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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
MitoBreak Resource Report Resource Website 10+ mentions |
MitoBreak (RRID:SCR_012949) | MitoBreak | storage service resource, service resource, data repository, data or information resource, database | Database with curated datasets of mitochondrial DNA (mtDNA) rearrangements. Users may submit new mtDNA rearrangements. | mitochondrial dna rearrangement, mitochondrial dna, deletion, duplication, linear, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:24170808 | Free, The community can contribute to this resource | biotools:mitobreak, OMICS_01640 | https://bio.tools/mitobreak | SCR_012949 | 2026-08-06 09:28:02 | 10 | ||||||
|
minfi Resource Report Resource Website 100+ mentions |
minfi (RRID:SCR_012830) | minfi | software resource, data analysis software, data processing software, data visualization software, software application | Software tools for analyzing and visualizing Illumina''s 450k array data. | Illumina, array data, Analyze Illumina Infinium DNA methylation arrays, DNA methylation array, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: SWAN has parent organization: Bioconductor |
PMID:28035024 | Free, Available for download, Freely available | biotools:minfi, OMICS_00799, BioTools:minfi | https://bio.tools/minfi, https://bio.tools/minfi, https://bio.tools/minfi | SCR_012830 | 2026-08-06 09:28:04 | 390 | ||||||
|
affy Resource Report Resource Website 1000+ mentions |
affy (RRID:SCR_012835) | Affy | data analysis software, software application, software resource, data processing software | Software R package of functions and classes for the analysis of oligonucleotide arrays manufactured by Affymetrix. Used to process probe level data and for exploratory oligonucleotide array analysis. | analysis, oligonucleotide, array, Affymetrix, process, probe, data, function, bio.tools |
is listed by: OMICtools is listed by: Bioconductor is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: affydata is related to: R Project for Statistical Computing is related to: OMICtools |
Danish Biotechnology Instrument Center | PMID:14960456 | Free, Available for download, Freely available | BioTools:affy, OMICS_00740, biotools:affy | https://bio.tools/affy, https://sources.debian.org/src/r-bioc-affy/ | SCR_012835 | Affymetrix, analysis of Affymetrix GeneChip data at the probe level, analysis of Affymetrix GeneChip data | 2026-08-06 09:28:04 | 2996 | ||||
|
AcroMine Resource Report Resource Website |
AcroMine (RRID:SCR_013196) | service resource, data access protocol, web service, software resource | An acronym dictionary which can be used to find distinct expanded forms of acronyms from MEDLINE. This freely available service can be used through your browser or by integrating it with your applications using the ReSTful service. Acromine identifies abbreviation definitions by assuming a word sequence co-occurring frequently with a parenthetical expression to be a potential expanded form. Applied to the whole MEDLINE (9,635,599 abstracts), the implemented system extracted 68,007 abbreviation candidates and recognized 467,402 expanded forms. The current Acromine achieves 99% precision and 82-95% recall on our evaluation corpus that roughly emulates the whole MEDLINE. | acronym, abbreviation, disambiguation, computational linguistics, text mining |
is listed by: FORCE11 is listed by: OMICtools has parent organization: University of Manchester; Manchester; United Kingdom |
JISC ; BBSRC ; EPSRC |
PMID:20360059 PMID:17050571 |
Free, Public | OMICS_01169, nif-0000-10215 | SCR_013196 | Acromine | 2026-08-06 09:28:05 | 0 | ||||||
|
Cufflinks Resource Report Resource Website 5000+ mentions |
Cufflinks (RRID:SCR_014597) | sequence analysis software, software resource, data analysis software, data processing software, software application | Software tool for transcriptome assembly and differential expression analysis for RNA-Seq. Includes script called cuffmerge that can be used to merge together several Cufflinks assemblies. It also handles running Cuffcompare as well as automatically filtering a number of transfrags that are likely to be artifacts. If the researcher has a reference GTF file, the researcher can provide it to the script to more effectively merge novel isoforms and maximize overall assembly quality. | transcriptome, rna-seq, rna seq, cuffmerge, cufflink, cuffcompare, transfrags, artifacts, gtf file, transcriptome assembly, expression analysis, bio.tools, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools is listed by: SoftCite works with: GeneScissors is hosted by: GitHub |
DOI:10.1038/nbt.1621 | Acknowledgement requested, Source code available on GitHub | biotools:cufflinks, OMICS_01304, SCR_013307 | https://github.com/cole-trapnell-lab/cufflinks, https://bio.tools/cufflinks, https://sources.debian.org/src/cufflinks/ | SCR_014597 | 2026-08-06 09:28:23 | 8838 | |||||||
|
Skylign Resource Report Resource Website 10+ mentions |
Skylign (RRID:SCR_001176) | Skylign | software resource, service resource, production service resource, data analysis service, analysis service resource | A tool for creating logos representing both sequence alignments and profile hidden Markov models. The interactive logos enable scrolling, zooming, and inspection of underlying values. Skylign can avoid sampling bias in sequence alignments by down-weighting redundant sequences and by combining observed counts with informed priors. It also simplifies the representation of gap parameters, and can optionally scale letter heights based on alternate calculations of the conservation of a position. | sequence alignment, profile, logo, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Janelia Research |
PMID:24410852 | Creative Commons Attribution License, v3 Unported | biotools:skylign, OMICS_02182 | https://bio.tools/skylign | SCR_001176 | Skylign - Interactive logos for alignments and profile HMMs | 2026-08-06 09:25:20 | 13 | |||||
|
WiggleTools Resource Report Resource Website 1+ mentions |
WiggleTools (RRID:SCR_001170) | WiggleTools | software resource, software library, software toolkit, data processing software, software application | A multithreaded software library that computes statistics on large numbers of datasets, generating statistical summaries within minutes with limited memory requirements, whether on the whole genome or on selected regions. | visualization, statistical analysis, parallel processing, genome |
is listed by: OMICtools has parent organization: European Bioinformatics Institute |
PMID:24363377 | Apache License, v2 | OMICS_02188 | SCR_001170 | 2026-08-06 09:25:20 | 1 | |||||||
|
sim4cc Resource Report Resource Website |
sim4cc (RRID:SCR_001204) | software resource, image analysis software, alignment software, data processing software, software application | Software tool as cross species spliced alignment program.Heuristic sequence alignment tool for comparing cDNA sequence with genomic sequence containing homolog of gene in another species. | Cross species spliced alignment, unix, sequence alignment, cdna sequence, genomic sequence, homolog, gene, splice, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Johns Hopkins University; Maryland; USA |
NSF CLS20163A; Sloan Research Fellowship ; NLM R01 LM006845 |
PMID:19429899 | Free, Available for download, Freely available | biotools:sim4cc, OMICS_02145 | https://bio.tools/sim4cc | SCR_001204 | 2026-08-06 09:25:20 | 0 | ||||||
|
Omixon Target Data Analysis Resource Report Resource Website |
Omixon Target Data Analysis (RRID:SCR_001207) | Omixon Target | software resource, data analysis software, software toolkit, data processing software, software application, commercial organization | Software application suite to help clinical labs adopt next generation sequencing for the analysis of diagnostic gene targets. | next-generation sequencing, gene target, windows, linux, mac, gene, diagnostic |
is listed by: OMICtools is parent organization of: Omixon Target HLA Typing |
License required | OMICS_02141 | SCR_001207 | 2026-08-06 09:25:20 | 0 | ||||||||
|
bsseq Resource Report Resource Website 1+ mentions |
bsseq (RRID:SCR_001072) | sequence analysis software, software resource, data analysis software, data processing software, software application | R package with tools for analyzing and visualizing bisulfite sequencing data. | bisulfite sequencing, analyze, r, sequence analysis software, data analysis software, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_01847, biotools:bsseq | https://bio.tools/bsseq | SCR_001072 | bsseq - Analyze manage and store bisulfite sequencing data | 2026-08-06 09:25:19 | 8 | |||||||
|
MmPalateMiRNA Resource Report Resource Website 1+ mentions |
MmPalateMiRNA (RRID:SCR_001070) | source code, software resource, data analysis software, data processing software, software application | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software R package written for analysis of murine palate miRNA two-color expression data. | murine, palate, mirna, two color expression, open source, r |
is listed by: OMICtools is hosted by: Bioconductor |
PMID:23298515 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00788 | SCR_001070 | 2026-08-06 09:25:20 | 1 | ||||||||
|
R453Plus1Toolbox Resource Report Resource Website 1+ mentions |
R453Plus1Toolbox (RRID:SCR_001105) | sequence analysis software, software resource, data analysis software, software toolkit, data processing software, software application | R software toolbox of functions for the analysis of data generated by Roche's 454 sequencing platform. Additional functions are included for quality assurance, annotation and visualization of detected variants, complementing the software tools shipped by Roche with their product. A pipeline for the detection of structural variants is provided. | genome, sequence, visualization, structural variants, r, sequence analysis software |
is listed by: OMICtools is hosted by: Bioconductor |
PMID:21349869 | Free, Available for download, Freely available | OMICS_01354 | SCR_001105 | 2026-08-06 09:25:20 | 4 | ||||||||
|
RmiR Resource Report Resource Website |
RmiR (RRID:SCR_001069) | RmiR | sequence analysis software, software resource, data analysis software, data processing software, software application | R package that contains functions to merge microRNA and respective targets using different databases. | micro rna, mrna, function, target, r, sequence analysis software |
is listed by: OMICtools has parent organization: Bioconductor |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00789 | https://rdrr.io/bioc/RmiR/ | SCR_001069 | 2026-08-06 09:25:19 | 0 | |||||||
|
CGEN Resource Report Resource Website 10+ mentions |
CGEN (RRID:SCR_001251) | CGEN | data analysis software, software application, software resource, data processing software | Software R package for analysis of case-control studies in genetic epidemiology. | genetic, epidemiology, r, case-control, clustering, multiple comparison, snp |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:21387464 | Free, Available for download, Freely available | OMICS_02089 | SCR_001251 | CGEN - An R package for analysis of case-control studies in genetic epidemiology | 2026-08-06 09:25:22 | 17 | ||||||
|
SplitSeek Resource Report Resource Website 1+ mentions |
SplitSeek (RRID:SCR_001012) | sequence analysis software, software resource, data analysis software, data processing software, software application | THIS RESOURCE IS NO LONGER IN SERVICE, documented September 20, 2016. A program for de novo prediction of splice junctions in RNA-seq data. | bioinformatics alignment, sequence analysis software, de novo, prediction, rna seq, rna, splice junction, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:20236510 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:splitseek, OMICS_01253 | https://bio.tools/splitseek | http://www.uppmax.uu.se/software/splitseek | SCR_001012 | 2026-08-06 09:25:18 | 1 | ||||||
|
Jmosaics Resource Report Resource Website |
Jmosaics (RRID:SCR_001094) | sequence analysis software, software resource, data analysis software, data processing software, software application | R software that detects enriched regions of ChIP-seq data sets jointly. | chip seq, data, genomics, sequencing, r, sequence analysis software |
is listed by: OMICtools is hosted by: Bioconductor |
Free, Available for download, Freely available | OMICS_00445 | SCR_001094 | 2026-08-06 09:25:19 | 0 | |||||||||
|
GDC Resource Report Resource Website 1+ mentions |
GDC (RRID:SCR_001007) | GDC | software resource, data analysis software, data management software, data processing software, software application | A C++ application designed for compression of genome collections from the same species. | compression, genome collection, c++, genome, software |
is listed by: OMICtools is hosted by: GitHub |
DOI:10.1038/srep11565 | Source code available for download | OMICS_00958 | https://github.com/refresh-bio/GDC2 | SCR_001007 | GDC 2, Genome Differential Compressor, Genome Differential Compressor (GDC) | 2026-08-06 09:25:18 | 1 | |||||
|
Mutation Surveyor Resource Report Resource Website 500+ mentions |
Mutation Surveyor (RRID:SCR_001247) | sequence analysis software, software resource, data analysis software, data processing software, software application | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software for DNA sequencing analysis that integates with Sanger Sequencing files generated by Applied Biosystems Genetic Analyzers, MegaBACE, and Beckman CEQ electrophoresis systems. It can be used to find single nucleotide polymorphisms (SNPs), insertions and deletions (INDELS), and somatic mutations in direct sequencing, PCR sequencing, mitochondrial DNA sequencing, and resequencing projects. | dna, sequencing, dna-seq, sanger sequencing, sequence analysis software | is listed by: OMICtools | PMID:21780000 PMID:20938837 |
Restricted | OMICS_01816 | Mutation Surveyor software version 5.0 | http://www.softgenetics.com/mutationSurveyor.html | SCR_001247 | 2026-08-06 09:25:21 | 668 | ||||||
|
AutoAssemblyD Resource Report Resource Website |
AutoAssemblyD (RRID:SCR_001087) | sequence analysis software, software resource, data analysis software, data processing software, software application | Software which performs local and remote genome assembly by several assemblers based on an XML Template which can replace the large command lines required by most assemblers. | genome, genome assembly, xml, sequence analysis software, local genome assembly, remote genome assembly, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:24143057 | Free, Available for download, Freely available | biotools:autoassemblyd, OMICS_00874 | https://bio.tools/autoassemblyd | SCR_001087 | 2026-08-06 09:25:20 | 0 | |||||||
|
GenoSet Resource Report Resource Website |
GenoSet (RRID:SCR_001275) | GenoSet | data analysis software, software application, software resource, data processing software | Software package to load, manipulate, and plot copynumber and BAF data by providing classes similar to ExpressionSet for copy number analysis. The class extends ExpressionSet by adding a locData slot for a RangedData or GRanegs object. This object contains feature genome location data and provides for efficient subsetting on genome location. CNSet and BAFSet extend GenoSet and require assayData matrices for Copy Number (cn) or Log-R Ratio (lrr) and B-Allele Frequency (baf) data. Implements and provides convenience functions for processing of copy number and B-Allele Frequency data. | copy number variation, data representation, infrastructure, microarray, snp |
is listed by: OMICtools has parent organization: Bioconductor |
Artistic License, v2 | OMICS_02063 | SCR_001275 | genoset - Provides classes similar to ExpressionSet for copy number analysis | 2026-08-06 09:25:21 | 0 |
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