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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
3D-footprint Resource Report Resource Website |
3D-footprint (RRID:SCR_015713) | data or information resource, database | Database of DNA-binding protein structures that is updated with Protein Data Bank complexes. It provides structure-based binding specificities and sequence logos, classification and clusters of protein-DNA interfaces, and downloads/stats. | dna binding protein structure, protein data bank, sequencing, protein-dna interface, bio.tools |
is listed by: Debian is listed by: bio.tools works with: footprintDB |
CSIC 200720I038 | PMID:19767616 | Freely available, Free for academic use, Tutorial available | biotools:3d-footprint | https://bio.tools/3d-footprint | SCR_015713 | 2026-09-19 12:57:35 | 0 | ||||||
|
ProteomicsDB Resource Report Resource Website 100+ mentions |
ProteomicsDB (RRID:SCR_015562) | data or information resource, database | Database for the identification of the human proteome and its use across the scientific community. Users can browse proteins and chromosomes and contribute to the data repository. | human proteome, human proteomics, proteomics database, human proteomics database, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools is related to: ProteomeTools has parent organization: Technical University of Munich; Bavaria; Germany |
PMID:24870543 | The research community can contribute to this resource | r3d100013408, biotools:proteomicsdb | https://bio.tools/proteomicsdb, https://doi.org/10.17616/R31NJMU8 | SCR_015562 | 2026-09-19 12:57:35 | 180 | |||||||
|
EGSEA Resource Report Resource Website 50+ mentions |
EGSEA (RRID:SCR_015036) | software resource, software toolkit, source code | Method developed for RNA-sequencing data. EGSEA combines results from twelve algorithms and calculates collective gene set scores to improve the biological relevance of the highest ranked gene sets. | gene set, rna sequencing, analysis method, r package, bio.tools |
is listed by: Debian is listed by: bio.tools is hosted by: Bioconductor |
Victorian State Government Operational Infrastructure Support ; Australian Government NHMRC IRIISS ; NHMRC GNT1050661; NHMRC GNT1045936; NHMRC GNT1057854; NHMRC GNT1104924 |
PMID:27694195 | Free, Available for download | biotools:egsea | https://bio.tools/egsea | SCR_015036 | Ensemble of Gene Set Enrichment Analyses (EGSEA), Ensemble of Gene Set Enrichment Analyses | 2026-09-19 12:57:34 | 64 | |||||
|
Datasets2Tools Resource Report Resource Website 1+ mentions |
Datasets2Tools (RRID:SCR_016174) | data or information resource, database | Database for the discovery and evaluation of biomedical digital objects. It includes a wide variety of enrichment analyses, gene interaction networks, interactive data visualizations, datasets, and computational tools. | biomedical, digital, bioinformatics, dataset, rna seq, computation, microarray, proteomic, bio.tools |
is listed by: bio.tools is listed by: Debian |
Public, Freely available | biotools:datasets2tools | https://bio.tools/datasets2tools | SCR_016174 | 2026-09-19 12:57:35 | 1 | ||||||||
|
TransmiR Resource Report Resource Website 100+ mentions |
TransmiR (RRID:SCR_017499) | data or information resource, database | Collection of transcription factor microRNA regulations. TransmiR v2.0 manually curated TF-miRNA regulations from publications during 2013-2017 and included ChIP-seq-derived TF-miRNA regulation data. | Transcription, factor, miRNA, regulation, manually, curated, TF-miRNA, ChIPseq, derived, TF-miRNA, data, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian has parent organization: Peking University; Beijing; China |
Restricted | biotools:transmir | https://bio.tools/transmir/ | SCR_017499 | TransmiR v2.0 | 2026-09-19 12:57:36 | 123 | |||||||
|
HmtVar Resource Report Resource Website 10+ mentions |
HmtVar (RRID:SCR_017288) | data or information resource, database, service resource | Manually curated database offering variability and pathogenicity information about mtDNA variants. Human mitochondrial variants data of healthy and diseased subjects.Data and text mining pipeline to annotate human mitochondrial variants with functional and clinical information. | manually, curated, data, variability, mitochondria, pathogenicity, mtDNA, variant, human, bio.tools |
uses: HmtDB - Human Mitochondrial DataBase uses: 1000 Genomes Project and AWS uses: MITOMAP - A human mitochondrial genome database uses: MutPred uses: SNPsandGO is listed by: Debian is listed by: bio.tools is affiliated with: University of Bologna; Bologna; Italy has parent organization: University of Bari; Bari; Italy |
DHOMOS Worldwide Cancer Research ; DISCO TRIP ; Italian Ministry of Health ; Rosa Maria Massari fellowship from the Italian Association for Cancer Research |
PMID:30371888 PMID:31821723 |
Free, Freely available | biotools:HmtVar | https://bio.tools/HmtVar | SCR_017288 | 2026-09-19 12:57:36 | 12 | ||||||
|
Blood Exposome Database Resource Report Resource Website 10+ mentions |
Blood Exposome Database (RRID:SCR_017610) | data or information resource, database | Collection of chemical compounds and associated information that were automatically extracted by text mining content of PubMed and PubChem databases. Unifies chemical lists from metabolomics, systems biology, environmental epidemiology, occupational expossure, toxiology and nutrition fields. | Chemical, compound, collection, extracted, text, mining, PubMed chemical compounds list, PubChem chemical compounds list, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: University of California at Davis; California; USA |
NIAID U54 AI138370; NIA U19 AG023122; NIEHS U2C ES030158 |
PMID:31557052 | Free, Available for download, Freely available | biotools:blood-exposome-db | https://github.com/barupal/exposome, https://bio.tools/blood-exposome-db | SCR_017610 | The Blood Exposome Database, exposome | 2026-09-19 12:57:37 | 11 | |||||
|
PEPPER Resource Report Resource Website 1+ mentions |
PEPPER (RRID:SCR_000431) | PEPPER | software application, software resource | A Cytoscape app designed to identify protein pathways / complexes as densely connected subnetworks from seed lists of proteins derived from pull-down assays (i.e AP-MS...). | plugin, protein-protein interaction, network, bio.tools |
is listed by: OMICtools is listed by: Cytoscape is listed by: bio.tools is listed by: Debian |
PMID:25138169 | Free, Available for download, Freely available | biotools:pepper, OMICS_05485 | https://bio.tools/pepper | SCR_000431 | Protein complex Expansion using Protein-Protein intERaction networks, Protein complex Expansion using Protein-Protein intERactions | 2026-09-19 12:57:41 | 1 | |||||
|
LOCUSMAP Resource Report Resource Website |
LOCUSMAP (RRID:SCR_000840) | LOCUSMAP | software application, software resource | Software package designed for rapid linkage analysis and map construction of loci with a variety of inheritance modes. (entry from Genetic Analysis Software) | gene, genetic, genomic, fortran 90/95, ms-windows, linux, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
nlx_154434, biotools:locusmap | https://bio.tools/locusmap | SCR_000840 | 2026-09-19 12:57:42 | 0 | ||||||||
|
circlize Resource Report Resource Website 1000+ mentions |
circlize (RRID:SCR_002141) | software application, software resource, standalone software | Software package that implements and enhances circular visualization in R. Due to natural born feature of R to draw statistical graphics, this package can provide more general and flexible way to visualize huge information in circular style. | circular visualization, draw statistical graphics, circular style graphics, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: CRAN |
PMID:24930139 | Free, Available for download, Freely available | OMICS_04658, biotools:circlize | https://github.com/jokergoo/circlize, https://bio.tools/circlize | SCR_002141 | circlize: Circular Visualization in R | 2026-09-19 12:57:44 | 1289 | ||||||
|
GERMLINE Resource Report Resource Website 100+ mentions |
GERMLINE (RRID:SCR_001720) | GERMLINE | software application, software resource | Software application for discovering long shared segments of Identity by Descent (IBD) between pairs of individuals in a large population. It takes as input genotype or haplotype marker data for individuals (as well as an optional known pedigree) and generates a list of all pairwise segmental sharing., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, genetic, genomic, c++, linux, bio.tools |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian has parent organization: Columbia University; New York; USA |
PMID:18971310 | Free, Available for download, Freely available | biotools:germline, OMICS_00202, nlx_154080 | https://bio.tools/germline | http://www1.cs.columbia.edu/~gusev/germline/ | SCR_001720 | 2026-09-19 12:57:44 | 451 | |||||
|
BREAKDANCER Resource Report Resource Website 100+ mentions |
BREAKDANCER (RRID:SCR_001799) | BreakDancer | software application, software resource | A Perl/C++ software package that provides genome-wide detection of structural variants from next generation paired-end sequencing reads. BreakDancerMax predicts five types of structural variants: insertions, deletions, inversions, inter- and intra-chromosomal translocations from next-generation short paired-end sequencing reads using read pairs that are mapped with unexpected separation distances or orientation. (entry from Genetic Analysis Software) | gene, genetic, genomic, perl, c++, next generation sequencing, structural variant, insertion, deletion, inversion, inter-chromosomal translocation, intra-chromosomal translocation, chromosomal translocation, indel, bio.tools |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian is listed by: SoftCite has parent organization: Washington University School of Medicine in St. Louis; Missouri; USA |
PMID:19668202 | Free, Available for download, Freely available | biotools:breakdancer, nlx_154253, OMICS_00307 | https://bio.tools/breakdancer | SCR_001799 | 2026-09-19 12:57:44 | 390 | ||||||
|
HAPLOPAINTER Resource Report Resource Website 10+ mentions |
HAPLOPAINTER (RRID:SCR_001710) | HaploPainter | software application, software resource | A pedigree drawing program, suitable in processing haplotype outputs from GENEHUNTER, ALLEGRO, MERLIN, and SIMWALK (entry from Genetic Analysis Software) | gene, genetic, genomic, perl, pedigree, haplotype, draw, bio.tools |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:15377505 | Free, Freely Available | nlx_154062, OMICS_00209, biotools:haplopainter | https://bio.tools/haplopainter | http://haplopainter.sourceforge.net/html/ManualIndex.htm | SCR_001710 | 2026-09-19 12:57:44 | 48 | |||||
|
PEDHUNTER Resource Report Resource Website 1+ mentions |
PEDHUNTER (RRID:SCR_002031) | PedHunter | software application, software resource | Software package that facilitates creation and verification of pedigrees within large genealogies. The pedigrees are produced as files in LINKAGE format ready for linkage analysis and for drawing with a variety of drawing programs, such as PEDDRAW and cranefoot. | gene, genetic, genomic, genealogy, pedigree, bio.tools |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian has parent organization: NCBI |
PMID:20433770 PMID:9521925 |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:pedhunter, OMICS_00211, nlx_154518 | https://bio.tools/pedhunter | SCR_002031 | 2026-09-19 12:57:44 | 2 | ||||||
|
NGSUtils Resource Report Resource Website 10+ mentions |
NGSUtils (RRID:SCR_001236) | NGSUtils | software resource, software toolkit | A suite of software tools for analyzing and manipulating next-generation sequencing datasets, such as FASTQ, BED and BAM format files. These tools provide a stable and modular platform for data management and analysis. | mac os x, linux, next-generation sequencing, illumia, solid, 454, ion torrent, pac bio, sequencing, dna resequcing, rna resequcing, chip-seq, clip-seq, targeted resequencing, agilent exome capture, pcr targeting, dna, rna, mapping pipeline, python, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Indiana University School of Medicine; Indiana; USA |
PMID:23314324 | Free, Available for download, Freely available | biotools:ngsutils, OMICS_02104 | https://bio.tools/ngsutils | SCR_001236 | NGSUtils - Tools for next-generation sequencing analysis | 2026-09-19 12:57:43 | 40 | |||||
|
TDT-PC Resource Report Resource Website |
TDT-PC (RRID:SCR_001116) | TDT-PC | software application, software resource | Software program to compute the statistical power of the Transmission/Disequilibrium Test (TDT) analytically, based on the most accurate asymptotic algorithms up to date, and is applicable in very general situations, where different parental disease status, multiple children, mixed family type and recombination events are considered. Routine algorithms for Monte Carlo simulations with significant improvements are also implemented in this program. (entry from Genetic Analysis Software) | gene, genetic, genomic, c++, ms-windows, ms-dos, unix, solaris, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
PMID:11443734 | nlx_154677, biotools:tdt_power_calculator | https://bio.tools/tdt_power_calculator | SCR_001116 | Transmission Disequilibrium Test Power Calculator, TDT Power Calculator | 2026-09-19 12:57:43 | 0 | ||||||
|
khmer Resource Report Resource Website 10+ mentions |
khmer (RRID:SCR_001156) | software resource, software toolkit | Software library and suite of command line tools for working with DNA sequence that takes a k-mer-centric approach to sequence analysis. It is primarily aimed at short-read sequencing data such as that produced by the Illumina platform. | dna sequence, short-read, sequencing, dna, illumina, sequence analysis, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
NHGRI R01HG007513 | PMID:26535114 DOI:10.12688/f1000research.6924.1 |
Free, Available for download, Freely available | SciRes_000166, OMICS_02560, biotools:khmer | https://github.com/dib-lab/khmer, https://bio.tools/khmer, https://sources.debian.org/src/khmer/ | https://github.com/ged-lab/khmer, http://ged.msu.edu/papers/2012-diginorm/ | SCR_001156 | khmer project, khmer - k-mer counting & filtering FTW, khmer - k-mer counting and filtering FTW, khmer: k-mer counting filtering and graph traversal FTW | 2026-09-19 12:57:43 | 25 | ||||
|
nondetects Resource Report Resource Website 1+ mentions |
nondetects (RRID:SCR_001702) | software application, software resource, standalone software | Software R package to model and impute non-detects in results of qPCR experiments.Used to directly model non-detects as missing data. | mac os x, unix/linux, windows, r, assay domain, gene expression, preprocessing, technology, workflow step, qpcr, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
Edelman-Gardner Foundation ; NCI CA009363; NCI CA138249; NHGRI HG006853 |
PMID:24764462 | Free, Available for download, Freely available | OMICS_03938, biotools:nondetects | https://bio.tools/nondetects | SCR_001702 | nondetects - Non-detects in qPCR data | 2026-09-19 12:57:44 | 1 | |||||
|
pRESTO Resource Report Resource Website 50+ mentions |
pRESTO (RRID:SCR_001782) | pRESTO | software resource, software toolkit | Software toolkit for processing raw reads from high-throughput sequencing of lymphocyte repertoires. | lymphocyte, high throughput sequencing, processing, raw reads, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Yale School of Medicine; Connecticut; USA |
EMD/Merck/Serono ; United States-Israel Binational Science Foundation 2009046; NCRR RR19895; NLM T15 LM07056; NIAAA U19AI089992; NIAAA U19AI050864 |
PMID:24618469 | Free, Freely available | SCR_001782 | REpertoire Sequencing TOolkit | 2026-09-19 12:57:44 | 72 | ||||||
|
Subread Resource Report Resource Website 1000+ mentions |
Subread (RRID:SCR_009803) | data processing software, software application, software resource | Software package for high-performance read alignment, quantification and mutation discovery.General purpose read aligner which can be used to map both genomic DNA-seq reads and RNA-seq reads. Subread aligner as fast, accurate and scalable read mapping by seed-and-vote.These programs were also implemented in Bioconductor R package Rsubread. | read alignment, DNA-seq reads mapping, RNA-seq reads mapping, mutation discovery, , bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Rsubread has parent organization: University of Melbourne; Victoria; Australia |
Australian Government ; Australian National Health and Medical Research Council ; Victorian State Government Operational Infrastructure Support |
PMID:23558742 | Free, Freely available | OMICS_01255, biotools:subread | https://bio.tools/subread, https://sources.debian.org/src/subread/ | SCR_009803 | 2026-09-19 12:56:00 | 2138 |
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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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