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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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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 | 2026-09-19 12:54:05 | 86 | ||||||
|
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 | 2026-09-19 12:54:05 | 12 | ||||||
|
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 | 2026-09-19 12:54:03 | 3 | |||||||
|
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 | 2026-09-19 12:54:03 | 87 | ||||||||
|
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 | 2026-09-19 12:54:04 | 47 | |||||||
|
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 | 2026-09-19 12:54:04 | 1213 | |||||||
|
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 | 2026-09-19 12:54:04 | 2879 | ||||||
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ImJoy Resource Report Resource Website 1+ mentions |
ImJoy (RRID:SCR_020935) | data analysis software, data processing software, software application, software resource | Software tool as plugin powered hybrid computing platform for deploying deep learning applications such as advanced image analysis tools. Runs on mobile and desktop environment cross different operating systems, can run in the browser, localhost, remote and cloud servers. | Deep learning, flexible plugin system, deploying deep learning applications, advanced image analysis, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download,Freely available | biotools:ImJoy | https://github.com/imjoy-team/ImJoy, https://bio.tools/ImJoy | SCR_020935 | SciCrunch Registry | 2026-09-19 12:54:46 | 3 | ||||||||
|
UEA sRNA Workbench Resource Report Resource Website 10+ mentions |
UEA sRNA Workbench (RRID:SCR_020947) | data analysis software, data processing software, software application, software resource | Software package for analysing small RNA data. Software suite of tools for analyzing miRNAs and sRNAs. Performs analysis of single or multiple sample small RNA datasets from both plants and animals. | Analysing small RNA data, analyzing miRNAs, profiling small RNA expression patterns, genetic data, bio.tools, bio.tools, bio.tools |
lists: VisSR is listed by: bio.tools is listed by: Debian has parent organization: University of East Anglia; Norwich; United Kingdom |
BBSRC BB/L021269/1 | PMID:29722807 | Free, Available for download, Freely available | biotools:siloco, biotools:mircat | https://github.com/sRNAworkbenchuea/UEA_sRNA_Workbench, https://bio.tools/mircat, https://bio.tools/siloco, | SCR_020947 | SciCrunch Registry | UEA small RNA Workbench | 2026-09-19 12:54:46 | 10 | |||||
|
PhenStat Resource Report Resource Website 10+ mentions |
PhenStat (RRID:SCR_021317) | data analysis software, data processing software, software application, software resource, software toolkit | Software R package for statistical analysis of phenotypic data.Tool kit for standardized analysis of high throughput phenotypic data. | Statistical analysis, phenotypic data, standardized analysis, bio.tools, Bioconductor |
is listed by: Bioconductor is listed by: bio.tools |
NHGRI U54 HG006370; Wellcome Trust |
PMID:26147094 | Free, Available for download, Freely available | biotools:phenstat | https://bio.tools/phenstat | SCR_021317 | SciCrunch Registry | 2026-09-19 12:54:51 | 11 | ||||||
|
vcflib Resource Report Resource Website 100+ mentions |
vcflib (RRID:SCR_001231) | vcflib | software library, software resource, software toolkit | A C++ library for parsing and manipulating Variant Call Format (VCF) files, and many command-line utilities. The API provides a quick and extremely permissive method to read and write VCF files. Extensions and applications of the library provided in the included utilities (*.cpp) comprise the vast bulk of the library's utility for most users. | c++, sequence variation, genomic variation, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
Free, Available for download, Freely available | biotools:vcflib, OMICS_02112 | https://bio.tools/vcflib, https://sources.debian.org/src/libvcflib-dev/ | https://sources.debian.org/src/libvcflib-dev/ | SCR_001231 | SciCrunch Registry | 2026-09-19 12:55:04 | 129 | ||||||
|
CSDeconv Resource Report Resource Website |
CSDeconv (RRID:SCR_000016) | CSDeconv | data analysis software, data processing software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software application that maps transcription factor binding sites from ChIP-seq data to high resolution using a blind deconvolution approach. | sequence analysis software, transcription factor binding site, chip-seq, blind deconvolution, transcription binding, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Rutgers University; New Jersey; USA has parent organization: University of South Australia; Adelaide; Australia |
PMID:20028542 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00436, biotools:csdeconv | https://bio.tools/csdeconv | SCR_000016 | SciCrunch Registry | 2026-09-19 12:55:03 | 0 | ||||||
|
fastqz Resource Report Resource Website |
fastqz (RRID:SCR_001006) | data management software, software application, software resource, source code | Source code used to compress FASTQ files. FASTQ is DNA sequencing machine output. | compress, source code, fastq output, fastq dna, fastq sequencing, fastq compress, fastq compressor, fastq files, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:23533605 | Free, Available for download, Freely available | OMICS_00956, biotools:fastqz | https://bio.tools/fastqz | SCR_001006 | SciCrunch Registry | 2026-09-19 12:55:03 | 0 | |||||||
|
SeqEM Resource Report Resource Website 1+ mentions |
SeqEM (RRID:SCR_002021) | algorithm resource, data analysis software, data processing software, sequence analysis software, software application, software resource, web application | Online tool for utilizing a genotype calling algorithm for next-generation sequence data. | genotype, algorithm, sequence, rna, dna, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Miami Miller School of Medicine; Florida; USA |
PMID:20861027 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00074, biotools:seqem | https://bio.tools/seqem | SCR_002021 | SciCrunch Registry | 2026-09-19 12:55:04 | 1 | |||||||
|
BeetleBase Resource Report Resource Website 50+ mentions |
BeetleBase (RRID:SCR_001955) | BEETLEBASE | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | A centralized sequence database and community resource for Tribolium genetics, genomics and developmental biology containing genomic sequence scaffolds mapped to 10 linkage groups, genetic linkage maps, the official gene set, Reference Sequences from NCBI (RefSeq), predicted gene models, ESTs and whole-genome tiling array data representing several developmental stages. The current version of Beetlebase is built on the Tribolium castaneum 3.0 Assembly (Tcas 3.0) released by the Human Genome Sequencing Center at the Baylor College of Medicine. The database is constructed using the upgraded Generic Model Organism Database (GMOD) modules. The genomic data is stored in a PostgreSQL relational database using the Chado schema and visualized as tracks in GBrowse. The genetic map is visualized using the comparative genetic map viewer CMAP. To enhance search capabilities, the BLAST search tool has been integrated with the GMOD tools. Tribolium castaneum is a very sophisticated genetic model organism among higher eukaryotes. As the member of a primitive order of holometabolous insects, Coleoptera, Tribolium is in a key phylogenetic position to understand the genetic innovations that accompanied the evolution of higher forms with more complex development. Coleoptera is also the largest and most species diverse of all eukaryotic orders and Tribolium offers the only genetic model for the profusion of medically and economically important species therein. The genome sequences may be downloaded. | red flour beetle, tribolium castaneum, sequence data, gene, mutant, genetic marker, expressed sequence tag, genome, blast, model organism, insect, developmental biology, genomics, genetics, entomology, development, bio.tools, FASEB list |
is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: RefSeq has parent organization: Kansas State University; Kansas; USA |
NCRR P20 RR16475 | PMID:18362917 PMID:17090595 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02599, biotools:beetlebase, r3d100010921 | https://bio.tools/beetlebase, https://doi.org/10.17616/R3G61K | http://bioinformatics.k-state.edu/BeetleBase/, http://www.bioinformatics.ksu.edu/BeetleBase/ | SCR_001955 | SciCrunch Registry | 2026-09-19 12:55:04 | 82 | ||||
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SGA Resource Report Resource Website 10+ mentions |
SGA (RRID:SCR_001982) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software package that functions as a de novo genome assembler based on the concept of string graphs. It is designed as a modular set of programs used to assemble large genomes from high coverage short read data. | string, graph assembler, de novo assembly, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
DOI:10.1101/gr.126953.111 | Free, Available for download, Freely available | OMICS_00028, biotools:sga | https://bio.tools/sga, https://sources.debian.org/src/sga/ | SCR_001982 | SciCrunch Registry | String Graph Assembler (SGA), String Graph Assembler | 2026-09-19 12:55:04 | 18 | ||||||
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GSNAP Resource Report Resource Website 500+ mentions |
GSNAP (RRID:SCR_005483) | GSNAP | alignment software, data processing software, image analysis software, software application, software resource | Software to align single and paired end reads as short as 14 nt and of arbitrarily long length. Can detect short and long distance splicing, including interchromosomal splicing, in individual reads, using probabilistic models or database of known splice sites. Permits SNP-tolerant alignment to reference space of all possible combinations of major and minor alleles, and can align reads from bisulfite-treated DNA for study of methylation state. | next-generation sequencing, bio.tools, FASEB list |
is used by: Gsnap2Augustus is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:20147302 | OMICS_00665, biotools:gsnap | https://bio.tools/gsnap | SCR_005483 | SciCrunch Registry | Genomic Short-read Nucleotide Alignment Program | 2026-09-19 12:55:08 | 802 | ||||||
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EMAGE Gene Expression Database Resource Report Resource Website 10+ mentions |
EMAGE Gene Expression Database (RRID:SCR_005391) | EMAGE | atlas, data or information resource, data repository, database, service resource, storage service resource | A database of in situ gene expression data in the developing mouse embryo and an accompanying suite of tools to search and analyze the data. mRNA in situ hybridization, protein immunohistochemistry and transgenic reporter data is included. The data held is spatially annotated to a framework of 3D mouse embryo models produced by EMAP (e-Mouse Atlas Project). These spatial annotations allow users to query EMAGE by spatial pattern as well as by gene name, anatomy term or Gene Ontology (GO) term. The conceptual framework which houses the descriptions of the gene expression patterns in EMAGE is the EMAP Mouse Embryo Anatomy Atlas. This consists of a set of 3D virtual embryos at different stages of development, as well as an accompanying ontology of anatomical terms found at each stage. The raw data images can be conventional 2D photographs (of sections or wholemount specimens) or 3D images of wholemount specimens derived from Optical Projection Tomography (OPT) or confocal microscopy. Users may submit data using a Data submission tool or without. | genetics, 3d model, anatomy, development, mouse morphology, molecular neuroanatomy resource, gene expression, in situ hybridization, immunohistochemistry, embryo, in situ reporter, embryonic mouse, optical projection tomography, confocal microscopy, annotation, pathway, gene association, protein, theiler stage, gene expression, embryology, dna, protein, protein-protein interaction, protein binding, gene, embryology, anatomy, genetics, bio.tools |
is listed by: re3data.org is listed by: Debian is listed by: bio.tools is related to: HUDSEN Electronic Atlas of the Developing Human Brain is related to: eMouseAtlas is related to: eMouseAtlas is related to: HUDSEN Human Gene Expression Spatial Database is related to: aGEM is related to: Eurexpress is related to: Gene Expression Database is related to: Gene Ontology is related to: NIDDK Information Network (dkNET) is related to: GUDMAP Ontology |
MRC | PMID:19767607 | Except where noted, Creative Commons Attribution License, The community can contribute to this resource | biotools:emage, nif-0000-00080, r3d100010564 | https://bio.tools/emage, https://doi.org/10.17616/R3860B | SCR_005391 | SciCrunch Registry | Emage (e-Mouse Atlas of Gene Expression), e-Mouse Atlas of Gene Expression | 2026-09-19 12:55:08 | 25 | ||||
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ATRHUNTER Resource Report Resource Website 1+ mentions |
ATRHUNTER (RRID:SCR_006480) | ATRHUNTER | analysis service resource, data analysis service, production service resource, service resource, software resource | Software that finds and displays approximate tandem repeats in DNA sequences. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:16201913 | biotools:atrhunter, OMICS_00102 | https://bio.tools/atrhunter | SCR_006480 | SciCrunch Registry | 2026-09-19 12:55:09 | 1 | |||||||
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LAST Resource Report Resource Website 100+ mentions |
LAST (RRID:SCR_006119) | LAST | analysis service resource, data analysis service, data processing software, production service resource, service resource, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software tool for aligning sequences, similar to BLAST 2 sequences that colour-codes the alignments by reliability. Another useful feature of LAST is that it can compare huge (vertebrate-genome-sized) datasets. Unfortunately, this only applies to the downloadable version of LAST, not the web service. The web service can just about handle bacterial genomes, but it will take a few minutes and the output will be large. LAST can: * Handle big sequence data, e.g: ** Compare two vertebrate genomes ** Align billions of DNA reads to a genome * Indicate the reliability of each aligned column. * Use sequence quality data properly. * Compare DNA to proteins, with frameshifts. * Compare PSSMs to sequences * Calculate the likelihood of chance similarities between random sequences. LAST cannot (yet): * Do spliced alignment., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | sequence alignment, align, vertebrate, genome, sequence, alignment, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: RecountDB has parent organization: National Institute of Advanced Industrial Science and Technology |
National Genome Research Network ; INTEuropean Union Systems Institute ; Japanese Ministry of Education Culture Sports Science and Technology MEXT |
PMID:21209072 PMID:20144198 PMID:20110255 DOI:10.1093/nar/gkq010 |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_151594, OMICS_15813, biotools:last | https://bio.tools/last, https://sources.debian.org/src/last-align/ | SCR_006119 | SciCrunch Registry | 2026-09-19 12:55:08 | 403 |
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