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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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BadMedicine Resource Report Resource Website 1+ mentions |
BadMedicine (RRID:SCR_018879) | software application, code testing framework, software library, software resource, software development tool, software toolkit | Software library and command line tool for generating realistic looking synthetic Electronic Health Records data for testing purposes. | Electronic Health Record, electronic health record data generation, health data, testing health data, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Freely available | biotools:badmedicine | https://bio.tools/badmedicine | SCR_018879 | 2026-07-28 09:44:51 | 1 | ||||||||
|
fracridge Resource Report Resource Website 1+ mentions |
fracridge (RRID:SCR_019045) | software application, data analysis software, software resource, data processing software, time-series analysis software, 1d time-series analysis software | Software tool as regularization technique that penalizes L2-norm of coefficients in linear regression. Available in two programming languages MATLAB and Python. | Generalized linear model, hyperparameters, regularization technique, coefficient, linear regression, L2 norm, bio.tools |
is listed by: Debian is listed by: bio.tools |
Free, Available for download, Freely available | biotools:fracridge | https://bio.tools/fracridge | SCR_019045 | fractional ridge regression | 2026-07-28 09:44:54 | 1 | |||||||
|
ScanITD Resource Report Resource Website 1+ mentions |
ScanITD (RRID:SCR_018886) | software application, data analysis software, sequence analysis software, software resource, data processing software | Open source software Python tool for detecting internal tandem duplication with variant allele frequency estimation. | Internal tandem duplication, FLT3, acute myeloid leukemia, TCGA, chimeric alignment, variant allele frequency, variant allele, frequency estimation, , bio.tools |
is listed by: Debian is listed by: bio.tools |
Acute Myeloid Leukemia | DOI:10.5524/100775 | Free, Available for download, Freely available | biotools:ScanItD | https://bio.tools/ScanITD, http://gigadb.org/dataset/100775 | SCR_018886 | Scan Internal Tandem Duplications | 2026-07-28 09:45:01 | 1 | |||||
|
STAMP Resource Report Resource Website 500+ mentions |
STAMP (RRID:SCR_018887) | software application, data analysis software, software resource, data processing software, data visualization software, software toolkit | Open source software package for analyzing taxonomic or metabolic profiles that promotes best practices in choosing appropriate statistical techniques and reporting results. Graphical software package that provides statistical hypothesis tests and exploratory plots for analyzing taxonomic and functional profiles. Supports tests for comparing pairs of samples or samples organized into two or more treatment groups. | Statistical analysis, taxonomic profile, functional profile, metabolic profile, statistical hypothesis test, plot, sample, sample group, sample pair comparison, bio.tools |
is listed by: Debian is listed by: bio.tools |
Genome Atlantic ; Natural Sciences and Engineering Research Council of Canada ; Australian Research Council ; Canada Foundation for Innovation ; Canada Research Chairs program ; Dalhousie Faculty of Computer Science ; Dalhousie Centre for Comparative Genomics and Evolutionary Bioinformatics ; Tula Foundation Killam Trust |
PMID:25061070 | Free, Freely available | biotools:stamp-metagenomic | https://github.com/dparks1134/STAMP, https://github.com/dparks1134/STAMP/releases, https://bio.tools/stamp-metagenomic | SCR_018887 | STAMP v2.1.3, statistical analysis of taxonomic and functional profiles | 2026-07-28 09:44:47 | 504 | |||||
|
SynergyFinder Resource Report Resource Website 500+ mentions |
SynergyFinder (RRID:SCR_019318) | software application, software resource, data processing software, data visualization software, software toolkit | 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 | 2026-07-28 09:45:01 | 510 | ||||||
|
BiG-SLiCE Resource Report Resource Website 1+ mentions |
BiG-SLiCE (RRID:SCR_019130) | software application, software resource, data analysis software, data processing software | Software tool to perform large scale clustering analysis of Biosynthetic Gene Cluster data. | Biosynthetic Gene, gene clusters, super linear clustering, clustering data analysis, bio.tools |
is listed by: bio.tools is listed by: Debian |
Netherlands eScience Center Accelerating Scientific Discoveries Grant ; Graduate School for Experimental Plant Sciences Netherlands |
DOI:10.1101/2020.08.17.240838 | Free, Available for download, Freely available | biotools:big_slice | https://bio.tools/big_slice | SCR_019130 | Biosynthetic Gene clusters - Super Linear Clustering Engine | 2026-07-28 09:44:56 | 5 | |||||
|
Parliament2 Resource Report Resource Website 1+ mentions |
Parliament2 (RRID:SCR_019187) | software application, data analysis software, software resource, data processing software, software toolkit | Software tool to identify structural variants in given sample relative to reference genome. Runs combination of tools to generate structural variant calls on whole genome sequencing data. | structural variants identification, reference genome, structural variant calls generation, whole genome sequencing data, sequencing data, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:parliament2 | https://bio.tools/parliament2 | SCR_019187 | 2026-07-28 09:44:54 | 5 | ||||||||
|
long-read-tools Resource Report Resource Website 10+ mentions |
long-read-tools (RRID:SCR_019116) | data or information resource, software repository, database, software resource | Interactive database of software tools for analysis of long read sequencing data.Catalogue of long-read sequencing data analysis tools. Catalogue of downstream analysis tools of real and synthetic long-read technologies. | Software tools collection, long read sequencing data, long read sequencing, data analysis, data analysis tools, bio.tools |
is listed by: bio.tools is listed by: Debian |
PMID:32033565 | Free, Freely available | biotools:long-read-tools | https://github.com/shaniAmare/long_read_tools, https://bio.tools/long-read-tools | SCR_019116 | Long-Read-Tools, long-read-tools.org | 2026-07-28 09:44:56 | 11 | ||||||
|
variancePartition Resource Report Resource Website 50+ mentions |
variancePartition (RRID:SCR_019204) | software application, data analysis software, software resource, data processing software, data analytics 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 | 2026-07-28 09:45:04 | 52 | ||||||
|
CiteFuse Resource Report Resource Website 1+ mentions |
CiteFuse (RRID:SCR_019321) | software application, software resource, 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 | 2026-07-28 09:45:01 | 2 | ||||||
|
ChiRA Resource Report Resource Website 1+ mentions |
ChiRA (RRID:SCR_019219) | software application, narrative resource, data or information resource, software resource, data processing software, workflow, software toolkit, training material | 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 | 2026-07-28 09:44:55 | 4 | |||||||
|
fgsea Resource Report Resource Website 100+ mentions |
fgsea (RRID:SCR_020938) | software application, software resource, data analysis software, data processing software | Software R package for fast preranked gene set enrichment analysis. Allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction. | Gene set enrichment analysis, preranked gene set, multiple hypothesis correction, bio.tools |
is listed by: Bioconductor is listed by: bio.tools is listed by: Debian |
DOI:10.1101/060012 | Free, Available for download, Freely available | biotools:fgsea | https://github.com/ctlab/fgsea/, https://bio.tools/fgsea | SCR_020938 | fast gene set enrichment analysis, Fast Gene Set Enrichment Analysis, FGSEA | 2026-07-28 09:45:03 | 185 | ||||||
|
Omics Data Paper Generator Resource Report Resource Website 1+ mentions |
Omics Data Paper Generator (RRID:SCR_019809) | software application, workflow software, data access protocol, software resource, data processing software, documentation generation software, software development tool, web service | Software package for streamlined import of omics metadata from European Nucleotide Archive into OMICS Data Paper manuscript. Omics Data Paper R Shiny app demonstrates workflow for automatic import of ENA genomic metadata into omics data paper manuscript. Streamlined conversion of metadata into manuscript facilitates authoring of omics data papers, which allow omics dataset creators to receive credit for their work and to improve description and visibility of their datasets. | Workflow, genomics, omics, FAIR data, data paper, G Power, European Nucleotide Archive, genomic metadata, omics data paper manuscript, streamlined conversion, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: Shiny |
Horizon 2020 764840 | Free, Available for download, Freely available | biotools:omics-data-paper-shinyapp-golem | https://mdmtrv.shinyapps.io/Omics_data_paper/, https://bio.tools/omics-data-paper-shinyapp-golem | SCR_019809 | omicsdatapaper | 2026-07-28 09:45:06 | 1 | ||||||
|
Bs-Seeker2 Resource Report Resource Website 1+ mentions |
Bs-Seeker2 (RRID:SCR_020948) | software application, data analysis software, sequence analysis software, software resource, data processing software | Software tool as versatile aligning pipeline for bisulfite sequencing data. Used for mapping bisulfite sequencing data and generating DNA methylomes. Improves mappability over existing aligners by using local alignment. Maps reads from RRBS library by building special indexes with improved efficiency and accuracy. Provides additional function for filtering out reads with incomplete bisulfite conversion, which is useful in minimizing overestimation of DNA methylation levels. | Versatile aligning pipeline, bisulfite sequencing data, mapping bisulfite sequencing data, generating DNA methylomes, DNA methylation level, reads mapping, Reduced Represented Bisulfite Sequencing library, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: BS Seeker has parent organization: University of California at Los Angeles; California; USA |
Institute of Genomics and Proteomics at UCLA ; NBRPC 2012CB316503; China Scholarship Council |
PMID:24206606 | Free, Available for download, Freely available | biotools:bs-seeker2 | http://pellegrini.mcdb.ucla.edu/BS_Seeker2/, https://bio.tools/bs-seeker2 | SCR_020948 | Bisulfite Sequencing Seeker2, BS Seeker2 | 2026-07-28 09:44:59 | 2 | |||||
|
Biological General Repository for Interaction Datasets (BioGRID) Resource Report Resource Website 1000+ mentions |
Biological General Repository for Interaction Datasets (BioGRID) (RRID:SCR_007393) | BioGRID | data or information resource, database | 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 | 2026-07-28 09:41:48 | 2554 | ||||
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VISTA Enhancer Browser Resource Report Resource Website 100+ mentions |
VISTA Enhancer Browser (RRID:SCR_007973) | VISTA Enhancer Browser | service resource, data or information resource, data repository, database, storage service resource | Resource for experimentally validated human and mouse noncoding fragments with gene enhancer activity as assessed in transgenic mice. Most of these noncoding elements were selected for testing based on their extreme conservation in other vertebrates or epigenomic evidence (ChIP-Seq) of putative enhancer marks. Central public database of experimentally validated human and mouse noncoding fragments with gene enhancer activity as assessed in transgenic mice. Users can retrieve elements near single genes of interest, search for enhancers that target reporter gene expression to particular tissue, or download entire collections of enhancers with defined tissue specificity or conservation depth. | human, noncoding fragment, mutant mouse strain, molecular neuroanatomy resource, image, telencephalon, development, genome, enhancer, dna fragment, embryo, embryonic mouse, brain, neural tube, eye, ear, heart, tail, limb, nose, cranial nerve, trigeminal, dorsal root ganglia, face, branchial arch, gene expression, annotation, vector, transgenic embryo, lacz reporter vector, lacz, biomaterial supply resource, in vivo, image collection, transcriptional enhancer, chip-seq, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools is related to: NIF Data Federation is related to: One Mind Biospecimen Bank Listing is related to: OMICtools has parent organization: Lawrence Berkeley National Laboratory |
American Heart Association ; NIDCR ; NHLBI HL066681; NHGRI HG003988; DOE contract DE-AC02-05CH11231; NINDS NS062859; DOE DE020060 |
PMID:17130149 | Free, Freely available | nif-0000-03637, OMICS_01568, biotools:vista_enhancer_browser | https://bio.tools/vista_enhancer_browser | SCR_007973 | 2026-07-28 09:42:00 | 233 | |||||
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T1DBase Resource Report Resource Website 100+ mentions |
T1DBase (RRID:SCR_007959) | service resource, resource, data or information resource, data repository, database, storage service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 26,2019. In October 2016, T1DBase has merged with its sister site ImmunoBase (https://immunobase.org). Documented on March 2020, ImmunoBase ownership has been transferred to Open Targets (https://www.opentargets.org). Results for all studies can be explored using Open Targets Genetics (https://genetics.opentargets.org). Database focused on genetics and genomics of type 1 diabetes susceptibility providing a curated and integrated set of datasets and tools, across multiple species, to support and promote research in this area. The current data scope includes annotated genomic sequences for suspected T1D susceptibility regions; genetic data; microarray data; and global datasets, generally from the literature, that are useful for genetics and systems biology studies. The site also includes software tools for analyzing the data. | genetics, beta cell, gene, variant, region, genomics, gene expression, genome-wide association study, data analysis service, bio.tools |
is used by: NIF Data Federation is used by: NIDDK Information Network (dkNET) is listed by: NIDDK Information Network (dkNET) is listed by: Debian is listed by: bio.tools is related to: dkCOIN has parent organization: University of Cambridge; Cambridge; United Kingdom |
Type 1 diabetes. Diabetes | Wellcome Trust ; NIDDK ; Juvenile Diabetes Research Foundation |
PMID:20937630 | THIS RESOURCE IS NO LONGER IN SERVICE. | nif-0000-03531, biotools:t1dbase | https://bio.tools/t1dbase | SCR_007959 | T1DBase - Type 1 Diabetes Database | 2026-07-28 09:41:57 | 145 | ||||
|
QIIME Resource Report Resource Website 10000+ mentions |
QIIME (RRID:SCR_008249) | software application, software resource, data analysis software, data processing software | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 23,2023.Software package for comparison and analysis of microbial communities, primarily based on high-throughput amplicon sequencing data, but also supporting analysis of other types of data. QIMME analyzes and transforms raw sequencing data generated on Illumina or other platforms to publication quality graphics and statistics. | microbiome, microbial community, sequence data, data analysis software, bio.tools |
is used by: SortMeRNA is used by: Nephele is listed by: OMICtools is listed by: Human Microbiome Project is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: University of Colorado Boulder; Colorado; USA |
DOI:10.1038/nmeth.f.303 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01118, SCR_011948, OMICS_01521, biotools:qiime | https://bio.tools/qiime | SCR_008249 | Quantitative Insights Into Microbial Ecology | 2026-07-28 09:42:06 | 11036 | ||||||
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dbEST Resource Report Resource Website 100+ mentions |
dbEST (RRID:SCR_008132) | service resource, data or information resource, data repository, database, storage service resource | Database as a division of GenBank that contains sequence data and other information on single-pass cDNA sequences, or Expressed Sequence Tags, from a number of organisms. | data, sequence, single, pass, cDNA, express, tag, bio.tools, gold standard |
is listed by: Debian is listed by: bio.tools has parent organization: NCBI |
PMID:8401577 | biotools:dbest, nif-0000-20937, r3d100010648 | http://www.ncbi.nlm.nih.gov/dbEST/, https://bio.tools/dbest, https://doi.org/10.17616/R3FG8P | SCR_008132 | database Expressed Sequence Tag (EST), database Expressed Sequence Tag | 2026-07-28 09:42:03 | 179 | |||||||
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ActiveDriver Resource Report Resource Website 10+ mentions |
ActiveDriver (RRID:SCR_008104) | ActiveDriver | software application, data analysis software, sequence analysis software, software resource, data processing software | A statistical method for interpreting variations in protein sequence (e.g. coding SNPs in the population, SNVs in cancer genomes) in the context of protein post-translational signaling modifications. | Protein sequence variation, variation interpretation, protein sequence, protein post-translational signaling modifications, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
Free, Available for download, Freely available | biotools:ActiveDriver, OMICS_00140 | http://reimandlab.org/software/activedriver/, https://cran.r-project.org/web/packages/ActiveDriver/ActiveDriver.pdf, https://bio.tools/ActiveDriver | SCR_008104 | 2026-07-28 09:42:02 | 25 |
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