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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Cuffdiff Resource Report Resource Website 1000+ mentions |
Cuffdiff (RRID:SCR_001647) | Cuffdiff | software resource | Software that estimates expression at transcript-level resolution and controls for variability evident across replicate libraries. | differential expression, rna-seq, transcript, splicing, promoter, coding sequence, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Cufflinks has parent organization: University of Maryland; Maryland; USA |
PMID:23222703 | Free, Available for download, Freely available | biotools:cuffdiff, OMICS_01969 | https://bio.tools/cuffdiff | SCR_001647 | Cuffdiff 2 | 2026-09-19 12:49:44 | 3925 | |||||
|
MetaBase Resource Report Resource Website 50+ mentions |
MetaBase (RRID:SCR_001762) | MB | data or information resource, database, narrative resource, wiki | User-contributed list of biological databases available on the internet. Currently there are 1,801 entries, each describing a different database. The databases are described in a semi-structured way by using templates and entries can carry various user comments and annotations. Entries can be searched, listed or browsed by category. The site uses the same MediaWiki technology that powers Wikipedia, The Mediawiki system allows users to participate on many different levels, ranging from authors and editors to curators and designers. MetaBase aims to be a flexible, user-driven (user-created) resource for the biological database community. The main focuses of MetaBase are: * As a basic requirement, MB contains a list of databases, URLs and descriptions of the most commonly used biological databases currently available on the internet. * The system should be flexible, allowing users to contribute, update and maintain the data in different ways. * In the future we aim to generate more communication between the database developer and user communities. | biological, mediawiki, biology, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian has parent organization: Genome Research Foundation |
MKE - Ministry of Knowledge Economy | PMID:22139927 | Free, Freely available | biotools:metabase, nif-0000-10293 | https://bio.tools/metabase | http://biodatabase.org/index.php?title=Main_Page&oldid=8972 | SCR_001762 | MetaBase (MB) | 2026-09-19 12:49:46 | 87 | |||
|
PennSeq Resource Report Resource Website 1+ mentions |
PennSeq (RRID:SCR_001763) | PennSeq | software resource | Software for isoform-specific gene expression quantification in RNA-Seq by modeling non-uniform read distribution. Instead of making parametric assumptions, they give adequate weight to the underlying data by the use of a non-parametric approach. The rationale is that regardless what factors lead to non-uniformity, whether it is due to hexamer priming bias, local sequence bias, positional bias, RNA degradation, mapping bias or other unknown reasons, the probability that a fragment is sampled from a particular region will be reflected in the aligned data. This empirical approach thus maximally reflects the true underlying non-uniform read distribution. | isoform, gene expression, rna-seq, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:24362841 | Free, Available for download, Freely available | biotools:pennseq, OMICS_01946 | https://bio.tools/pennseq | SCR_001763 | 2026-09-19 12:49:46 | 4 | ||||||
|
Chilibot: Gene and Protein relationships from MEDLINE Resource Report Resource Website 10+ mentions |
Chilibot: Gene and Protein relationships from MEDLINE (RRID:SCR_001705) | Chilibot | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | Data analysis service that searches PubMed literature database (abstracts) about specific relationships between proteins, genes, or keywords using a NLP-based text-mining approach. The results are returned as a graph. The synonym database used in Chilibot is available, without fee, for academic use only. Several different search methods are supported including: * searching for relationship between two genes, proteins or keywords * searching for relationships between many genes, proteins, or keywords * searching for relationships between two lists of genes, proteins, or keywords Advanced options include: * Automated hypothesis generation (graph) * Restricting context using keywords * Providing your own synonyms * Modifying synonyms provided by Chilibot * Color coding nodes with gene expression values * Special search: modulation | drug, gene, literature, natural language processing, protein, text-mining, network, keyword, biological concept, graph, bio.tools |
is listed by: OMICtools is listed by: 3DVC is listed by: bio.tools is listed by: Debian is related to: PubMed has parent organization: University of Tennessee Health Science Center; Tennessee; USA |
PHS DA-03977 | PMID:15473905 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01176, nif-0000-10196, biotools:chilibot | https://bio.tools/chilibot | SCR_001705 | Chilibot - Mining PubMed for relationships | 2026-09-19 12:49:46 | 33 | ||||
|
PhosphoSitePlus: Protein Modification Site Resource Report Resource Website 1000+ mentions |
PhosphoSitePlus: Protein Modification Site (RRID:SCR_001837) | PSP | data or information resource, knowledge environment resource, portal | A freely accessible on-line systems biology resource devoted to all aspects of protein modification, as well as other post-translational modifications. It provides valuable and unique tools for both cell biologists and mass spectroscopists. PhosphoSite is a human- and mouse-centric database. It includes features such as: viewing the locations of modified residues on molecular models; browsing and searching MS2 records by disease, tissue, and cell line; submitting lists of peptides to identify previously reported genes; searching by sub-cellular localization, treatment, tissues, cell types, cell lines and diseases, and protein types and protein domains; searching for experimentally-verified kinase substrates and viewing preferred substrate motifs; and viewing MS2 spectra for peptides and sites not previously published. | portal, mass spectroscopist, molecular model, mouse, post translational, subcellular localization, protein modification, post-translational modification, protein phosphorylation, protein structure, protein function, ubiquitinylation, acetylation, cellular component, cell type, visualization, data repository, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian is related to: Cytoscape is related to: ConsensusPathDB has parent organization: Cell Signaling Technology |
NCI ; NIAAA R44 AA014848; NIGMS R43 GM65768 |
PMID:22135298 | Free, Freely available | biotools:phosphositeplus, nif-0000-10399 | https://bio.tools/phosphositeplus | SCR_001837 | PhosphoSitePlus, PhosphoSite | 2026-09-19 12:49:48 | 1003 | ||||
|
R Project for Statistical Computing Resource Report Resource Website 10000+ mentions |
R Project for Statistical Computing (RRID:SCR_001905) | R | software resource | Software environment and programming language for statistical computing and graphics. R is integrated suite of software facilities for data manipulation, calculation and graphical display. Can be extended via packages. Some packages are supplied with the R distribution and more are available through CRAN family.It compiles and runs on wide variety of UNIX platforms, Windows and MacOS. | R software, statistical, computing, graphics, programming, language, bio.tools |
is used by: UTR is used by: MSstats is used by: CummeRbund is used by: deFuse is used by: JASP is used by: Boruta is used by: NMRProcFlow is used by: PlotsOfData is used by: rtransparent is used by: shinyCircoss is listed by: OMICtools is listed by: bio.tools is listed by: Debian is affiliated with: CRAN is affiliated with: factoextra is affiliated with: dendsort is affiliated with: viridis is affiliated with: RColorBrewer is affiliated with: statmod is related to: Sweave is related to: rOpenSci is related to: R Manuals is related to: Bioconductor is related to: ggplot2 is related to: madsim is related to: Solas is related to: braincog is related to: clustree is related to: PhenoSpD is related to: geomorph is related to: NeuroAnatomy Toolbox is related to: dplyr is related to: glmmADMB is related to: clusterProfiler is related to: ropls is related to: mixOmics is related to: FlowSOM is related to: Rtsne is related to: scran is related to: Rsubread is related to: riboSeqR is related to: Biostrings is related to: riboWaltz is related to: GenomicFeatures is related to: devtools is related to: affy is related to: affydata is related to: Heatmapper is related to: toxprofileR is related to: LTRpred is related to: RaceID is related to: PRSice is related to: Genomic Ranges is related to: Goseq is related to: GAGE is related to: metagear is related to: pagoda2 is related to: dndSCV is related to: tidyr is related to: ClustVis is related to: IDR is related to: NeuroAnatomy Toolbox is related to: rjags is related to: gProfiler2 is related to: knitr is related to: EpiEstim is related to: Minimum-Hypergeometric Test is related to: Network-Based R-Statistics is related to: seqpac is related to: survminer is related to: Vector Generalized Linear and Additive Models is related to: LEA is related to: StAMPP is related to: Betareg is related to: Harrell Miscellaneous is related to: simplePHENOTYPES is related to: Bayesian Generalized Linear Regression is related to: ranger is related to: h2o4gpu is related to: ridge regression Best Linear Unbiased Prediction is related to: Classification And Regression Training is related to: Rphenograph is related to: Peptides is related to: taxize is related to: seqinr is related to: reshape2 is related to: monaLisa is related to: mia is related to: Rtsne is related to: R package:stats-package is related to: R package: maxstat is related to: stats |
PMID:18252159 | SCR_021974, nif-0000-10474, OMICS_01147, biotools:r | https://cran.r-project.org/src/base/R-3/, https://bio.tools/r | SCR_001905 | R software, The R Project for Statistical Computing, R project, R Project, R, R version 3.5.1, R Package, R-3, R version 3.6.1, R Project for Statistical Computing | 2026-09-19 12:49:49 | 52118 | ||||||
|
Pecan Resource Report Resource Website 50+ mentions |
Pecan (RRID:SCR_001909) | software resource | A Java consistency based multiple sequence alignment software program. | java, sequence, alignment, consistency, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of California at Santa Cruz; California; USA |
PMID:18849524 | Free, Available for download, Freely available | OMICS_03739, biotools:pecan | http://hgwdev.cse.ucsc.edu/~benedict/code/Pecan.html, https://bio.tools/pecan | SCR_001909 | 2026-09-19 12:49:49 | 51 | |||||||
|
Ray Resource Report Resource Website 1+ mentions |
Ray (RRID:SCR_001916) | Ray | software resource | Software that assembles reads obtained with new sequencing technologies (Illumina, 454, SOLiD) using MPI 2.2. | mpi, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:20958248 DOI:10.1089/cmb.2009.0238 |
Free, Available for download, Freely available | OMICS_00027, biotools:ray | https://bio.tools/ray, https://sources.debian.org/src/ray/ | SCR_001916 | Ray - a de novo assembler using MPI 2.2, Ray - Parallel genome assemblies for parallel DNA sequencing | 2026-09-19 12:49:50 | 1 | |||||
|
GATK Resource Report Resource Website 10000+ mentions |
GATK (RRID:SCR_001876) | GATK | data analysis software, data processing software, software application, software library, software resource, software toolkit | A software package to analyze next-generation resequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size. This software library makes writing efficient analysis tools using next-generation sequencing data very easy, and second it's a suite of tools for working with human medical resequencing projects such as 1000 Genomes and The Cancer Genome Atlas. These tools include things like a depth of coverage analyzers, a quality score recalibrator, a SNP/indel caller and a local realigner. (entry from Genetic Analysis Software) | gene, genetic, genomic, next-generation resequencing, bio.tools |
is used by: Halvade Somatic is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: SnpEff is related to: GATK HaplotypeCaller is related to: GATK VariantFiltration has parent organization: Broad Institute |
PMID:21478889 | Free, Available for download, Freely available | nlx_154324, OMICS_00286, biotools:gatk | http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit, https://bio.tools/gatk | SCR_001876 | Genome Analysis ToolKit | 2026-09-19 12:49:49 | 18211 | |||||
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TCW Resource Report Resource Website 1+ mentions |
TCW (RRID:SCR_001875) | TCW | software resource | Software package for assembling, annotating, querying, and comparing transcript and expression level data that consists of two parts: * singleTCW (sTCW): Single transcript sets or assemblies; annotation; differential expression (EdgeR, DEGSeq, DESeq, GoSeq) * multiTCW (mTCW): Comparison of multiple transcript sets; ortholog grouping (e.g., OrthoMCL) It has been tested on Linux and uses Java, mySQL and optionally R. | transcript, assembly annotation, differential expression, transcript set, ortholog, expression, linux, java, mysql, r, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Arizona; Arizona; USA |
NSF IOS-1044821 | PMID:23874959 | Free, Available for download, Freely available | OMICS_01940, biotools:tCW | https://bio.tools/TCW | SCR_001875 | Transcriptome Computational Workbench, TCW: Transcriptome Computational Workbench | 2026-09-19 12:49:49 | 2 | ||||
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SPP Resource Report Resource Website 1+ mentions |
SPP (RRID:SCR_001790) | data analysis software, data processing software, software application, software resource | R analysis and processing package for Illumina platform Chip-Seq data. | chip seq data, illummina, r package, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite |
NHGRI U01HG004258; NIGMS R01GM082798; NCRR UL1RR024920 |
DOI:10.1038/nbt.1508 | Free, Available for download, Freely available | OMICS_00425, biotools:spp | https://bio.tools/spp | https://sites.google.com/a/brown.edu/bioinformatics-in-biomed/spp-r-from-chip-seq | SCR_001790 | SPP Package | 2026-09-19 12:49:47 | 9 | ||||
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myExperiment Resource Report Resource Website 10+ mentions |
myExperiment (RRID:SCR_001795) | myExperiment | community building portal, data or information resource, data processing software, data repository, database, portal, service resource, software application, software resource, storage service resource, workflow software | Community repository and virtual research environment where scientists can safely publish their workflows and experiment plans, share them with groups and find and use those of others. Workflows, other digital objects and collections (called Packs) can be swapped, sorted and searched. It supports Linked data, has a SPARQL Endpoint and REST API and is based on an open source Ruby on Rails codebase. Scientific workflows in various formats can be uploaded. Specific support is provided for Taverna workflows for which the system displays relevant metadata, components and visual previews, that are retrieved directly from workflow files. Version history for workflows is collected. This feature allows the contributor to keep previous versions of the workflow available, when the latest one is uploaded. This brings additional benefit for the users by allowing them to view the development stages of the workflow towards its latest implementation. | workflow, pipeline, platform, component, data sharing, publish, digital object, experimental method, workflow management, virtual research environment, collaborative computing, taverna workflow workbench, bioinformatics, web service, bio.tools |
is listed by: FORCE11 is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: Taverna is related to: Workflow4Ever is related to: Biocatalogue - The Life Science Web Services Registry has parent organization: University of Southampton; Southampton; United Kingdom has parent organization: University of Manchester; Manchester; United Kingdom has parent organization: University of Oxford; Oxford; United Kingdom |
JISC ; Microsoft Technical Computing Initiative ; EPSRC |
PMID:20501605 | Free, Freely available | nif-0000-10309, r3d100010473, biotools:myexperiment | https://www.force11.org/node/4638, https://bio.tools/myexperiment | SCR_001795 | my experiment | 2026-09-19 12:49:47 | 23 | ||||
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TEMP Resource Report Resource Website 100+ mentions |
TEMP (RRID:SCR_001788) | software resource | Software package for detecting transposable elements (TEs) insertions and excisions from pooled high-throughput sequencing data. | standalone software, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Massachusetts Medical School; Massachusetts; USA |
PMID:24753423 | Free, Available for download, Freely available | OMICS_03821, biotools:temp | https://bio.tools/temp | SCR_001788 | 2026-09-19 12:49:47 | 216 | |||||||
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AffyPipe Resource Report Resource Website 1+ mentions |
AffyPipe (RRID:SCR_002032) | software resource | An open-source software pipeline for Affymetrix Axiom genotyping workflow. | affymetrix, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
Italian Ministry of Education University and Research 505/Ric; project GenHome ; European Union FP7 project Gene2Farm 289592 |
PMID:25028724 | Free, Available for download, Freely available | biotools:affypipe, OMICS_05203 | https://bio.tools/affypipe | SCR_002032 | AffyPipe: an open-source pipeline for Affymetrix Axiom genotyping workflow | 2026-09-19 12:49:52 | 5 | |||||
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Addgene Resource Report Resource Website 10000+ mentions |
Addgene (RRID:SCR_002037) | data or information resource, material storage repository, organization portal, portal, service resource, storage service resource | Non-profit plasmid repository dedicated to helping scientists around the world share high-quality plasmids. Facilitates archiving and distributing DNA-based research reagents and associated data to scientists worldwide. Repository contains over 65,000 plasmids, including special collections on CRISPR, fluorescent proteins, and ready-to-use viral preparations. There is no cost for scientists to deposit plasmids, which saves time and money associated with shipping plasmids themselves. All plasmids are fully sequenced for validation and sequencing data is openly available. We handle the appropriate Material Transfer Agreements (MTA) with institutions, facilitating open exchange and offering intellectual property and liability protection for depositing scientists. Furthermore, we curate free educational resources for the scientific community including a blog, eBooks, video protocols, and detailed molecular biology resources. | RIN, Resource Information Network, plasmid, molecular biology, sequence alignment, repository, bio.tools, FASEB list, RRID Community Authority |
uses: GenomeCompiler is used by: NIF Data Federation is used by: NIDDK Information Network (dkNET) is used by: Structural Genomics Consortium is used by: ZCre is listed by: One Mind Biospecimen Bank Listing is listed by: DataCite is listed by: re3data.org is listed by: bio.tools is listed by: Debian is listed by: Resource Information Network is related to: zfishbook is related to: GenomeCompiler is related to: Phoenix is related to: Integrated Manually Extracted Annotation is related to: Genetic Tools Atlas is parent organization of: Vector Database |
Fees collected from plasmid sales support operation of the repository | DOI:10.1093/nar/gku893 | Free (deposit of plasmids), Limited (Some available to academic and non-profits, For-profit entities, Commercial license), Material Transfer Agreement, Non-commercial, Acknowledgement required, Copyrighted, For informational purposes only, Commercial with written consent, The community can contribute to this resource | ISNI: 0000 0004 5912 0787, Wikidata: Q4681063, grid.482682.2, biotools:Addgene, nif-0000-11872 | https://ror.org/01nn1pw54, https://bio.tools/Addgene | SCR_002037 | Addgene Repository, Addgene Plasmid Database | 2026-09-19 12:49:52 | 54912 | |||||
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CanSNPer Resource Report Resource Website 10+ mentions |
CanSNPer (RRID:SCR_001980) | software resource | Software that is a hierarchical genotype classifier of clonal pathogens. | python, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:24574113 | Free, Available for download, Freely available | biotools:cansnper, OMICS_03706 | https://bio.tools/cansnper | SCR_001980 | 2026-09-19 12:49:52 | 18 | |||||||
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Candida Genome Database Resource Report Resource Website 500+ mentions |
Candida Genome Database (RRID:SCR_002036) | CGD, CGD LOCUS, CGD REF | data or information resource, data repository, database, service resource, storage service resource | Database of genetic and molecular biological information about Candida albicans. Contains information about genes and proteins, descriptions and classifications of their biological roles, molecular functions, and subcellular localizations, gene, protein, and chromosome sequence information, tools for analysis and comparison of sequences and links to literature information. Each CGD gene or open reading frame has an individual Locus Page. Genetic loci that are not tied to DNA sequence also have Locus Pages. Provides Gene Ontology, GO, to all its users. Three ontologies that comprise GO (Molecular Function, Cellular Component, and Biological Process) are used by multiple databases to annotate gene products, so that this common vocabulary can be used to compare gene products across species. Development of ontologies is ongoing in order to incorporate new information. Data submissions are welcome. | protein, chromosome, classification, gene, genome, candidiasis, thrush, yeast, yeast gene, yeast genome, candida albicans, candida glabrata, data analysis service, biological role, molecular function, subcellular localization, chromosome sequence, bio.tools, FASEB list |
is used by: NIF Data Federation is listed by: bio.tools is listed by: Debian is related to: AmiGO is related to: ASPGD is related to: Gene Ontology has parent organization: Stanford University School of Medicine; California; USA |
NIDCR DE015873 | PMID:19808938 | Free, Available for download, Freely available | biotools:cgd, nif-0000-02634, r3d100010617 | https://bio.tools/cgd | SCR_002036 | 2026-09-19 12:49:53 | 506 | |||||
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InteroPorc Resource Report Resource Website 1+ mentions |
InteroPorc (RRID:SCR_002067) | InteroPorc | analysis service resource, data analysis service, data analysis software, data or information resource, data processing software, database, production service resource, service resource, software application, software resource, source code | Automatic prediction tool to infer protein-protein interaction networks, it is applicable for lots of species using orthology and known interactions. The interoPORC method is based on the interolog concept and combines source interaction datasets from public databases as well as clusters of orthologous proteins (PORC) available on Integr8. Users can use this page to ask InteroPorc for all species present in Integr8. Some results are already computed and users can run InteroPorc to investigate any other species. Currently, the following databases are processed and merged (with datetime of the last available public release for each database used): IntAct, MINT, DIP, and Integr8. | orthology, prediction, protein interaction, tool, sequenced genome, proteinprotein interaction, inferred interaction, molecular interaction, interaction, protein, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: Integr8 : Access to complete genomes and proteomes is related to: IntAct is related to: MINT is related to: Database of Interacting Proteins (DIP) is related to: PSICQUIC Registry has parent organization: CEA; Gif sur Yvette; France |
European Union FELICS 021902 RII3; Marie Curie Fellowship ; French National Agency of Research ANR Biosys06_134823 SULFIRHOM; French Atomic Energy Commission |
PMID:18508856 | Open unspecified license, Acknowledgement requested | nif-0000-20816, biotools:interoporc | https://bio.tools/interoporc | SCR_002067 | InteroPorc: Automatic molecular interaction predictions, Automatic molecular interaction predictions | 2026-09-19 12:49:52 | 6 | ||||
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SNVer Resource Report Resource Website 50+ mentions |
SNVer (RRID:SCR_002061) | data analysis software, data processing software, software application, software resource | Statistical software tool for calling common and rare variants in analysis of pool or individual next-generation sequencing data. This software is optimized for analysis of whole-exome sequencing data and whole-genome sequencing data. | statistical analysis software, sequencing, dna, whole-exome, whole-genome, variant, bio.tools |
lists: SAMTOOLS is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:21813454 | Free, Available for download, Freely available | OMICS_00076, biotools:snver | https://sourceforge.net/projects/snver/, https://bio.tools/snver | SCR_002061 | 2026-09-19 12:49:52 | 52 | |||||||
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Kalign Resource Report Resource Website 100+ mentions |
Kalign (RRID:SCR_011810) | Kalign | software resource | A fast and accurate multiple sequence alignment algorithm. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: European Bioinformatics Institute |
PMID:16343337 DOI:10.1093/bioinformatics/btz795 |
Free | OMICS_00978, biotools:kalign | https://bio.tools/kalign, https://sources.debian.org/src/kalign/ | SCR_011810 | 2026-09-19 12:52:18 | 123 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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