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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Osprey Resource Report Resource Website 10+ mentions |
Osprey (RRID:SCR_003627) | Osprey | software resource | Oligonucleotide design software that calculates optimal oligonucleotides for a range of tasks: sequence assembly, differential expression, and microarrays (cDNA and spotted oligos)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. |
is listed by: OMICtools has parent organization: University of Calgary; Alberta; Canada |
PMID:15456895 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00832 | SCR_003627 | Osprey: Oligonucleotide Design Software | 2026-08-08 11:58:08 | 47 | |||||||
|
UEA sRNA toolkit Resource Report Resource Website 10+ mentions |
UEA sRNA toolkit (RRID:SCR_003620) | UEA sRNA toolkit | software resource | Software tools for the analysis of high-throughput small RNA data. | is listed by: OMICtools | PMID:22628521 | OMICS_00369 | SCR_003620 | 2026-08-08 11:58:03 | 34 | |||||||||
|
RINS Resource Report Resource Website 10+ mentions |
RINS (RRID:SCR_003652) | RINS | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 6, 2023. An intersection-based pathogen detection workflow that utilizes a user-provided custom reference genome set for identification of nonhuman sequences in deep sequencing datasets. This is a package recommended for advanced users only. | virus, rna-seq, dna-seq, viral integration, clipped-sequence, paired-end, reconstruction, fusion transcript, sequence, perl |
is listed by: OMICtools has parent organization: Stanford University School of Medicine; California; USA |
PMID:22377895 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00223 | SCR_003652 | 2026-08-08 11:58:08 | 26 | |||||||
|
J-Express Resource Report Resource Website 50+ mentions |
J-Express (RRID:SCR_003609) | J-Express | software resource | Gene expression analysis software using Java. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is parent organization of: Mini Analysis Guide for Microarrays |
PMID:11301307 | Acknowledgement requested | biotools:j-express, OMICS_00767 | https://bio.tools/j-express | SCR_003609 | J-Express: Gene expression analysis software | 2026-08-08 11:58:07 | 87 | |||||
|
QuasiRecomb Resource Report Resource Website 10+ mentions |
QuasiRecomb (RRID:SCR_008812) | QuasiRecomb | software resource | A jumping hidden Markov model that describes the generation of the viral quasispecies and a method to infer its parameters by analysing next generation sequencing data. | haplotype, next-generation sequencing, virus, parameter, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:23383997 | OMICS_00229, biotools:quasirecomb | https://bio.tools/quasirecomb | SCR_008812 | QuasiRecomb - Probabilistic inference of viral Quasispecies | 2026-08-08 11:59:20 | 33 | ||||||
|
isva Resource Report Resource Website 1+ mentions |
isva (RRID:SCR_008772) | isva | software resource | An algorithm for feature selection in the presence of potential confounding factors. | is listed by: OMICtools | OMICS_00860 | SCR_008772 | Independent Surrogate Variable Analysis, isva: Independent Surrogate Variable Analysis | 2026-08-08 11:59:07 | 3 | |||||||||
|
svd Resource Report Resource Website |
svd (RRID:SCR_008805) | svd | software resource | Interfaces to various state-of-art SVD and eigensolvers. | is listed by: OMICtools | OMICS_00862 | SCR_008805 | 2026-08-08 11:59:08 | 0 | ||||||||||
|
XPN Resource Report Resource Website 1+ mentions |
XPN (RRID:SCR_008845) | XPN | software resource | Merging Two Gene Expression Studies via Cross Platform Normalization. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA |
OMICS_00863, biotools:xpn | https://bio.tools/xpn | SCR_008845 | 2026-08-08 11:59:21 | 2 | ||||||||
|
MuSiC Resource Report Resource Website 100+ mentions |
MuSiC (RRID:SCR_008792) | MuSiC | software resource | A set of tools aimed at determining the significance of somatic mutations discovered within a given cohort of cancer samples, incorporating the cohort''s alignment data, variant lists and any relevant clinical data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Washington University in St. Louis; Missouri; USA |
PMID:22759861 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:MuSiC2, OMICS_00152 | https://bio.tools/MuSiC2, https://github.com/ding-lab/MuSiC2/blob/master/README.md | SCR_008792 | Mutational Significance In Cancer | 2026-08-08 11:59:08 | 485 | |||||
|
Roadmap Epigenomics Project Resource Report Resource Website 100+ mentions |
Roadmap Epigenomics Project (RRID:SCR_008924) | Roadmap Epigenomics Project | data or information resource, consortium, project portal, portal, organization portal | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 11, 2022. Project for human epigenomic data from experimental pipelines built around next-generation sequencing technologies to map DNA methylation, histone modifications, chromatin accessibility and small RNA transcripts in stem cells and primary ex vivo tissues selected to represent normal counterparts of tissues and organ systems frequently involved in human disease. Consortium expects to deliver collection of normal epigenomes that will provide framework or reference for comparison and integration within broad array of future studies. Consortium is also committed to development, standardization and dissemination of protocols, reagents and analytical tools to enable research community to utilize, integrate and expand upon this body of data. | epigenomics, genome, genetic variation, gene regulation, genomics, stem cell, primary cell, tissue, blood, lung, heart, gastrointestinal tract, brain, embryonic stem cell, fetus, adult, cell, epigenome, methylome, chip-seq, rna, breast, muscle, connective, gastrointestinal, genitourinary, fat, hematopoietic stem cell, thymus, spleen, placenta, kidney, adrenal, induced pluripotent stem cell, skin, angular gyrus, anterior caudate, cingulate gyrus, hippocampus, inferior temporal lobe, mid frontal lobe, substantia nigra, dna methylation, histone modification, chromatin, rna transcript, dna, methylation, histone, data set |
is used by: NIF Data Federation is used by: VizHub is used by: Integrated Data Annotation is listed by: 3DVC is listed by: OMICtools is related to: NCBI Epigenomics is related to: Gene Expression Omnibus is related to: Spark is related to: Deep Blue Epigenomic Data Server has parent organization: NIH Common Fund is parent organization of: Human Epigenome Atlas is parent organization of: WashU Epigenome Browser is parent organization of: VizHub |
PMID:22690667 PMID:20944595 PMID:20944597 |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_151644, OMICS_01564 | SCR_008924 | Epigenomics Program, Common Fund Epigenomics, NIH Roadmap Epigenomics Program, NIH Roadmap Epigenomics Project, Common Fund Epigenomics Program, NIH Common Fund Epigenomics, NIH Common Fund Epigenomics Program, Common Fund Roadmap Epigenomics Program | 2026-08-08 11:59:18 | 323 | ||||||
|
Gzip Resource Report Resource Website 10+ mentions |
Gzip (RRID:SCR_009291) | Gzip | software resource | A compression utility designed to be a replacement for compress. | is listed by: OMICtools | OMICS_00961 | SCR_009291 | GNU zip | 2026-08-08 11:59:23 | 32 | |||||||||
|
SeqSaw Resource Report Resource Website |
SeqSaw (RRID:SCR_009185) | SeqSaw | software resource | A package for mapping of spliced reads and unbiased detection of novel splice junctions from RNA-seq data. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:21575597 | biotools:seqsaw, OMICS_01250 | https://bio.tools/seqsaw | SCR_009185 | SeqSaw - Short Spliced Sequence Mapping Tool | 2026-08-08 11:59:11 | 0 | ||||||
|
GAAS Resource Report Resource Website 500+ mentions |
GAAS (RRID:SCR_008967) | GAAS | software resource | An integrated software framework for efficient management, analysis and visualization of large amounts of gene expression data across replicated experiments., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. |
is listed by: OMICtools has parent organization: Polytechnic University of Milan; Milan; Italy |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00757 | SCR_008967 | Gene Array Analyzer Software | 2026-08-08 11:59:18 | 721 | ||||||||
|
DELIMINATE Resource Report Resource Website 1+ mentions |
DELIMINATE (RRID:SCR_008956) | DELIMINATE | software resource | A practical implementation of a novel compression approach that can rapidly compress FASTA files containing genomic sequence data in a loss-less fashion. | is listed by: OMICtools | PMID:22833526 | OMICS_00953 | SCR_008956 | DELIMINATE: A fast and efficient method for loss-less compression of genomic sequences | 2026-08-08 11:59:10 | 1 | ||||||||
|
CMAP Resource Report Resource Website 100+ mentions |
CMAP (RRID:SCR_009034) | CMap | software resource, software application, data analysis software, data processing software | Web-based tool that allows users to view comparisons of genetic and physical maps. The package also includes tools for curating map data. (entry from Genetic Analysis Software) | gene, genetic, genomic, perl, unix, solaris, freebsd, linux, sequence, FASEB list |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: SoftCite has parent organization: Generic Model Organism Database Project works with: Drug Gene Budger |
PMID:19648141 | GNU General Public License | nlx_153998, OMICS_00933 | https://sourceforge.net/projects/gmod/files/cmap/ | http://www.gmod.org/cmap/, http://gmod.org/wiki/Cmap | SCR_009034 | , GMOD Comparative Mapping (CMap) tool, Comparative Mapping tool, genetic and comparative maps | 2026-08-08 11:59:19 | 417 | ||||
|
DNAzip Resource Report Resource Website 1+ mentions |
DNAzip (RRID:SCR_009032) | DNAzip | software resource | DNA sequence compression using a reference genome. |
is listed by: OMICtools has parent organization: University of California at Irvine; California; USA |
OMICS_00954 | SCR_009032 | 2026-08-08 11:59:11 | 1 | ||||||||||
|
CLIIQ Resource Report Resource Website 1+ mentions |
CLIIQ (RRID:SCR_009972) | CLIIQ | software resource | An algorithm to simultaneously identify and quantify expressed isoforms based on RNA-Seq data from multiple sample(s) in a population. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_01272 | SCR_009972 | 2026-08-08 11:59:16 | 1 | ||||||||||
|
MSbind Resource Report Resource Website |
MSbind (RRID:SCR_009910) | MSbind | software resource | Software tool that calculates features of meta-stable RNA secondary structure target sites. |
is listed by: OMICtools has parent organization: King's College London; London; United Kingdom |
PMID:24292936 | OMICS_00390 | SCR_009910 | Msbind - Accessibility of microRNA binding sites in meta-stable RNA secondary structures in the presence of SNPs | 2026-08-08 11:59:27 | 0 | ||||||||
|
RNASEQR Resource Report Resource Website |
RNASEQR (RRID:SCR_009871) | RNASEQR | software resource | A streamlined and accurate RNA-seq sequence analysis program. | is listed by: OMICtools | OMICS_01263 | SCR_009871 | RNASEQR-a streamlined and accurate RNA-seq sequence analysis program | 2026-08-08 11:59:27 | 0 | |||||||||
|
isomiRID Resource Report Resource Website 1+ mentions |
isomiRID (RRID:SCR_009809) | isomiRID | software resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on 4/1/14. Software providing a framework to find isomiRNAs, templated and non-templated modifications in microRNAs. |
is listed by: OMICtools has parent organization: Federal University of Rio Grande do Sul; Rio Grande do Sul; Brazil |
PMID:23946501 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00387 | SCR_009809 | 2026-08-08 11:59:24 | 5 |
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