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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
GPU-Meta-Storms Resource Report Resource Website 1+ mentions |
GPU-Meta-Storms (RRID:SCR_012029) | GPU-Meta-Storms | software resource | Optimized GPU-based software to efficiently measure the quantitative phylogenetic similarity among massive amount of microbial community samples. | c++, parallel computation 4, cuda, structure similarity, metagenomic, phylogenetic, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Chinese Academy of Sciences; Beijing; China |
PMID:24363375 | OMICS_02187, biotools:meta-storms | https://bio.tools/meta-storms | SCR_012029 | 2026-07-25 12:07:25 | 1 | |||||||
|
COBRApy Resource Report Resource Website 100+ mentions |
COBRApy (RRID:SCR_012096) | software resource | Software Python package that provides support for basic COnstraint-Based Reconstruction and Analysis (COBRA) methods. | software package, mac os x, unix/linux, windows, python, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:23927696 DOI:10.1186/1752-0509-7-74 |
OMICS_05190, biotools:cobrapy | https://bio.tools/cobrapy | https://sources.debian.org/src/python3-cobra/ | SCR_012096 | COBRA for Python | 2026-07-25 12:07:28 | 311 | ||||||
|
NetCoffee Resource Report Resource Website 1+ mentions |
NetCoffee (RRID:SCR_012095) | software resource | A fast and accurate algorithm which allows to find a global alignment of multiple protein-protein interaction networks. | standalone software, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Google Code |
PMID:24336806 | GNU General Public License | biotools:netcoffee, OMICS_05172 | https://bio.tools/netcoffee | SCR_012095 | 2026-07-25 12:07:27 | 3 | |||||||
|
Cell motility Resource Report Resource Website |
Cell motility (RRID:SCR_012120) | software resource | An open source Java application that provides a clear and concise analysis workbench for large amounts of cell motion data. | applet, java, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Google Code |
PMID:16762054 | Apache License, v2 | biotools:cell-motility, OMICS_05660 | https://bio.tools/cell-motility | SCR_012120 | Cell_motility | 2026-07-25 12:07:27 | 0 | ||||||
|
ISDTool Resource Report Resource Website |
ISDTool (RRID:SCR_012125) | software resource | Software that implements a computational model for predicting immunosuppressive domains (ISDs). The software could be used to identify typical ISDs in retroviruses including HERV, HTLV, HIV, STLV, SIV and MLV. | standalone software, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:25008418 | OMICS_05696, biotools:isdtool | https://bio.tools/isdtool | SCR_012125 | 2026-07-25 12:07:32 | 0 | ||||||||
|
A5-miseq Resource Report Resource Website 100+ mentions |
A5-miseq (RRID:SCR_012148) | software resource | Software that produces high quality microbial genome assemblies on a laptop computer without any parameter tuning. A5-miseq does this by automating the process of adapter trimming, quality filtering, error correction, contig and scaffold generation, and detection of misassemblies. Unlike the original A5 pipeline, A5-miseq can use long reads from the Illumina MiSeq, use read pairing information during contig generation, and includes several improvements to read trimming. | standalone software, illumina, unix/linux, mac os x, bio.tools |
is used by: Nephele is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:25338718 | GNU General Public License | OMICS_06339, biotools:a5-miseq | https://bio.tools/a5-miseq | SCR_012148 | 2026-07-25 12:07:32 | 189 | |||||||
|
PLEK Resource Report Resource Website 100+ mentions |
PLEK (RRID:SCR_012132) | software resource | An alignment-free software tool which uses a computational pipeline based on an improved k-mer scheme and a support vector machine (SVM) algorithm to distinguish lncRNAs from messenger RNAs (mRNAs), in the absence of genomic sequences or annotations. It is especially suitable for PacBio or 454 sequencing data and large-scale transcriptome data. | standalone software, roche, pacific biosciences, unix/linux, c, python, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:25239089 | GNU General Public License | biotools:plek, OMICS_05839 | https://bio.tools/plek | SCR_012132 | PLEK: predictor of long non-coding RNAs and messenger RNAs based on an improved k-mer scheme | 2026-07-25 12:07:32 | 122 | ||||||
|
REDItools Resource Report Resource Website 100+ mentions |
REDItools (RRID:SCR_012133) | software resource | A suite of python scripts to perform high-throughput investigation of RNA editing using next-generation sequencing data. | standalone software, illumina, roche, pacific biosciences, life technologies, python, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Google Code |
PMID:23742983 | MIT License | biotools:reditools, OMICS_05860 | https://bio.tools/reditools | SCR_012133 | 2026-07-25 12:07:28 | 141 | |||||||
|
iceLogo Resource Report Resource Website 100+ mentions |
iceLogo (RRID:SCR_012137) | software resource | Software that builds on probability theory to visualize significant conserved sequence patterns in multiple peptide sequence alignments against background (reference) sequence sets that can be tailored to the studied system and the used protocol. | standalone software, web app, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Google Code |
PMID:19876014 | Apache License | biotools:icelogo, OMICS_05885 | https://bio.tools/icelogo | SCR_012137 | 2026-07-25 12:07:29 | 176 | |||||||
|
AMS Resource Report Resource Website |
AMS (RRID:SCR_012140) | software resource | Software that predicts the wide selection of 88 different types of the single amino acid post-translational modifications (PTM) in protein sequences. The source code and precompiled binaries of brainstorming tool are available under Apache licensing. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Google Code |
PMID:22555647 | Apache License | OMICS_05934, biotools:ams | https://bio.tools/ams | SCR_012140 | AutoMotif Service | 2026-07-25 12:07:29 | 0 | ||||||
|
PhosphoSiteAnalyzer Resource Report Resource Website |
PhosphoSiteAnalyzer (RRID:SCR_012142) | software resource | A bioinformatical software tool for analyzing (quantitative) phosphoproteome datasets. The program retrieves kinase-substrate predictions from NetworKIN and contains various statistical modules for futher analysis. | standalone software, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:22471441 | Free, Public | biotools:phosphositeanalyzer, OMICS_05951 | https://bio.tools/phosphositeanalyzer | SCR_012142 | 2026-07-25 12:07:28 | 0 | |||||||
|
DNAcopy Resource Report Resource Website 100+ mentions |
DNAcopy (RRID:SCR_012560) | DNAcopy | software resource | Software that segments DNA copy number data using circular binary segmentation to detect regions with abnormal copy number. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
OMICS_00720, biotools:dnacopy | https://bio.tools/dnacopy, https://sources.debian.org/src/r-bioc-dnacopy/ | SCR_012560 | 2026-07-25 12:07:33 | 334 | ||||||||
|
DNaseR Resource Report Resource Website |
DNaseR (RRID:SCR_012819) | DNaseR | software resource | A R package that enables the identification of protein binding footprints in DNase I hypersensitive sites sequencing (DNase-seq) data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
PMID:23118738 | Free | biotools:dnaser, OMICS_00517 | https://bio.tools/dnaser | SCR_012819 | DNaseR: DNase I footprinting analysis of DNase-seq data | 2026-07-25 12:07:37 | 0 | |||||
|
Krona Resource Report Resource Website 50+ mentions |
Krona (RRID:SCR_012785) | Krona | software resource | Software that allows hierarchical data to be explored with zoomable pie charts. | bio.tools |
is listed by: bio.tools has parent organization: SourceForge |
PMID:21961884 | OMICS_01498, biotools:krona | https://bio.tools/krona | SCR_012785 | Krona - Hierarchical data browser | 2026-07-25 12:07:36 | 89 | ||||||
|
IsaCGH Resource Report Resource Website |
IsaCGH (RRID:SCR_008375) | IsaCGH | software resource | Software to analyze CNV that will now normalize arrays CGH and it will visually integrate different genome annotations. | microarray, array cgh, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
OMICS_00727, biotools:isacgh | https://bio.tools/isacgh | SCR_008375 | 2026-07-25 12:06:50 | 0 | ||||||||
|
CAT Resource Report Resource Website 10+ mentions |
CAT (RRID:SCR_008421) | CAT | software resource | A repository of tools for analysis and annotation of CAZYmes (Carbohydrate Active enZYmes)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01676, biotools:CAt | https://bio.tools/CAT | SCR_008421 | 2026-07-25 12:06:52 | 13 | |||||||
|
FGDP Resource Report Resource Website |
FGDP (RRID:SCR_008910) | FGDP | software resource | A Java-based, Microarray or Genechip data analysis system. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Fox Chase Cancer Center |
PMID:14734324 | GNU General Public License | OMICS_00756, biotools:fgdp | https://bio.tools/fgdp | SCR_008910 | Functional Genomics Data Pipeline (FGDP), Functional Genomics Data Pipeline | 2026-07-25 12:06:56 | 0 | |||||
|
iMir Resource Report Resource Website 10+ mentions |
iMir (RRID:SCR_009496) | iMir | software resource | A modular pipeline for comprehensive analysis of smallRNA-Seq data, comprising specific tools for adapter trimming, quality filtering, DE analysis, target prediction by integrating multiple open source modules and resources in an automated workflow. | unix/linux, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:24330401 | Apache License | OMICS_00358, biotools:imir | https://bio.tools/imir | SCR_009496 | 2026-07-25 12:06:58 | 11 | ||||||
|
SpliceMap Resource Report Resource Website 10+ mentions |
SpliceMap (RRID:SCR_009650) | SpliceMap | software resource | A de novo splice junction discovery and alignment tool. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Stanford University; Stanford; California |
PMID:25577377 PMID:20371516 |
OMICS_01252, biotools:splicemap | https://bio.tools/splicemap | SCR_009650 | 2026-07-25 12:06:59 | 21 | |||||||
|
Biological General Repository for Interaction Datasets (BioGRID) Resource Report Resource Website 1000+ mentions |
Biological General Repository for Interaction Datasets (BioGRID) (RRID:SCR_007393) | BioGRID | database, data or information resource | Curated protein-protein and genetic interaction repository of raw protein and genetic interactions from major model organism species, with data compiled through comprehensive curation efforts. | budding yeast, fission yeast, protein, gene, protein interaction, genetic interaction, model organism, interaction, dataset, gene annotation, phenotype, orthologous interaction, yeast, cellular interaction network, physical interaction, protein-peptide, protein-rna, protein-protein interaction, genetics, publication, raw protein, genetic interaction, web service, pathway, network, biology, gene mapping, statistics, bio.tools, FASEB list |
is used by: NIF Data Federation is recommended by: National Library of Medicine is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: re3data.org is listed by: OMICtools is listed by: DataCite is listed by: NIH Data Sharing Repositories is listed by: bio.tools is listed by: Debian is related to: TissueNet - The Database of Human Tissue Protein-Protein Interactions is related to: Pathway Commons is related to: Cytoscape is related to: Interaction Reference Index is related to: ConsensusPathDB is related to: FlyMine is related to: IMEx - The International Molecular Exchange Consortium is related to: Integrated Molecular Interaction Database is related to: PSICQUIC Registry is related to: PSI-MI is related to: NIH Data Sharing Repositories is related to: Agile Protein Interactomes DataServer is related to: Integrated Manually Extracted Annotation has parent organization: Princeton University; New Jersey; USA has parent organization: University of Edinburgh; Scotland; United Kingdom has parent organization: University of Montreal; Quebec; Canada works with: IMEx - The International Molecular Exchange Consortium |
NCRR R01 RR024031; NHGRI HG02223; Canadian Institutes of Health Research ; BBSRC ; NIH Office of the Director R24 OD011194 |
PMID:23203989 PMID:21071413 PMID:16381927 PMID:12620108 |
Free, Freely available | nif-0000-00432, r3d100010350, OMICS_01901, biotools:the_grid | https://orip.nih.gov/comparative-medicine/programs/genetic-biological-and-information-resources, https://bio.tools/the_grid, https://doi.org/10.17616/R34C7G | SCR_007393 | , BioGRID, Biological General Repository for Interaction Datasets | 2026-07-25 12:06:40 | 2554 |
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