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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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EBCall Resource Report Resource Website 10+ mentions |
EBCall (RRID:SCR_006791) | EBCall | software resource | A software package for somatic mutation detection (including InDels). EBCall uses not only paired tumor/normal sequence data of a target sample, but also multiple non-paired normal reference samples for evaluating distribution of sequencing errors, which leads to an accurate mutaiton detection even in case of low sequencing depths and low allele frequencies. | mutation, cancer, genome, sequencing, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Tokyo; Tokyo; Japan |
PMID:23471004 | Copyright conditions, Acknowledgement required | biotools:ebcall, OMICS_00084 | https://bio.tools/ebcall | SCR_006791 | EBCall (Empirical Baysian mutation Calling), Empirical Baysian mutation Calling | 2026-09-12 12:56:45 | 20 | |||||
|
Proteomics Identifications (PRIDE) Resource Report Resource Website 500+ mentions |
Proteomics Identifications (PRIDE) (RRID:SCR_003411) | PRIDE | data or information resource, data repository, database, service resource, storage service resource | Centralized, standards compliant, public data repository for proteomics data, including protein and peptide identifications, post-translational modifications and supporting spectral evidence. Originally it was developed to provide a common data exchange format and repository to support proteomics literature publications. This remit has grown with PRIDE, with the hope that PRIDE will provide a reference set of tissue-based identifications for use by the community. The future development of PRIDE has become closely linked to HUPO PSI. PRIDE encourages and welcomes direct user submissions of protein and peptide identification data to be published in peer-reviewed publications. Users may Browse public datasets, use PRIDE BioMart for custom queries, or download the data directly from the FTP site. PRIDE has been developed through a collaboration of the EMBL-EBI, Ghent University in Belgium, and the University of Manchester. | proteomics, protein, peptide, mass spectrometry, annotation, standard, spectra, protein-protein interaction, amino acid, amino acid sequence, post-translational modification, biomart, bio.tools |
is used by: ProteomeXchange is used by: BioSample Database at EBI is recommended by: NIDDK Information Network (dkNET) is listed by: Biositemaps is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: HUPO Proteomics Standards Initiative is related to: ProteomeXchange has parent organization: European Bioinformatics Institute |
Wellcome Trust WT085949MA; European Union FP7 LSHG-CT-2006-036814; European Union FP7 260558; European Union FP7 262067; European Union FP7 202272; BBSRC BB/I024204/1 |
PMID:23203882 PMID:19662629 |
Free, Available for download, Freely available | nif-0000-03336, biotools:pride, r3d100011515 | https://www.ebi.ac.uk/pride/archive/, https://bio.tools/pride, https://doi.org/10.17616/R3F330 | SCR_003411 | PRoteomics IDEntifications database, PRIDE Archive - proteomics data repository, PRIDE Archive, PRIDE, Proteomics Identifications, Proteomics Identifications (PRIDE), PRoteomics IDEntifications database (PRIDE) | 2026-09-12 12:55:57 | 811 | ||||
|
ALDEx2 Resource Report Resource Website 500+ mentions |
ALDEx2 (RRID:SCR_003364) | software resource | Software tool to examine compositional high-throughput sequence data with Welch's t-test. A differential relative count abundance analysis for the comparison of two conditions. For example, single-organism and meta-rna-seq high-throughput sequencing assays, or of selected and unselected values from in-vitro sequence selections. Uses a Dirichlet-multinomial model to infer abundance from counts, that has been optimized for three or more experimental replicates. Infers sampling variation and calculates the expected Benjamini-Hochberg false discovery rate given the biological and sampling variation using several parametric and non-parametric tests. Can to glm and Kruskal-Wallace tests on one-way ANOVA style designs. | standalone software, r, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: aldex has parent organization: Western University; Ontario; Canada |
PMID:24910773 | Free, Available for download, Freely available | biotools:aldex2, OMICS_04634 | https://bio.tools/aldex2 | SCR_003364 | 2026-09-12 12:55:57 | 609 | |||||||
|
ggbio Resource Report Resource Website 10+ mentions |
ggbio (RRID:SCR_003313) | software resource | An R package for extending the grammar of graphics for genomic data. The graphics are designed to answer common scientific questions, in particular those often asked of high throughput genomics data. All core Bioconductor data structures are supported, where appropriate. The package supports detailed views of particular genomic regions, as well as genome-wide overviews. Supported overviews include ideograms and grand linear views. High-level plots include sequence fragment length, edge-linked interval to data view, mismatch pileup, and several splicing summaries. | standalone software, unix/linux, mac os x, windows, r, infrastructure, visualization, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
PMID:22937822 | Free, Available for download, Freely available | biotools:ggbio, OMICS_04660 | http://www.tengfei.name/ggbio/, https://bio.tools/ggbio | SCR_003313 | ggbio - Visualization tools for genomic data | 2026-09-12 12:55:55 | 16 | ||||||
|
deFuse Resource Report Resource Website 50+ mentions |
deFuse (RRID:SCR_003279) | data analysis software, data processing software, sequence analysis software, software application, software resource, software toolkit | Software package for gene fusion discovery using RNA-Seq data. It uses clusters of discordant paired end alignments to inform a split read alignment analysis for finding fusion boundaries. | rna sequencing, gene fusion, paired end alignment, split read, fusion boundary, bio.tools |
uses: SAMTOOLS uses: Bowtie uses: BLAT uses: GMAP uses: R Project for Statistical Computing is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
British Columbia Cancer Foundation ; Vancouver General Hospital Foundation ; Genome Canada ; Michael Smith Foundation for Health Research ; Canadian Breast Cancer Foundation ; Canadian Institutes of Health Research's Bioinformatics Training Program |
PMID:21625565 | Free, Available for download, Freely available | biotools:defuse, OMICS_01345 | https://sourceforge.net/projects/defuse/, http://compbio.bccrc.ca/software/defuse/, https://bio.tools/defuse | http://sourceforge.net/apps/mediawiki/defuse/index.php?title=Main_Page | SCR_003279 | 2026-09-12 12:55:55 | 95 | |||||
|
PrimerSeq Resource Report Resource Website 1+ mentions |
PrimerSeq (RRID:SCR_003295) | PrimerSeq | software resource | Software that designs RT-PCR primers that evaluate alternative splicing events by incorporating RNA-Seq data. It is particularly advantageous for designing a large number of primers for validating alternative splicing events found in RNA-Seq data. It incorporates RNA-Seq data in the design process to weight exons by their read counts. Essentially, the RNA-Seq data allows primers to be placed using actually expressed transcripts. This could be for a particular cell line or experimental condition, rather than using annotations that incorporate transcripts that are not expressed for the data. Alternatively, you can design primers that are always on constitutive exons. PrimerSeq does not limit the use of gene annotations and can be used for a wide array of species. | primer, rna-seq, rt-pcr, windows, mac os x, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:24747190 | Free, Available for download, Freely available | biotools:primerseq, OMICS_02328 | https://bio.tools/primerseq | SCR_003295 | Primer Seek in RNA-Seq | 2026-09-12 12:55:55 | 7 | |||||
|
MIPgen Resource Report Resource Website 50+ mentions |
MIPgen (RRID:SCR_003325) | software resource | Software for a fast, simple way to generate designs for MIP assays targeting hundreds or thousands of genomic loci in parallel. Packaged with MIPgen are scripts that aid in visualization of MIP designs and processing of MIP sequence reads to SAM files that can then be passed through any standard variant calling pipeline. | standalone software, c++, python, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Washington; Seattle; USA |
PMID:24867941 | Free, Available for download, Freely available | OMICS_04657, biotools:mipgen | https://github.com/shendurelab/MIPGEN, https://bio.tools/mipgen | SCR_003325 | MIPgen - One stop MIP design and analysis | 2026-09-12 12:55:56 | 52 | ||||||
|
Snakemake Resource Report Resource Website 100+ mentions |
Snakemake (RRID:SCR_003475) | Snakemake | software resource | A Python based language and execution environment for make-like workflows. The system supports the use of automatically inferred multiple named wildcards (or variables) in input and output filenames. | python, workflow, bio.tools |
is used by: RiboSnake is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Google Code |
PMID:22908215 DOI:10.1093/bioinformatics/bts480 |
Free, Available for download, Freely available | OMICS_02299, biotools:snakemake | https://snakemake.github.io/ | SCR_003475 | snakemake - A Python based language and execution environment for make-like workflows | 2026-09-12 12:55:58 | 465 | |||||
|
PheWAS R Package Resource Report Resource Website 1+ mentions |
PheWAS R Package (RRID:SCR_003512) | software resource | Software package contains methods for performing Phenome-Wide Association Study. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Vanderbilt University; Tennessee; USA |
PMID:20335276 | Free | OMICS_00242, biotools:phewas | https://bio.tools/phewas | SCR_003512 | Phenome-Wide Association Study | 2026-09-12 12:55:59 | 7 | ||||||
|
Cell Image Library (CIL) Resource Report Resource Website 10+ mentions |
Cell Image Library (CIL) (RRID:SCR_003510) | CIL | data or information resource, data repository, database, image repository, service resource, storage service resource | Freely accessible, public repository of vetted and annotated microscopic images, videos, and animations of cells from a variety of organisms, showcasing cell architecture, intracellular functionalities, and both normal and abnormal processes. Explore by Cell Process, Cell Component, Cell Type or Organism. The Cell includes images acquired from historical and modern collections, publications, and by recruitment. | microscopic image repository, microscopic video repository, cell animation repository, bio.tools |
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: bio.tools is listed by: Debian is related to: Cell Centered Database is related to: Cell Centered Database is related to: OME-TIFF Format is related to: Integrated Manually Extracted Annotation has parent organization: American Society for Cell Biology has parent organization: University of California; San Diego;National Center for Microscopy and Imaging Research - NCMIR has parent organization: University of California at San Diego; California; USA is parent organization of: Biological Imaging Methods Ontology |
NIGMS RC2 GM092708 | PMID:34218671 PMID:34218673 |
Free, Freely available | biotools:cellimagelibrary, nif-0000-37639, r3d100011601 | http://www.cellimagelibrary.org/pages/about, https://bio.tools/cellimagelibrary, https://doi.org/10.17616/R3N92J | SCR_003510 | Cell Image Library. CIL, Cell Image Library (CIL) | 2026-09-12 12:55:59 | 22 | ||||
|
Bpipe Resource Report Resource Website 10+ mentions |
Bpipe (RRID:SCR_003471) | Bpipe | software resource | Software tool for running and managing bioinformatics pipelines. It specializes in enabling users to turn existing pipelines based on shell scripts or command line tools into highly flexible, adaptable and maintainable workflows with a minimum of effort. Bpipe ensures that pipelines execute in a controlled and repeatable fashion and keeps audit trails and logs to ensure that experimental results are reproducible. Requiring only Java as a dependency, it is fully self-contained and cross-platform, making it very easy to adopt and deploy into existing environments. | genetics, dna, analysis, cluster, workflow, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Google Code |
PMID:22500002 | Free, Available for download, Freely available | biotools:bpipe, OMICS_02301 | https://github.com/ssadedin/bpipe | SCR_003471 | bpipe - A tool for running and managing bioinformatics pipelines | 2026-09-12 12:55:58 | 13 | |||||
|
Parseq Resource Report Resource Website 1+ mentions |
Parseq (RRID:SCR_003464) | Parseq | software resource | Statistical software for transcription landscape reconstruction at a basepair resolution from RNA Seq read counts. It is based on a state-space model which describes, in terms of abrupt shifts and more progressive drifts, the transcription level dynamics along the genome. Alongside variations of transcription level, it incorporates a component of short-range variation to pull apart local artifacts causing correlated dispersion. Reconstruction of the transcription level relies on a conditional sequential Monte Carlo approach that is combined with parameter estimation in a Markov chain Monte Carlo algorithm known as particle Gibbs. The method allows to estimate the local transcription level, to call transcribed regions, and to identify the transcript borders. | rna-seq, genome, transcription, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Sorbonne University; Paris; France |
PMID:24470570 | Free, Available for download, Freely available | biotools:parseq, OMICS_02302 | https://bio.tools/parseq | SCR_003464 | 2026-09-12 12:55:58 | 2 | ||||||
|
MultiPhen Resource Report Resource Website 10+ mentions |
MultiPhen (RRID:SCR_003498) | software resource | Software package that performs genetic association tests between SNPs (one-at-a-time) and multiple phenotypes (separately or in joint model). | standalone software, r, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: CRAN |
PMID:22567092 | GNU General Public License, v2 | biotools:multiphen, OMICS_04397 | https://bio.tools/multiphen | SCR_003498 | MultiPhen: a package for the genetic association testing of multiple phenotypes | 2026-09-12 12:55:59 | 31 | ||||||
|
EBSeq Resource Report Resource Website 500+ mentions |
EBSeq (RRID:SCR_003526) | EBSeq | software resource | Software R package for RNA-Seq Differential Expression Analysis. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Wisconsin-Madison; Wisconsin; USA |
PMID:23428641 DOI:10.1093/bioinformatics/btt087 |
biotools:ebseq, OMICS_01307 | https://bio.tools/ebseq, https://sources.debian.org/src/r-bioc-ebseq/ | SCR_003526 | 2026-09-12 12:55:59 | 590 | |||||||
|
Reactome Resource Report Resource Website 1000+ mentions |
Reactome (RRID:SCR_003485) | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | Collection of pathways and pathway annotations. The core unit of the Reactome data model is the reaction. Entities (nucleic acids, proteins, complexes and small molecules) participating in reactions form a network of biological interactions and are grouped into pathways (signaling, innate and acquired immune function, transcriptional regulation, translation, apoptosis and classical intermediary metabolism) . Provides website to navigate pathway knowledge and a suite of data analysis tools to support the pathway-based analysis of complex experimental and computational data sets. | pathway, interaction, reaction, nucleic acid, protein, complex, small molecule, signaling pathway, immune function, transcriptional regulation, translation, apoptosis, metabolism, ortholog, visualization, protein-protein interaction, web service, book, biomart, gold standard, bio.tools, FASEB list |
is used by: NIF Data Federation is used by: DisGeNET is used by: Pathway Analysis Tool for Integration and Knowledge Acquisition is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: WikiPathways is related to: Pathway Commons is related to: ConsensusPathDB is related to: FlyMine is related to: AmiGO is related to: PSICQUIC Registry is related to: Integrated Molecular Interaction Database is related to: NCBI BioSystems Database is related to: MOPED - Model Organism Protein Expression Database is related to: KOBAS is related to: PSICQUIC Registry is related to: Pathway Interaction Database is related to: hiPathDB - human integrated Pathway DB with facile visualization is related to: Algal Functional Annotation Tool has parent organization: Ontario Institute for Cancer Research has parent organization: Cold Spring Harbor Laboratory has parent organization: European Bioinformatics Institute has parent organization: New York University School of Medicine; New York; USA works with: PathwayMatcher |
European Molecular Biology Laboratory ; European Union FP6 ENFIN LSHG-CT-2005-518254; NHGRI P41 HG003751; NIGMS GM080223; NIGMS R01 GM100039; Ontario Research Fund |
PMID:21082427 PMID:21067998 |
Open source, Public, Freely available | r3d100010285, nif-0000-03390, biotools:reactome | https://bio.tools/reactome, https://doi.org/10.17616/R3V59P | SCR_003485 | Reactome Functional Interaction Network | 2026-09-12 12:55:59 | 4810 | |||||
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L-Measure Resource Report Resource Website 10+ mentions |
L-Measure (RRID:SCR_003487) | LM | data processing software, image analysis software, image processing software, service resource, software application, software resource | A freely available software tool available for the Windows and Linux platform, as well as the Online version Applet, for the analysis, comparison and search of digital reconstructions of neuronal morphologies. For the quantitative characterization of neuronal morphology, LM computes a large number of neuroanatomical parameters from 3D digital reconstruction files starting from and combining a set of core metrics. After more than six years of development and use in the neuroscience community, LM enables the execution of commonly adopted analyses as well as of more advanced functions, including: (i) extraction of basic morphological parameters, (ii) computation of frequency distributions, (iii) measurements from user-specified subregions of the neuronal arbors, (iv) statistical comparison between two groups of cells and (v) filtered selections and searches from collections of neurons based on any Boolean combination of the available morphometric measures. These functionalities are easily accessed and deployed through a user-friendly graphical interface and typically execute within few minutes on a set of 20 neurons. The tool is available for either online use on any Java-enabled browser and platform or may be downloaded for local execution under Windows and Linux. | neuronal morphology, neuroinformatics, branching analysis, digital reconstruction, analysis, comparison, bio.tools |
is listed by: 3DVC is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is listed by: bio.tools has parent organization: Computational Neuroanatomy Group |
Human Brain Project ; NINDS R01 NS39600 |
PMID:18451794 | Public | nif-0000-00003, biotools:l-measure | http://www.nitrc.org/projects/lmeasure, https://bio.tools/l-measure | SCR_003487 | 2026-09-12 12:55:59 | 30 | |||||
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jmzTab Resource Report Resource Website 1+ mentions |
jmzTab (RRID:SCR_003481) | software resource | A Java interface to the mzTab data exchange format for reporting a summary of proteomics results. | standalone software, mac os x, unix/linux, java, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Google Code |
PMID:24659499 | Apache License, v2 | OMICS_04542, biotools:jmztab | https://bio.tools/jmztab | SCR_003481 | 2026-09-12 12:55:59 | 1 | |||||||
|
metagen Resource Report Resource Website 10+ mentions |
metagen (RRID:SCR_003443) | metagen | software resource | Software program providing a method for meta-analysis of case-control genetic association studies using random-effects logistic regression. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:17605724 | Free, Available for download, Freely available | OMICS_00238, biotools:metagen | https://www.rdocumentation.org/packages/meta/versions/4.9-6/topics/metagen | SCR_003443 | 2026-09-12 12:55:58 | 21 | ||||||
|
eTRIKS Resource Report Resource Website 10+ mentions |
eTRIKS (RRID:SCR_003765) | eTRIKS | consortium, data or information resource, organization portal, portal, service resource | Research informatics and analytics platform for the IMI OncoTrack consortium. | data sharing, drug discovery, translational research, informatics, knowledge management, metadata standard, platform, analytics, tool development, bio.tools |
uses: tranSMART is used by: U-BIOPRED is used by: Predict-TB is used by: OncoTrack is used by: ABIRISK is used by: RA MAP is listed by: Consortia-pedia is listed by: Debian is listed by: bio.tools is related to: Roche is related to: Janssen Research and Development is related to: Merck is related to: Pfizer Animal Genetics is related to: Imperial College London; London; United Kingdom is related to: French National Center for Scientific Research is related to: Clinical Data Interchange Standards Consortium is related to: University of Luxembourg; Luxembourg; Luxembourg is related to: IDBS is related to: BioSci Consulting is related to: TraIT is related to: EMIF is related to: Open PHACTS has parent organization: Imperial College London; London; United Kingdom |
Innovative Medicines Initiative ; EFPIA |
PMID:29482119 | biotools:eTRIKS, nlx_158034 | https://bio.tools/eTRIKS | SCR_003765 | European Translational Information and Knowledge Management Services, European Translational Information & Knowledge Management Services | 2026-09-12 12:56:02 | 11 | |||||
|
RAREMETAL Resource Report Resource Website 10+ mentions |
RAREMETAL (RRID:SCR_003573) | RAREMETAL | software resource | A software program that facilitates the meta-analysis of rare variants from genotype arrays or sequencing. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Michigan; Ann Arbor; USA |
PMID:24894501 | biotools:raremetal, OMICS_00243 | https://bio.tools/raremetal | SCR_003573 | 2026-09-12 12:56:00 | 22 |
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