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Resource Name
bio.tools
RRID:SCR_014695 RRID Copied      
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bio.tools (RRID:SCR_014695)
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Resource Information

URL: https://bio.tools

Proper Citation: bio.tools (RRID:SCR_014695)

Description: Community registry of software tools and data resources for life sciences. Tools and data services registry as community effort to document bioinformatics resources. Registry of software and databases, facilitating researchers from across spectrum of biological and biomedical science. When adding tools to registry, information including URL, contact information, resource function, field its relevant in, and its primary publication are required. Development is supported by ELIXIR - the European Infrastructure for Biological Information.

Resource Type: catalog, data or information resource, software resource, database, software repository

Defining Citation: DOI:10.1186/s13059-019-1772-6, PMID:26538599

Keywords: Registry, software registry, biological tool, data services registry, services discovery portal, bio.tools

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GUARDD

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GEOquery

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RNAcontext

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Patchwork

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SODOCK

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GENIE3

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MODENT - A Tool For Reconstructing Gene Regulatory Networks

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PeptideProphet

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Quant

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ProteinProphet

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Flicker

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Micro-Analyzer

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riboPicker

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dbSTS

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POPBAM

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flowPeaks

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cn.FARMS

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Sequence Search and Alignment by Hashing Algorithm

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SAMBLASTER

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Pindel

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Mfuzz

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TAPyR

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ContEst

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PGS

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PEPPER

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StringTie

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SOAP

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SplitSeek

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MUSCLE

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SplicePlot

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Illuminator

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GimmeMotifs

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Skylign

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BreakSeq

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Barrnap

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SLOPE

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CUDA-EC

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QualiMap

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massiR

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OmicsOffice for NGS SeqSolve

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QUAST

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GenomicTools

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NGSUtils

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TileQC

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Sequedex

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PARalyzer

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BFCounter

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TALLYMER

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SNPchip

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VAAL

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ProbRNA

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ADMIXTURE

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SABER

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piCALL

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CYCLE

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limmaGUI

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DEXUS

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wateRmelon

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NGSrich

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OLIN

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MACAT

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affylmGUI

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ToppCluster

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AnimalTFDB

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oneChannelGUI

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YinOYang

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Chilibot: Gene and Protein relationships from MEDLINE

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asSeq

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FARMS

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GERMLINE

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unifiedWMWqPCR

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HAPLOPAINTER

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Biocatalogue - The Life Science Web Services Registry

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HOMOZYGOSITYMAPPER

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MetaBase

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PyLOH

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InterMine

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myExperiment

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pRESTO

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Prediction of Amyloid Structure Aggregation

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PhosphoSitePlus: Protein Modification Site

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BREAKDANCER

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FACTA+.

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PEDIGRAPH

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CQN

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CanSNPer

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SamSPECTRAL

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TEMP

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MEME Suite - Motif-based sequence analysis tools

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SNPAAMapper

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Pecan

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InteroPorc

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AffyPipe

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ADaCGH2

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DINDEL

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ASPGD

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Candida Genome Database

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BISC

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PurBayes

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SNVer

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Cake

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S-MART

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SHORTY

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Pathway Commons

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TcoF

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BEETL-fastq

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SBARS

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cpnDB: A Chaperonin Database

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cisRED: cis-regulatory element

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FlyFactorSurvey

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pymzML

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EchoBASE

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Blood Group Antigen Gene Mutation Database

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WebGeSTer DB

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RUbioSeq

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COSMIC - Catalogue Of Somatic Mutations In Cancer

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MethylAid

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ExomeDepth

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ZOOM

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Iterative Signature Algorithm

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ShotGun

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Pathview

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T3DB

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Autophagy Database

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rBiopaxParser

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QualitySNPng

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CAMERA - Collection of annotation related methods for mass spectrometry data

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libCSAM

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RopeBWT2

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NetPathMiner

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BioNumbers

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leeHom

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tweeDEseq

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ProRata

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Coding Potential Calculator

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CPTRA

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MFEprimer

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Distant Regulatory Elements

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HGNC

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GATE

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SuperPred: Drug classification and target prediction

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hot scan

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AltAnalyze - Alternative Splicing Analysis Tool

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Primer3Plus

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pairheatmap

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BioJS

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ms lims

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Eukaryotic Linear Motif

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Proteome Analyst Specialized Subcellular Localization Server

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HYDEN

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drFAST

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GeneFisher

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GreenPhylDB

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MiST - Microbial Signal Transduction database

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Pipeliner

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Gene Set Enrichment Analysis

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Piano

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Weighted Gene Co-expression Network Analysis

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FastSNP

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Triplex

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mrsFAST

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GenePattern

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NovelSeq

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QDNAseq

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MutDB

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SplicingCompass

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deFuse

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Database of Interacting Proteins (DIP)

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Assembly Based ReAligner

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MAGE-TAB

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ggbio

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miR-PREFeR

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NanoStringNorm

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MIPgen

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HTqPCR

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Parseq

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T-profiler

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Bpipe

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jmzTab

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L-Measure

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Snakemake

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PoPoolation

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MultiPhen

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PheWAS R Package

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Quantitative Enrichment of Sequence Tags

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ALDEx2

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INMEX

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InsertionMapper

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BSRD

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SeWeR - SEquence analysis using WEb Resources

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Segway - a way to segment the genome

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Stem Cell Discovery Engine

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TagDust

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Kdetrees

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Tree and reticulogram REConstruction

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NEWT

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DER Finder

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BioPig

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Selectome: a Database of Positive Selection

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Distributed String Mining Framework

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PILGRM

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Apo and Holo structures DataBase

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MLTreeMap

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MG-RAST

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miRNAKey

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SVseq

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Small Molecule Pathway Database

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Information Hyperlinked Over Proteins

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SVMerge

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BioSample Database at EBI

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MetaPhyler

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SOPRA

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NCBI BioSystems Database

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SLIQ

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G-BLASTN

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SSPACE

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AmphoraNet

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NCBI Structure: Cn3D

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DELLY

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RUM

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STING Report

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SoyBase

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SINA

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Strelka

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RNA-eXpress

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Percolator: Semi-supervised learning for peptide identification from shotgun proteomics datasets

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VFS

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ShoRAH

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READSCAN

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ERANGE

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GeneTalk

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ORMAN

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SEECER

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Scripture

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SPOT - Biological prioritization after a SNP association study

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NCBO Annotator

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CoPub

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SolexaQA

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PHAge Search Tool

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Knime4Bio

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MethPipe

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Bis-SNP

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GobyWeb

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EMAGE Gene Expression Database

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FusionMap

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Yabi

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GSNAP

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rQuant

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MethylViewer

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DistMap

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PASS

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mrFAST

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Kismeth

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Stampy

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TreQ

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FLASH

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SAMStat

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PRINSEQ

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MethylomeDB

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SOAPaligner/soap2

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TMA Navigator

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TRANSFAC

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SeqMap

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Bambino

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MicrobesOnline

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DMRforPairs

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TIGRFAMS

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CLIPZ

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SNPsandGO

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ToppGene Suite

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SeqTrace

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GoSurfer

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Jellyfish

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GoFish

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WEGO - Web Gene Ontology Annotation Plot

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ngsTools

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GraphProt

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SerbGO

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GoPubMed

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ccPDB - Compilation and Creation of datasets from PDB

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DOMMINO - Database Of MacroMolecular INteractiOns

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SOURCE

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DistiLD - Diseases and Traits in LD

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PePr

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Expression Profiler

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eQuilibrator

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DiseaseMeth

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Dr.VIS - Human Disease-Related Viral Integration Sites

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FunTree

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DBETH - Database for Bacterial ExoToxins for Humans

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BLESS

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GWASdb

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HFV Database

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IndelFR - Indel Flanking Region Database

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MIPModDB

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Europe PubMed Central

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CharProtDB: Characterized Protein Database

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IDEAL - Intrinsically Disordered proteins with Extensive Annotations and Literature

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MMMDB - Mouse Multiple tissue Metabolome DataBase

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ICEberg

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VirHostNet: Virus-Host Network

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Cascade

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Polbase

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VIRsiRNAdb

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959 Nematode Genomes

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OGEE - Online GEne Essentiality database

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ProPortal

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SNPedia

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Newtomics

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HotRegion - A Database of Cooperative Hotspots

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SitEx

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ScerTF

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HMM-TM

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NRG-CING

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PRED-LIPO

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InterEvol database

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SpliceDisease

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RNA CoSSMos

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deepSNV

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PRED-GPCR

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RecountDB

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VICUNA

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ProRepeat

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MouseBook

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COEUS

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Predictive Networks

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PRED-SIGNAL

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Flycircuit

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COLT-Cancer

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ATRHUNTER

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GeneTrail

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epigenomix

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Pseudomonas Genome Database

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QCGWAS

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TSSer

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UMD-BRCA1/ BRCA2 databases

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PomBase

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Phytozome

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OMPdb

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GOEAST - Gene Ontology Enrichment Analysis Software Toolkit

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MSIsensor

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GWAMA

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SpliceTrap

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ViralZone

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waviCGH

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MyHits

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Decombinator

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CAPS Database

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ADGO

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zfishbook

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EagleView

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Gene Expression Database

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SRAdb

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BEDTools

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IMGT/GENE-DB

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RamiGO

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canSAR

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IMGT/LIGM-DB

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PLEXdb - Plant Expression Database

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COHCAP

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DARC - Database for Aligned Ribosomal Complexes

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Immune Epitope Database and Analysis Resource (IEDB)

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AutismKB

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RIKEN integrated database of mammals

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Myrna

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PhenoM - Phenomics of yeast Mutants

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BIGpre

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HIstome: The Histone Infobase

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TriTrypDB

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CuticleDB

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Midbody, Centrosome and Kinetochore

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SCOP: Structural Classification of Proteins

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Expression Database in 4D

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VIDA

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Database of Arabidopsis Transcription Factors

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Atlas of Genetics and Cytogenetics in Oncology and Haematology

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ESEfinder 3.0

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agriGO

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Taipan

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AgBase

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Chromosome 7 Annotation Project

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MEROPS

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T1DBase

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Hyper Cell Line Database

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GenoTan

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VISTA Browser

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lobSTR

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Candidate Genes to Inherited Diseases

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VISTA Enhancer Browser

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Gene Array Analyzer

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Network Analysis, Visualization and Graphing TORonto

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MuSiC

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MfunGD - MIPS Mouse Functional Genome Database

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eTBlast

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Single Nucleotide Polymorphism Spectral Decomposition (SNPSpD)

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FGDP

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hiPathDB - human integrated Pathway DB with facile visualization

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miRNEST

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neXtProt

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NetOGlyc

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QuasiRecomb

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GMAP

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iMir

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MaCH-Admix

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SeqBuster

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LegumeIP

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DNAtraffic

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MicroSNiPer

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Pathema

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BeeBase

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Geneious

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MOSCPHASER

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SNPinfo Web Server

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elastix

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MIRA

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NEBcutter

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CopySeq

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CUPSAT

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Atlas2

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ALLPATHS-LG

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Velvet

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HomSI

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SVDetect

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omiRas

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HMCan

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HapFABIA

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WEBLOGO

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ZINBA

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SICER

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kmer-SVM

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MAnorm

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Pedimap

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nucleR

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CEQer

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MutSig

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DIANA-LncBase

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MethMarker

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PeakRanger

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PlnTFDB

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CloudBurst

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NPS

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MutationTaster

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ProDesign

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OligoArray

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ArrayAnalysis.org

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PatMaN

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SEAL

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Asterias

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RACE

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RobiNA

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CANGS

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PlantTFcat

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LitInspector

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HSLPred

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PSAR-Align

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CancerResource

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JiffyNet

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ECHO

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GPU-Meta-Storms

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GenoREAD

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TopHat-Fusion

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GeneStitch

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FABIA

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CPFP

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MFPaQ

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ICPL ESIQuant

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easyRNASeq

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PREDDIMER

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NetCoffee

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SlideSort-BPR

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miRPlant

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AlienTrimmer

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PRIDE Converter 2

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SNP ratio test

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compomics-utilities

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Allim

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PLEK

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ISDTool

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OBI-Warp

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LocalAli

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iceLogo

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multiplierz

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AMS

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NGSmethDB

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PoolHap

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DNaseR

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Btrim

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COBRApy

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NAIL

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CAZy- Carbohydrate Active Enzyme

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A5-miseq

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ANNOVAR

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GENSCAN

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PhosphoSiteAnalyzer

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MethylCoder

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featureCounts

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LOCAS

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Scalpel

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Cell motility

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Mouse Genome Database

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CloudAligner

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HeurAA

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GSA-SNP

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seqMINER

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PolyPhen: Polymorphism Phenotyping

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rqubic

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PlantNATsDB - Plant Natural Antisense Transcripts DataBase

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MitoBreak

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Cube-DB

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Death Domain database

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Telescoper

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Crossbow

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MToolBox

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GENE-counter

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BEADS

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PLAN2L

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INCLUSive

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CSAR

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ApiDB CryptoDB

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MACS

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NNcon

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KAVIAR

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GeneSigDB

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psRNATarget

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Composition Profiler

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MINAS - Metal Ions in Nucleic AcidS

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EGSEA

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Crystallography and NMR System (CNS)

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Morpheus

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IUPHAR/BPS Guide to Pharmacology

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RAST Server

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ProteomicsDB

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SPEX2

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LTR_Finder

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SCRATCH

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DSAP

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PALEOMIX

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Buccaneer

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QuantiSNP

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ProtTest

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MultiQC

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GeneWise

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DISEASES

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Off-Spotter

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oligo

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3D-footprint

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SC3

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MS-GF+

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TISSUES

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TFBS

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CHiCAGO

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Poretools

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Membrane Protein Explorer

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FATCAT

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Bio-tradis

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ALTER

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HISAT2

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MetaMapR

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PhyD3

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Exonerate

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primers4clades

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Fastml

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Bamtools

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Genesis

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DISULFIND

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EnrichmentMap

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LoRDEC

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mentha

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IDEPI - IDentify EPItopes

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Oufti

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FluxModeCalculator

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eXpression2Kinases

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SMAGEXP

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ProCon - PROteomics CONversion

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Lifebit Deploit

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TRANSIT

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Splicing Express

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Microscopy Image Browser

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SARTools

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SPICE

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DINIES

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OmicsNet

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ngsRelate

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clusterProfiler

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NetworkAnalyst

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FRETBursts

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Thunder STORM

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ANOCVA

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ConsensusClusterPlus

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CIBERSORT

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CCTOP

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scran

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Rsubread

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Heatmapper

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BinPacker

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Subread

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UMI-tools

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Goseq

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PRSice

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ScaffMatch

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EMBOSSMatcher

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JAMM

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CentroidFold

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Gigwa

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FastProject

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GeSeq

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ComplexHeatmap

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PatchDock

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Proovread

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trimAl

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ExPASy ABCD database

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shinyGEO

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AmoebaDB

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Blood Exposome Database

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STRUCTURE

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NetPhos

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Geneshot

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ProtParam Tool

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HiC-Pro

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HingeProt

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Mousebytes

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iTOL

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ChiCMaxima

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SWISS-MODEL

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PASTEClassifier

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R/qtl2

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FlowCal

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Signaling Pathways Project

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GPS-SUMO

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Roary

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SpydrPick

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ProSA-web

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SIGNOR

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MaxAlign

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REDIportal

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EpiModel

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Protein Interactions Calculator

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rVista

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Minimap2

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PrognoScan

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Batch Web CD-Search Tool

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AlgPred

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GOnet

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GalaxyWEB

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GalaxyRefine

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Annotree

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khmer

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E-CRISP

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Robetta

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D-GENIES

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aroma.light

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Clustal Omega

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DESeq

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VICMpred

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Ray

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Apollo

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STAMP

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discoSnp

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vcflib

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IgBLAST

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BioPerl

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Genome BioInformatics Research Lab - gff2ps

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Rainbow

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Predictions for Entire Proteomes

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Stacks

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Clustal W2

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RNAhybrid

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Primer3

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SAMtools/BCFtools

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EBSeq

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biobambam

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DIALIGN

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Unipro UGENE

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Bowtie 2

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Artemis: Genome Browser and Annotation Tool

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WHAM

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Database of Secondary Structure Assignments

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Minia

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HTSeq

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RAxML

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Sickle

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Segemehl

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Staden Package

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Bismark

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NCBI BLAST

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Vienna RNA

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GBrowse

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ea-utils

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AmpliconNoise

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COILS: Prediction of Coiled Coil Regions in Proteins

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BitSeq

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HilbertVis

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VARSCAN

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Regulatory Sequence Analysis Tools

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CD-HIT

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MACH

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SOAPsnp

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ProbCons

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BEAST

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Crux tandem mass spectrometry analysis software

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Pscan-ChIP

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BRIG

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tRNAscan-SE

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CGView

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Circos

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FreeBayes

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Glimmer

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T-Coffee

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Oases

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LIMMA

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cutadapt

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edgeR

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OpenMS

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Flexbar

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RSEM

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TopHat

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DNAcopy

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phyloseq

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Trinity

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FastTree

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Cufflinks

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CummeRbund

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minet

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Atac

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Pilon

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GMA

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Nanopolish

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Krona

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SeqPrep

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SortMeRNA

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THESIAS

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tximport

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StoatyDive

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rCASC

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precrec

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IMGT-ONTOLOGY

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KAT

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globaltest

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COPASI

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CheckM

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NiftyPET

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SeaView

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ASHLAR

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KisSplice

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metagen

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BUSCO

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HH-suite

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yaqcaffy

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seqbias

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ngs.plot

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Eoulsan

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bsseq

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genomation

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eTRIKS

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ascat

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GADMA

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ropls

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sabre

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icy

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plgem

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biobakery

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minfi

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MyGene.info

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ODAM

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MRIcron

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smashpp

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BSA4Yeast

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neuroelectro

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RepeatFiller

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ShinyLearner

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docker4seq

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CRISPR-ERA

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MAFFT

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RepeatScout

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Phenoscape

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PhenoMeNal

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multtest

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TransDecoder

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PlotTwist

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CRISPR-P

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Telescope

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charm

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Warp

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European Variation Archive (EVA)

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Eukaryote Genes

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Evolutionary Couplings Server

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NHLBI Exome Sequencing Project (ESP)

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ExpressYourself

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fgsea

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Full-Length cDNA Database

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FuncAssociate: The Gene Set Functionator

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