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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
ASC Resource Report Resource Website 1+ mentions |
ASC (RRID:SCR_001013) | ASC | software resource | Borrows information across sequences to establish prior distribution of sample variation, so that biological variation can be accounted for even when replicates are not available. | sample variation, rna, dna, biology, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Brown University; Rhode Island; USA |
biotools:sqn, OMICS_01298 | https://bio.tools/sqn | SCR_001013 | 2026-08-29 11:20:34 | 1 | ||||||||
|
Jmosaics Resource Report Resource Website |
Jmosaics (RRID:SCR_001094) | data analysis software, data processing software, sequence analysis software, software application, software resource | 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 | 2026-08-29 11:20:43 | 0 | |||||||||
|
GDC Resource Report Resource Website 1+ mentions |
GDC (RRID:SCR_001007) | GDC | data analysis software, data management software, data processing software, software application, software resource | 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) | 2026-08-29 11:20:34 | 1 | |||||
|
AutoAssemblyD Resource Report Resource Website |
AutoAssemblyD (RRID:SCR_001087) | data analysis software, data processing software, sequence analysis software, software application, software resource | 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 | 2026-08-29 11:20:42 | 0 | |||||||
|
jmzML Resource Report Resource Website 1+ mentions |
jmzML (RRID:SCR_001119) | software resource | A Java application programming interface (API) for the Proteomics Standards Initiative mzML data standard. | standalone software, mac os x, unix/linux, windows, java, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Google Code |
PMID:20127693 | Free, Available for download, Freely available | biotools:jmzml, OMICS_03340 | https://bio.tools/jmzml | SCR_001119 | 2026-08-29 11:20:59 | 1 | |||||||
|
massiR Resource Report Resource Website |
massiR (RRID:SCR_001157) | software resource | Software that predicts the sex of samples in gene expression microarray datasets. | standalone software, mac os x, unix/linux, windows, r, classification, clustering, gene expression, microarray, quality control, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:24659105 | Free, Available for download, Freely available | biotools:massir, OMICS_03638 | https://bio.tools/massir | SCR_001157 | massiR: MicroArray Sample Sex Identifier, MicroArray Sample Sex Identifier | 2026-08-29 11:20:44 | 0 | ||||||
|
Reaper - Demultiplexing trimming and filtering sequencing data Resource Report Resource Website 1+ mentions |
Reaper - Demultiplexing trimming and filtering sequencing data (RRID:SCR_001144) | Reaper | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23, 2022. Software program for demultiplexing, trimming and filtering short read sequencing data. | c, alignment, sequence, demultiplex, trim, filter, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: European Bioinformatics Institute |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:reaper, OMICS_02157 | https://bio.tools/reaper | SCR_001144 | 2026-08-29 11:20:44 | 1 | |||||||
|
Phred Resource Report Resource Website 10+ mentions |
Phred (RRID:SCR_001017) | Phred | data analysis software, data processing software, sequence analysis software, software application, software resource | A base calling program for DNA sequence traces. | base calling, sequence analysis software, dna, trace | is listed by: OMICtools | PMID:9521922 | Restricted | OMICS_01809 | SCR_001017 | 2026-08-29 11:20:34 | 13 | |||||||
|
Skylign Resource Report Resource Website 10+ mentions |
Skylign (RRID:SCR_001176) | Skylign | analysis service resource, data analysis service, production service resource, service resource, software 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 | 2026-08-29 11:20:37 | 13 | |||||
|
yaqcaffy Resource Report Resource Website 1+ mentions |
yaqcaffy (RRID:SCR_001295) | yaqcaffy | software resource | Software package for quality control of Affymetrix GeneChip expression data and reproducibility analysis of human whole genome chips with the MAQC reference datasets. | microarray, one channel, quality control, report writing, affymetrix, gene expression, 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 | BioTools:yaqcaffy, biotools:yaqcaffy, OMICS_02040 | http://www.bioconductor.org/packages/release/bioc/html/yaqcaffy.html | SCR_001295 | yaqcaffy - Affymetrix expression data quality control and reproducibility analysis | 2026-08-29 11:21:01 | 3 | ||||||
|
BSSim Resource Report Resource Website 1+ mentions |
BSSim (RRID:SCR_001212) | BSSim | software resource | Software to mimic various methylation level and bisulfite conversion rate in CpG, CHG and CHH context, respectively. It can also simulate genetic variations that are divergent from the reference sequence along with the sequencing error and quality distributions. In the output, both directional/non-directional, various read length, single/paired-end reads and alignment data in the SAM format can be generated. BSSim is a cross-platform BS-seq simulator offers output read datasets not only suitable for Illumina's Solexa, but also for Roche's 454 and Applied Biosystems' SOLiD. | bisulfite sequencing, simulator, next-generation sequencing, python, dna methylation, snp, read quality | is listed by: OMICtools | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02130 | SCR_001212 | BSSim: Bisulfite sequencing simulator for next-generation sequencing | 2026-08-29 11:21:00 | 1 | |||||||
|
SplicePlot Resource Report Resource Website |
SplicePlot (RRID:SCR_001172) | SplicePlot | software resource | A software tool for visualizing alternative splicing and the effects of splicing quantitative trait loci (sQTLs) from RNA-seq data. It provides a simple command line interface for drawing sashimi plots, hive plots, and structure plots of alternative splicing events from .bam, .gtf, and .vcf files. | visualization, alternative splicing, splicing quantitative trait loci, quantitative trait loci, rna-seq, hive plot, structure plot, sashmi plot, python, linux, mac os, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Stanford University School of Medicine; California; USA |
PMID:24363378 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02185, biotools:spliceplot | https://bio.tools/spliceplot | SCR_001172 | SplicePlot: a tool for visualizing alternative splicing | 2026-08-29 11:20:59 | 0 | |||||
|
ChIPsim Resource Report Resource Website 1+ mentions |
ChIPsim (RRID:SCR_001293) | ChIPsim | software resource | Software package providing a general framework for the simulation of ChIP-seq data. Although currently focused on nucleosome positioning the package is designed to support different types of experiments. | chip-seq, infrastructure, simulation |
is listed by: OMICtools has parent organization: Bioconductor |
GNU General Public License, v2 or newer | OMICS_02042 | SCR_001293 | ChIPsim - Simulation of ChIP-seq experiments | 2026-08-29 11:20:40 | 1 | |||||||
|
methyAnalysis Resource Report Resource Website 1+ mentions |
methyAnalysis (RRID:SCR_001290) | methyAnalysis | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software package for DNA methylation data analysis and visualization. A new class is defined to keep the chromosome location information together with the data. The current version of the package mainly focuses on analyzing the Illumina Infinium methylation array data, but most methods can be generalized to other methylation array or sequencing data. | dna methylation, microarray, visualization |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:21159174 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02046 | SCR_001290 | methyAnalysis - DNA methylation data analysis and visualization | 2026-08-29 11:20:40 | 9 | ||||||
|
WiggleTools Resource Report Resource Website 1+ mentions |
WiggleTools (RRID:SCR_001170) | WiggleTools | data processing software, software application, software library, software resource, software toolkit | 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 | 2026-08-29 11:20:37 | 2 | |||||||
|
les Resource Report Resource Website |
les (RRID:SCR_001291) | les | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software package that estimates Loci of Enhanced Significance (LES) in tiling microarray data. These are regions of regulation such as found in differential transcription, CHiP-chip, or DNA modification analysis. The package provides a universal framework suitable for identifying differential effects in tiling microarray data sets, and is independent of the underlying statistics at the level of single probes. | loci of enhanced significance, tiling microarray, tiling, microarray, chip-chip, dna modification, probe, dna methylation, differential expression, microarray, transcription, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:les, OMICS_02045 | https://bioconductor.org/packages/les/, https://bio.tools/les | SCR_001291 | les package: Identifying Differential Effects in Tiling Microarray Data, Loci of Enhanced Significance | 2026-08-29 11:20:49 | 0 | ||||||
|
sim4cc Resource Report Resource Website |
sim4cc (RRID:SCR_001204) | alignment software, data processing software, image analysis software, software application, software resource | 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 |
NLM R01 LM006845; NSF CLS20163A; Sloan Research Fellowship |
PMID:19429899 | Free, Available for download, Freely available | biotools:sim4cc, OMICS_02145 | https://bio.tools/sim4cc | SCR_001204 | 2026-08-29 11:20:37 | 0 | ||||||
|
QualiMap Resource Report Resource Website 10+ mentions |
QualiMap (RRID:SCR_001209) | QualiMap | software resource | Software application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data. It examines sequencing alignment data in SAM / BAM files according to the features of the mapped reads and provides an overall view of the data that helps to the detect biases in the sequencing and/or mapping of the data and eases decision-making for further analysis. | next-generation sequencing, alignment, linux, macos, windows, quality control, sam, bam, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Principe Felipe Research Centre; Valencia; Spain |
Spanish Ministry of Economy and Competitiveness BIO2009-10799; EU funded program ERA-NET PathoGenoMics BIO2008-05266-E |
PMID:22914218 DOI:10.1093/bioinformatics/bts503 |
Free, Available for download, Freely available | OMICS_02133, biotools:qualimap | https://bio.tools/qualimap | https://sources.debian.org/src/qualimap/ | SCR_001209 | QualiMap - Evaluating next generation sequencing alignment data | 2026-08-29 11:20:46 | 48 | |||
|
Omixon Target Data Analysis Resource Report Resource Website |
Omixon Target Data Analysis (RRID:SCR_001207) | Omixon Target | commercial organization, data analysis software, data processing software, software application, software resource, software toolkit | 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 | 2026-08-29 11:20:59 | 0 | ||||||||
|
MetaPhyl Resource Report Resource Website |
MetaPhyl (RRID:SCR_001169) | MetaPhyl | software resource | Software implementing a supervised classification method for metagenomic samples that takes advantage of the natural structure of microbial community data encoded by phylogenetic trees. | c++, linux, mac osx, phylogenetic tree, command line, classification, metagenomic |
is listed by: OMICtools has parent organization: University of California at Riverside; California; USA |
PMID:24369151 | Free, Available for download, Freely available | OMICS_02189 | SCR_001169 | 2026-08-29 11:20:59 | 0 |
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