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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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MARRVEL Resource Report Resource Website 10+ mentions |
MARRVEL (RRID:SCR_016871) | MARRVEL | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | Web tool to search multiple public variant databases simultaneously and provide a unified interface to facilitate the search process. Used for integration of human and model organism genetic resources to facilitate functional annotation of the human genome. Used for analysis of human genes and variants by cross-disciplinary integration of records available in public databases to facilitate clinical diagnosis and basic research. | integration, database, model, genetic, resource, functional, annotation, genome, data, analysis, dataset, rare, variant, exploration, bio.tools |
uses: OMIM uses: ClinVar uses: DECIPHER uses: Geno2MP uses: Database of Genomic Variants is used by: Hypothesis Center is listed by: bio.tools is listed by: Debian |
Baylor College of Medicine Medical Scientist Training Program ; Belfer Foundation ; CPRIT RP170387; Houston Endowment ; Huffington Foundation ; NCI P30 CA06516; NCRR R24 RR032668; NHGRI U01 HG007709; NIGMS R01 GM067761; NIGMS R01 GM067858; NIGMS R01 GM084947; NIGMS R01 GM120033; NIH Office of the Director R24 OD021997; NIH Office of the Director R24 OD022005; NINDS 1U54NS093793; NINDS U54 NS093793; NSF DMS 1263932; Simons Foundation ; T T Chao Family Foundation ; The Robert and Janice McNair Foundation |
PMID:28502612 | Free, Public, Freely available | biotools:marrvel | https://bio.tools/marrvel | SCR_016871 | SciCrunch Registry | Model organism Aggregated Resources for Rare Variant ExpLoration | 2026-09-26 02:15:51 | 25 | ||||
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rnaSPAdes Resource Report Resource Website 50+ mentions |
rnaSPAdes (RRID:SCR_016992) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software tool for assembling transcripts from RNA-Seq data. Explores surprising computational parallels between assembly of transcriptomes and single cell genomes. Suitable for all kind of organisms. Part of SPAdes package since version 3.9. | assembling, transcript, RNA-Seq, data, single, cell, genome, analysis, sequence, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: SPAdes is related to: rnaQUAST |
Russian Science Foundation 14-50-00069 | DOI:10.1101/420208 | Free, Available for download, Freely available | biotools:rnaSPAdes_autogenerated | https://bio.tools/rnaSPAdes_autogenerated | SCR_016992 | SciCrunch Registry | 2026-09-26 02:15:54 | 58 | ||||||
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PathwayMatcher Resource Report Resource Website 1+ mentions |
PathwayMatcher (RRID:SCR_016759) | data analysis software, data processing software, network analysis software, software application, software resource | Software tool for multi omics pathway mapping and proteoform network generation. Open source software writen in Java to search for pathways related to a list of proteins in Reactome. | mapping, omics, data, pathways, network, analysis, proteoform, generate, Reactome, database, match, bio.tools |
is listed by: Galaxy is listed by: OMICtools is listed by: Debian is listed by: bio.tools works with: Reactome |
Bergen Research Foundation ; European Research Council ; NHGRI U41 HG003751; NIGMS U54 GM114833; Research Council of Norway |
DOI:10.1101/375097 | Free, Available for download, Freely available | BioTools:PathwayMatcher, biotools:PathwayMatcher | https://anaconda.org/bioconda/pathwaymatcher, https://toolshed.g2.bx.psu.edu/repository?repository_id=6d75f02b86acc421, https://bio.tools/PathwayMatcher, https://bio.tools/PathwayMatcher, https://bio.tools/PathwayMatcher | SCR_016759 | SciCrunch Registry | 2026-09-26 02:15:51 | 1 | ||||||
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sleuth Resource Report Resource Website 10+ mentions |
sleuth (RRID:SCR_016883) | data analysis software, data processing software, software application, software resource | Software tool for analysis of RNA-Seq experiments for which transcript abundances have been quantified with kallisto. Used for the differential analysis of gene expression data that utilizes bootstrapping in conjunction with response error linear modeling to decouple biological variance from inferential variance. | differential, analysis, RNA-Seq, data, gene, expression, bootstrapping, error, linear, modeling, decouple, biological, variance, inferential, bio.tools |
is listed by: Debian is listed by: bio.tools works with: kallisto |
NHGRI R01 HG006129; NIDDK R01 DK094699 |
PMID:28581496 | Free, Available for download, Freely available | biotools:sleuth, BioTools:sleuth | https://bio.tools/sleuth, https://bio.tools/sleuth, https://bio.tools/sleuth | SCR_016883 | SciCrunch Registry | 2026-09-26 02:15:52 | 28 | ||||||
|
ropls Resource Report Resource Website 10+ mentions |
ropls (RRID:SCR_016888) | R OPLS | data analysis software, data processing software, software application, software resource | Software R package for multivariate analysis and feature selection of omics data. Used for visualization, regression, classification, and feature selection of omics data where the number of variables exceeds the number of samples and with multicollinearity among variables. | multivariate, analysis, feature, selection, omics, data, visualization, regression, classification, variable, exceedes, number, sample, multicollinearity, bio.tools |
is listed by: Bioconductor is listed by: Debian is listed by: bio.tools is related to: R Project for Statistical Computing |
Free, Available for download, Freely available | BioTools:ropls, biotools:ropls | https://bio.tools/ropls, https://bio.tools/ropls, https://bio.tools/ropls | SCR_016888 | SciCrunch Registry | R Orthogonal Partial Least Squares | 2026-09-26 02:15:53 | 15 | ||||||
|
Goseq Resource Report Resource Website 100+ mentions |
Goseq (RRID:SCR_017052) | data analysis software, data processing software, software application, software resource | Software application for performing Gene Ontology analysis on RNAseq data and other length biased data. Used to reduce complexity and highlight biological processes in genome wide expression studies. | Gene, Ontology, analysis, RNAseq, data, sequencing, genome, expression, bio.tools |
is listed by: Bioconductor is listed by: Debian is listed by: bio.tools is related to: R Project for Statistical Computing |
PMID:20132535 | Free, Available for download, Freely available | biotools:goseq | https://bio.tools/goseq | SCR_017052 | SciCrunch Registry | 2026-09-26 02:15:55 | 382 | |||||||
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Genomic Ranges Resource Report Resource Website 1+ mentions |
Genomic Ranges (RRID:SCR_017051) | data analysis software, data processing software, software application, software resource, software toolkit | Software R package for computing and annotating genomic ranges. Used for storing and manipulating genomic intervals and variables defined along genome. | computing, annotating, genomic, range, storing, manipulating, interval, variable, bio.tools |
is listed by: Bioconductor is listed by: Debian is listed by: bio.tools is related to: R Project for Statistical Computing |
NHGRI P41 HG004059; NHGRI U41 HG004059; NHLBI R01 HL086601; NHLBI R01 HL093076; NHLBI R01 HL094635 |
PMID:23950696 | Free, Available for download, Freely available | biotools:genomicranges | https://bio.tools/genomicranges | SCR_017051 | SciCrunch Registry | 2026-09-26 02:15:54 | 2 | ||||||
|
XL-mHG Resource Report Resource Website |
XL-mHG (RRID:SCR_016846) | xlmhg | data analysis software, data processing software, software application, software resource | Software Python package as a semiparametric test for enrichment in ranked lists. Used for determining gene set enrichment. | semiparametric, test, enrichment, ranked, list, gene, bio.tools |
is listed by: Debian is listed by: bio.tools |
Free, Available for download, Freely available | BioTools:XL-mHG, biotools:XL-mHG | https://bio.tools/XL-mHG, https://bio.tools/XL-mHG, https://bio.tools/XL-mHG | SCR_016846 | SciCrunch Registry | xlminimumhypergeometric, XL-minimum HyperGeometric test, XL-minimum HyperGeometric, xlmhg, XL-mHG | 2026-09-26 02:15:52 | 0 | ||||||
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Bridger Resource Report Resource Website 1+ mentions |
Bridger (RRID:SCR_017039) | data analysis software, data processing software, software application, software resource | Software package as de novo trascriptome assembler for RNA-Seq data. Framework for de novo transcriptome assembly using RNA-seq data. Can assemble all transcripts from short reads without using reference. Input RNA-Seq reads in fasta or fastq format, and ouput all assembled candidate transcripts in fasta format. Operating system Unix/Linux. | de novo, transcripto, assembler, RNAseq, data, short, read, sequencing, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
NCRR P20 RR016460; NIGMS P20 GM103429; NSFC 61272016; NSFC 61432010 |
PMID:25723335 | Free, Available for download, Freely available | biotools:bridger, OMICS_07535 | https://bio.tools/bridger | SCR_017039 | SciCrunch Registry | 2026-09-26 02:15:55 | 6 | ||||||
|
RepeatFiller Resource Report Resource Website 10+ mentions |
RepeatFiller (RRID:SCR_017414) | alignment software, data processing software, image analysis software, software application, software resource | Software tool to incorporate newly detected repeat overlapping alignments into pairwise alignment chains. It only aligns local genomic regions that are bounded by colinear aligning blocks, as provided in chains, which makes it feasible to consider all seeds including those that overlap repetitive regions. Used to improve genome alignments by incorporating previously undetected local alignments between repetitive sequences. | Repeat, overlapping, alignment, pairwise, chain, local, genomic, region, colinear, block, sequence, undetected, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Max Planck Institute of Molecular Cell Biology and Genetics; Dresden; Germany |
DOI:10.1101/696922 | Free, Freely available | biotools:RepeatFiller, BioTools:RepeatFiller | https://bio.tools/RepeatFiller, https://bio.tools/RepeatFiller, https://bio.tools/RepeatFiller | SCR_017414 | SciCrunch Registry | 2026-09-26 02:15:58 | 16 | |||||||
|
trimAl Resource Report Resource Website 500+ mentions |
trimAl (RRID:SCR_017334) | data analysis software, data processing software, software application, software resource | Software tool for automated removal of spurious sequences or poorly aligned regions from multiple sequence alignment. Software package for automated alignment trimming in large scale phylogenetic analyses. | removal, spurious, sequence, poorly, aligned, region, multiple, alignment, trimming, large, scale, phylogenetic, analysis, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
FIS ; MEC |
PMID:19505945 | Free, Available for download, Freely available | biotools:trimal | https://vicfero.github.io/trimal/, https://bio.tools/trimal | SCR_017334 | SciCrunch Registry | 2026-09-26 02:15:57 | 673 | ||||||
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Human Neocortical Neurosolver Resource Report Resource Website 10+ mentions |
Human Neocortical Neurosolver (RRID:SCR_017437) | HNN | data analysis software, data processing software, simulation software, software application, software resource | Open source software package for circuit level interpretation of human EEG/MEG data. Software tool for interpreting cellular and network origin of human MEG/EEG data. Simulates electrical activity of neocortical cells and circuits that generate primary electrical currents underlying EEG/MEG recordings. Designed for researchers and clinicians, without computational neural modeling experience, to develop and test hypothesis on circuit origin of their data. | Neural, modeling, human, imaging, data, EEG, MEG, electrical, neocortical, cell, circuit, BRAIN Initiative, bio.tools |
is recommended by: BRAIN Initiative is listed by: Debian is listed by: bio.tools has parent organization: Brown University; Rhode Island; USA has parent organization: Yale University; Connecticut; USA has parent organization: Massachusetts General Hospital |
NIBIB R01 EB022889; NIDCD R01 DC012947 |
DOI:10.1101/740597 | Free, Available for download, Freely available | SCR_017678, biotools:HNN | https://github.com/jonescompneurolab/hnn, https://github.com/jonescompneurolab/hnn/tree/0.0.5, https://github.com/jonescompneurolab/hnn/tree/0.1.2, https://zenodo.org/record/2394296#.Xg4rCEdKiM9, https://bio.tools/HNN | SCR_017437 | SciCrunch Registry | 2026-09-26 02:15:59 | 13 | |||||
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FateID Resource Report Resource Website 1+ mentions |
FateID (RRID:SCR_017244) | data analysis software, data processing software, software application, software resource | Software R package for inference of cell fate bias from single cell RNA-seq data. Iterative supervised learning algorithm for probabilistic quantification of cell fate bias in progenitor populations. | inference, cell, fate, bias, single, RNAseq, data, iterative, supervised, learning, algorithm, probabilistic, quantification, progenitor, population, bio.tools |
is listed by: bio.tools is listed by: Debian |
PMID:29630061 | Free, Available for download, Freely available | biotools:fateid | https://bio.tools/fateid | SCR_017244 | SciCrunch Registry | 2026-09-26 02:15:56 | 2 | |||||||
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GEDIT Resource Report Resource Website 10+ mentions |
GEDIT (RRID:SCR_019277) | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | Software tool for accurate cell type quantification from gene expression data. Uses gene expression data to estimate cell type abundances. Allows user to supply custom reference matrices. | bio.tools |
is listed by: bio.tools is listed by: Debian |
DOI:10.1101/728493 | Free, Freely available | biotools:gedit | http://webtools.mcdb.ucla.edu/, https://bio.tools/gedit | SCR_019277 | SciCrunch Registry | Gene Expression Deconvolution Interactive Tool | 2026-09-26 02:16:16 | 12 | ||||||
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Gmove Resource Report Resource Website 1+ mentions |
Gmove (RRID:SCR_019132) | simulation software, software application, software resource | Software tool for genome annotation. Eukaryotic gene prediction tool focused on evidence supported by expressed sequences like transcripts and conserved proteins alignments. Can be used to reannotate genomes, to do comparative gene prediction and improve existing genome annotation. Can predict gene models with canonical and non-canonical splice sites. | Expressed sequences, RNAseq, conserved proteins, conserved proteins alignment, genome annotation, Eukaryotic gene prediction, gene prediction, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:gmove | https://github.com/institut-de-genomique/gmove, https://bio.tools/gmove | SCR_019132 | SciCrunch Registry | Gene MOdeling using Various Evidence | 2026-09-26 02:16:15 | 3 | |||||||
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SoupX Resource Report Resource Website 50+ mentions |
SoupX (RRID:SCR_019193) | data analysis software, data processing software, software application, software resource, software toolkit | Software R package for estimation and removal of cell free mRNA contamination in droplet based single cell RNA-seq data. | Estimation, removal, cell free mRNA contamination, droplet based, single cell RNA-seq data, RNA-seq data, data, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:soupx | https://bio.tools/soupx | SCR_019193 | SciCrunch Registry | 2026-09-26 02:16:16 | 87 | ||||||||
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ReactomePA Resource Report Resource Website 50+ mentions |
ReactomePA (RRID:SCR_019316) | data analysis software, data processing software, data visualization software, software application, software resource | Software R package provides functions for pathway analysis based on REACTOME pathway database. It implements enrichment analysis, gene set enrichment analysis and several functions for visualization. | pathway analysis, REACTOME pathway, REACTOME database, enrichment analysis, gene set enrichment analysis, bio.tools |
is listed by: Bioconductor is listed by: bio.tools is listed by: Debian |
PMID:26661513 | Free, Available for download, Freely available | biotools:reactomepa | https://bio.tools/reactomepa | SCR_019316 | SciCrunch Registry | Reactome Pathway Analysis | 2026-09-26 02:16:17 | 86 | ||||||
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tradeSeq Resource Report Resource Website 10+ mentions |
tradeSeq (RRID:SCR_019238) | data analysis software, data processing software, software application, software resource | Software tool as suite of tests for identifying dynamic temporal gene regulation using single cell RNA-seq data.Trajectory based differential expression analysis for sequencing data. | Dynamic temporal gene regulation, gene regulation identifying, gene regulation, single cell RNA-seq data, differential expression analysis, sequencing data, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:tradeseq | https://bioconductor.org/packages/tradeSeq/, https://bio.tools/tradeseq | SCR_019238 | SciCrunch Registry | TRAjectory-based Differential Expression analysis for SEQuencing data | 2026-09-26 02:16:16 | 47 | |||||||
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ShinyGO Resource Report Resource Website 1000+ mentions |
ShinyGO (RRID:SCR_019213) | data access protocol, software resource, web service | Software graphical gene set enrichment tool for animals and plants. Graphical web application to gain insights from gene sets. Features include graphical visualization of enrichment results and gene characteristics, and application program interface access to KEGG and STRING for retrieval of pathway diagrams and protein-protein interaction networks. | Graphical gene set enrichment, animal gene, plant gene, graphical visualization, enrichment results, gene characteristics, pathway diagrams retrieval, protein interaction network, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: Ensembl is related to: STRING is related to: KEGG has parent organization: South Dakota State University; South Dakota; USA |
PMID:31882993 | biotools:ShinyGO | https://bio.tools/ShinyGO | SCR_019213 | SciCrunch Registry | ShinyGO 0.77, ShinyGO 0.80, Shiny Gene Ontology, ShinyGO v0.61 | 2026-09-26 02:16:16 | 1213 | |||||||
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biomaRt Resource Report Resource Website 1000+ mentions |
biomaRt (RRID:SCR_019214) | data analysis software, data processing software, software application, software resource | Software package that integrates BioMart data resources with data analysis software in Bioconductor. Can annotate range of gene or gene product identifiers including Entrez Gene and Affymetrix probe identifiers with information such as gene symbol, chromosomal coordinates, Gene Ontology and OMIM annotation. Enables retrieval of genomic sequences and single nucleotide polymorphism information, which can be used in data analysis. | BioMart databases, Bioconductor, data analysis, BioMart data integration, gene annotation, gene product identifiers annotation, gene symbol retrival, chromosomal coordinates retrival, genomic sequence retrival, nucleotide polimorphism information, , bio.tools |
is listed by: Bioconductor is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: BioMart Project is related to: BioMart MartView is related to: Entrez Gene is related to: Affymetrix is related to: Gene Ontology is related to: OMIM is related to: Affymetrix |
PMID:16082012 | Free, Available for download, Freely available | biotools:biomart | https://bio.tools/biomart | SCR_019214 | SciCrunch Registry | biomaRt v 2.42.1 | 2026-09-26 02:16:16 | 2879 |
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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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