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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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AmpliconTagger Resource Report Resource Website 1+ mentions |
AmpliconTagger (RRID:SCR_019112) | workflow software, software resource, software application, data processing software | Software tool as rRNA marker gene amplicon pipeline coded in python framework that enables fine tuning and integration of virtually any potential rRNA gene amplicon bioinformatic procedure. Designed to work within HPC environment, supporting complex network of job dependencies with smart restart mechanism in case of job failure or parameter modifications. | High Performance Computing, HPC environment, rRNA gene amplicons, rRNA marker, gene amplicon pipeline, bio.tools |
is listed by: bio.tools is listed by: Debian |
PMID:31816087 | Free, Freely available | SCR_019113, biotools:amplicontagger | https://bitbucket.org/jtremblay514/nrc_pipeline_public/src/master/, https://jtremblay.github.io/amplicontagger_guide.html, https://bio.tolols/amplicontagger | SCR_019112 | 2026-08-08 12:01:27 | 3 | |||||||
|
variancePartition Resource Report Resource Website 50+ mentions |
variancePartition (RRID:SCR_019204) | software resource, software application, data analysis software, data analytics software, data processing software | Software R package to quantify and interpret divers of variation in multilevel gene expression experiments.Provides statistical and visualization framework for studying drivers of variation in RNA-seq datasets in many types of high throughput genomic assays including RNA-seq gene-, exon- and isoform-level quantification, splicing efficiency, protein quantification, metabolite quantification, metagenomic assays, methylation arrays and epigenomic sequencing assays. | Repeated measures, variation in gene expression, RNA-seq datasets, high throughput genomic assays, splicing efficiency, protein quantification, metabolite quantification, metagenomic assays, methylation arrays, epigenomic sequencing assays, bio.tools |
is listed by: Bioconductor is listed by: bio.tools is listed by: Debian is related to: CRAN |
NHLBI U01 HL107388; Icahn School of Medicine at Mount Sinai |
PMID:27884101 | Free, Available for download, Freely available | biotools:variancepartition | https://bio.tools/variancepartition | SCR_019204 | 2026-08-08 12:01:28 | 62 | ||||||
|
MP3 tool Resource Report Resource Website 1+ mentions |
MP3 tool (RRID:SCR_019282) | software resource, software application, simulation software | Software tool for prediction of pathogenic proteins in genomic and metagenomic data. Used for identification of partial pathogenic proteins predicted from short (100-150 bp) metagenomic reads and also performs on complete protein sequences., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | pathogenic proteins, pathogenic proteins prediction, genomic data, metagenomic data, partial pathogenic proteins, partial pathogenic proteins prediction, complete protein sequences, bio.tools |
is listed by: bio.tools is listed by: Debian |
Institutional Research Fund of IISER Bhopal | PMID:24736651 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:mp3 | https://bio.tools/mp3 | SCR_019282 | MP3 | 2026-08-08 12:01:29 | 2 | |||||
|
ChiRA Resource Report Resource Website 1+ mentions |
ChiRA (RRID:SCR_019219) | data or information resource, software toolkit, workflow, narrative resource, software resource, software application, training material, data processing software | Software tool suite to analyze RNA-RNA interactome experimental data such as CLASH, CLEAR-CLIP, PARIS, SPLASH, etc. | RNA-RNA interactome experimental data, experimental data analysis, miRNA, RNA-RNA interactome, RNA structurome, CLASH, CLEAR-CLIP, PARIS, SPLASH, chimeric read, read, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:chira | https://rna.usegalaxy.eu/, https://bio.tools/chira | SCR_019219 | Chimeric Read Analyzer | 2026-08-08 12:01:28 | 6 | |||||||
|
SynergyFinder Resource Report Resource Website 500+ mentions |
SynergyFinder (RRID:SCR_019318) | software toolkit, software resource, software application, data visualization software, data processing software | Software R package as efficient implementations for all popular synergy scoring models for drug combinations, including HSA, Loewe, Bliss and ZIP and visualization of synergy scores as either two dimensional or three dimensional interaction surface over dose matrix. Used to calculate and visualize synergy scores for drug combinations. | Synergy scores, drug combinations, popular synergy scoring models, dimensional interaction surface, dose matrix, bio.tools |
is listed by: Bioconductor is listed by: bio.tools is listed by: Debian is related to: SynergyFinder web application |
DOI:10.1007/978-1-4939-7493-1_17 | Free, Available for download, Freely available | biotools:synergyfinder | https://bio.tools/synergyfinder | SCR_019318 | synergyfinder | 2026-08-08 12:01:27 | 624 | ||||||
|
CiteFuse Resource Report Resource Website 1+ mentions |
CiteFuse (RRID:SCR_019321) | software resource, software application, data analysis software, data processing software | Software R package consisting of suite of tools for doublet detection, modality integration, clustering, differential RNA and protein expression analysis, antibody-derived tag evaluation, ligand-receptor interaction analysis and interactive web-based visualization of CITE-seq data. | Data pre processing, modality integration, clustering, differential RNA, ADT, expression analysis, ADT evaluation, ligand receptor interaction analysis, CITE-seq data, cellular indexing of transcriptomes and epitopes by sequencing, bio.tools |
is listed by: Bioconductor is listed by: bio.tools is listed by: Debian has parent organization: University of Sydney; Sydney; Australia |
PMID:32353146 | Free, Available for download, Freely available | biotools:citefuse | https://bioconductor.org/packages/CiteFuse/, https://github.com/SydneyBioX/CiteFuse/, http://shiny.maths.usyd.edu.au/CiteFuse/, https://bio.tools/CiteFuse | SCR_019321 | Cellular Indexing of Transcriptomes and Epitopes Fuse, Cellular indexing of transcriptomes and epitopes Fuse | 2026-08-08 12:01:24 | 3 | ||||||
|
MRIcron Resource Report Resource Website 1000+ mentions |
MRIcron (RRID:SCR_002403) | MRIcron | software resource, software application, data visualization software, data processing software | Software tool as a cross-platform NIfTI format image viewer. Used for viewing and exporting of brain images. MRIcroGL is a variant of MRIcron. | NIfTI, format, image, viewer, exporting, brain, image, processing, data, bio.tools |
is used by: XFSL: An FSL toolbox is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps is listed by: neurodebian is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: Colour maps for brain imaging has parent organization: University of South Carolina; South Carolina; USA |
PMID:17583985 PMID:11568431 |
BSD License | biotools:MRIcron, nif-0000-00122 | https://sources.debian.org/src/mricron/, http://www.mccauslandcenter.sc.edu/mricro/, http://www.nitrc.org/projects/mricron, http://neuro.debian.net/pkgs/mricron.html, https://bio.tools/MRIcron | SCR_002403 | mricron - magnetic resonance image conversion viewing and analysis | 2026-08-08 12:02:42 | 2312 | |||||
|
Multiple Myeloma survival predictor Resource Report Resource Website 1+ mentions |
Multiple Myeloma survival predictor (RRID:SCR_017651) | software resource, data access protocol, web service, service resource | Dockerized environment for winning algorithm in 2017 Multiple Myeloma DREAM Challenge, Sub-Challenge 3. | Multiple Myeloma, prognostic model, survival analysis, GuanRank, bio.tools |
is listed by: bio.tools is listed by: Debian |
Multiple Myeloma | Restricted | biotools:Multiple_Myeloma_survival_prediction | https://bio.tools/Multiple_Myeloma_survival_prediction | SCR_017651 | 2026-08-08 12:01:09 | 2 | |||||||
|
GADMA Resource Report Resource Website 1+ mentions |
GADMA (RRID:SCR_017680) | GADMA | software resource, software application, data analysis software, data processing software | Software tool to implement methods for automatic inferring joint demographic history of multiple populations from genetic data. Genetic algorithm for inferring demographic history of multiple populations from allele frequency spectrum data. | Inferring, demographic, history, population, genetic, data, allele, frequency, spectrum, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
DOI:10.1101/407734 | Free, Available for download, Freely available | biotools:GADMA | https://bio.tools/GADMA | SCR_017680 | Genetic Algorithm for Demographic Model Analysis | 2026-08-08 12:00:55 | 3 | |||||
|
CRISPy-web Resource Report Resource Website 10+ mentions |
CRISPy-web (RRID:SCR_017970) | software resource, data access protocol, web service | Web tool to design sgRNAs for CRISPR applications. Web tool based on CRISPy to design sgRNAs for any user-provided microbial genome. Implemented as standalone web application for Cas9 target prediction. | Design, sgRNA, CRISP, microbial, genome, Cas9, target, prediction, data, guide, single, editing, bio.tools |
is listed by: bio.tools is listed by: Debian |
Novo Nordisk Foundation | PMID:29062934 | Free, Freely available | biotools:crispy | https://bio.tools/crispy | SCR_017970 | single guide RNA desing | 2026-08-08 12:00:55 | 28 | |||||
|
PAFScaff Resource Report Resource Website 1+ mentions |
PAFScaff (RRID:SCR_017976) | sequence analysis software, software resource, software application, data analysis software, data processing software | Software as Pairwise mApping Format reference based Scaffold anchoring and super scaffolding tool. Dsigned for mapping genome assembly scaffolds to closely related chromosome level reference genome assembly. | Pairwise, mapping, reference, scaffold, genomics, scaffolding, assembly, genome, chromosome, bio.tools |
is listed by: Debian is listed by: bio.tools |
Free, Freely available | biotools:PAFScaff | https://github.com/slimsuite/pafscaff/blob/master/PAFScaff.md, https://slimsuite.github.io/pafscaff/, https://bio.tools/PAFScaff | SCR_017976 | Pairwise mApping Format reference-based Scaffold | 2026-08-08 12:01:12 | 4 | |||||||
|
CandiMeth Resource Report Resource Website 1+ mentions |
CandiMeth (RRID:SCR_017974) | CandiMeth | production service resource, software resource, software application, data analysis software, service resource, analysis service resource, data processing software | Software tool for visualisation and quantification of DNA methylation at candidate features. | DNA, methylation, candidate feature, visualisation, quantification, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Galaxy |
Medical Research Council ; ESRC/BBSRC |
Free, Freely available | biotools:CandiMeth | http://bit.do/candimeth, https://usegalaxy.org/u/sarajayne-thursby/w/candimeth-8, https://bio.tools/CandiMeth | SCR_017974 | CANDIdate feature METHylation | 2026-08-08 12:00:55 | 2 | |||||
|
VEnCode Resource Report Resource Website 1+ mentions |
VEnCode (RRID:SCR_018024) | VEnCode | software resource, software application, data analysis software, data processing software | Software tool to perform intersectional genetics-related operations to find VEnCodes using databases provided by FANTOM5 consortium, namely CAGE enhancer and transcription start site (TSS) databases. | FANTOM5 consortium, data, CAGE enhancer, transcription site database, intersectional genetics, bio.tools |
is listed by: Debian is listed by: bio.tools |
DOI:10.1101/552984 | Free, Available for download, Freely available | BioTools:VEnCode, biotools:VEnCode | https://bio.tools/VEnCode, https://bio.tools/VEnCode, https://bio.tools/VEnCode | SCR_018024 | Versatile Entry Codes | 2026-08-08 12:01:10 | 1 | |||||
|
fineSTRUCTURE Resource Report Resource Website 10+ mentions |
fineSTRUCTURE (RRID:SCR_018170) | software resource, software application, data analysis software, data processing software | Software tool as algorithm for identifying population structure using dense sequencing data. Can perform model based Bayesian clustering on large datasets, including full resequencing data. | Identifying population structure, dense sequencing data, Bayesian clustering, large dataset, data, analysis, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:finestructure | https://bio.tools/finestructure | SCR_018170 | FineSTRUCTURE version 2 | 2026-08-08 12:01:00 | 23 | |||||||
|
ChiCMaxima Resource Report Resource Website 1+ mentions |
ChiCMaxima (RRID:SCR_018178) | production service resource, web service, software resource, data access protocol, analysis service resource, service resource | Pipeline for analyzing and identificantion of chromatin loops in CHi-C promoters data. Used to capture Hi-C visualization and interaction calling. | Chromatin loop, CHi-C promoter, data, Hi-C visualization, interaction calling, data, analysis, bio.tools |
is listed by: Debian is listed by: bio.tools |
PMID:31118054 | Free, Freely available | biotools:ChiCMaxima | https://bio.tools/ChiCMaxima | SCR_018178 | 2026-08-08 12:01:00 | 2 | |||||||
|
SnpHub Resource Report Resource Website 1+ mentions |
SnpHub (RRID:SCR_018177) | web application, software resource | Web Shiny-based server framework for retrieving, analyzing and visualizing large genomic variations data. | Genomic, data, data visualization, data analysis, data retrieving, bio.tools |
is listed by: Debian is listed by: bio.tools |
National Natural Science Foundation of China 31701415; National Key Research and Development Program of China 2018YFD0100803; National Key Research and Development Program of China 2016YFD0100801 |
Free, Available for download, Freely available | biotools:SnpHub | http://guoweilong.github.io/SnpHub/, https://bio.tools/SnpHub | SCR_018177 | 2026-08-08 12:01:14 | 1 | |||||||
|
SpydrPick Resource Report Resource Website 1+ mentions |
SpydrPick (RRID:SCR_018176) | software resource, software application, data analysis software, data processing software | Software command line tool for performing direct coupling analysis of aligned categorical datasets. Used for analysis at scale of pan genomes of many bacteria. Incorporates correction for population structure, which adjusts for phylogenetic signal in data without requiring explicit phylogenetic tree. | Direct coupling analysis, aligned categorical datasets, analysis, genome, bacteria, phylogenetic signal, correction, phylogenetic tree, data, bio.tools |
is listed by: Debian is listed by: bio.tools |
COIN Center of Excellence ; Academy of Finland ; Wellcome Trust ; European Research Council |
PMID:31361894 | Free, Available for download, Freely available | biotools:SpydrPick | https://anaconda.org/bioconda/spydrpick, https://bio.tools/SpydrPick | SCR_018176 | 2026-08-08 12:01:00 | 3 | ||||||
|
CRISPRdirect Resource Report Resource Website 500+ mentions |
CRISPRdirect (RRID:SCR_018186) | production service resource, web service, software resource, data access protocol, analysis service resource, service resource | Software for designing CRISPR/Cas guide RNA with reduced off target sites. Used for rational design of CRISPR/Cas target. Web server for selecting rational CRISPR/Cas targets from input sequence. Server currently incorporates genomic sequences of human, mouse, rat, marmoset, pig, chicken, frog, zebrafish, Ciona, fruit fly, silkworm, Caenorhabditis elegans, Arabidopsis, rice, Sorghum and budding yeast. | CRISP/Cas guide RNA, reduced off target site, design of CRISP/Cas target, selecting rational target, sequence, genomic sequence, RNA, bio.tools |
is listed by: Debian is listed by: bio.tools |
Japan Science and Technology Agency ; Ministry of Education ; Culture ; Sports ; Science and Technology of Japan |
PMID:25414360 | Free, Freely available | biotools:CRISPRdirect | https://bio.tools/CRISPRdirect | SCR_018186 | 2026-08-08 12:01:14 | 588 | ||||||
|
Fcirc Resource Report Resource Website 1+ mentions |
Fcirc (RRID:SCR_018090) | Fcirc | workflow software, software resource, software application, data processing software | Software Python pipeline for linear and circular RNAs of known fusions exploration. Pipeline for exploring linear transcripts and circRNAs of known fusions based on RNA-Seq data. Known fusion genes are from multiple databases like COSMIC, ChimerDB, TicDB, FARE-CAFE and FusionCancer or user-added gene-pairs. | Fusion gene, linear and circular RNA, fusion exploration, RNAseq data, linear transcript, circRNA, gene, data, pipeline, bio.tools |
uses: HISAT2 uses: SAMTOOLS is listed by: Debian is listed by: bio.tools |
National Natural Science Foundation of China 31771469 ; National Natural Science Foundation of China 31571363 ; National Natural Science Foundation of China 81573023 ; National Key Research and Development Program 2017YFC0908500 |
Free, Available for download, Freely available | biotools:Fcirc | https://bio.tools/Fcirc | SCR_018090 | Comprehensive Pipeline for Exploration of Fusion Linear and Circular RNAs | 2026-08-08 12:01:13 | 2 | |||||
|
HingeProt Resource Report Resource Website 1+ mentions |
HingeProt (RRID:SCR_018136) | software resource, data access protocol, web service, service resource | Web server for predicting rigid protein parts and flexible hinge regions connecting them in native topology of protein chains by employing elastic network (EN) models. Automated prediction of hinges in protein structures. | Predicting protein hinges, flexible hinge region, native topology, rigid protein part, elastic network model, protein structure, bio.tools |
is listed by: Debian is listed by: bio.tools |
PMID:17847101 | Free, Available for download, Freely available | biotools:hingeprot | https://bio.tools/hingeprot | SCR_018136 | 2026-08-08 12:00:59 | 4 |
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