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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
TargetScore Resource Report Resource Website 1+ mentions |
TargetScore (RRID:SCR_012933) | TargetScore | software resource | Software to infer the posterior distributions of microRNA targets by probabilistically modelling the likelihood microRNA-overexpression fold-changes and sequence-based scores. |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:24135265 | Free | OMICS_00421 | SCR_012933 | TargetScore: Infer microRNA targets using microRNA-overexpression data and sequence information | 2026-02-14 02:02:44 | 3 | |||||||
|
OncoSNP Resource Report Resource Website 10+ mentions |
OncoSNP (RRID:SCR_012985) | OncoSNP | software resource | An analytical software tool for characterizing copy number alterations and loss-of-heterozygosity (LOH) events in cancer samples from SNP genotyping data. | is listed by: OMICtools | Cancer | Freely available for academic use, Non-commercial, Commercial with permission | OMICS_00728 | SCR_012985 | 2026-02-14 02:02:20 | 19 | ||||||||
|
RLMM Resource Report Resource Website 1+ mentions |
RLMM (RRID:SCR_012984) | RLMM | software resource | A Genotype Calling Algorithm for Affymetrix SNP Arrays. |
is listed by: OMICtools has parent organization: Bioconductor |
OMICS_00732 | SCR_012984 | 2026-02-14 02:02:49 | 5 | ||||||||||
|
IBDLD Resource Report Resource Website 10+ mentions |
IBDLD (RRID:SCR_013043) | IBDLD | software resource | A C++ software program for multipoint IBD estimation based on high density SNP genotype data. | c++ |
is listed by: OMICtools has parent organization: SourceForge |
PMID:21769932 | Free | OMICS_00204 | SCR_013043 | 2026-02-14 02:02:49 | 14 | |||||||
|
SolSNP Resource Report Resource Website 1+ mentions |
SolSNP (RRID:SCR_013045) | SolSNP | software resource | A Java-based DNA variant calling tool for Next-Generation Sequencing alignment data. |
is listed by: OMICtools has parent organization: SourceForge |
MIT License | OMICS_00079 | SCR_013045 | 2026-02-14 02:02:45 | 7 | |||||||||
|
HATS Resource Report Resource Website 10+ mentions |
HATS (RRID:SCR_013044) | HATS | software resource | A software tool that calls the amplified alleles, and thus amplified haplotype, in copy number aberration regions in next generation sequencing tumor data. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00200 | SCR_013044 | Haplotype Amplification in Tumor Sequences | 2026-02-14 02:02:21 | 37 | |||||||||
|
charm Resource Report Resource Website 50+ mentions |
charm (RRID:SCR_012992) | charm | software resource | Software package that implements analysis tools for DNA methylation data generated using Nimblegen microarrays and the McrBC protocol. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
biotools:charm, OMICS_00792 | https://bio.tools/charm | SCR_012992 | 2026-02-14 02:02:25 | 63 | ||||||||
|
ChIPOTle Peak Finder Resource Report Resource Website |
ChIPOTle Peak Finder (RRID:SCR_012991) | ChIPOTle Peak Finder | software resource | A peak-finding algorithm used to analyze ChIP-chip microarray data. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00803 | SCR_012991 | 2026-02-14 02:02:45 | 0 | ||||||||||
|
BiSeq Resource Report Resource Website 10+ mentions |
BiSeq (RRID:SCR_012993) | BiSeq | software resource | Software package that provides useful classes and functions to handle and analyze targeted bisulfite sequencing (BS) data such as reduced-representation bisulfite sequencing (RRBS) data. |
is listed by: OMICtools has parent organization: Bioconductor |
OMICS_00620 | SCR_012993 | 2026-02-14 02:02:49 | 30 | ||||||||||
|
Trinity Resource Report Resource Website 5000+ mentions |
Trinity (RRID:SCR_013048) | Trinity | software resource | Software for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge has parent organization: Broad Institute has parent organization: Hebrew University of Jerusalem; Jerusalem; Israel |
DOI:10.1038/nbt.1883 | biotools:trinity, OMICS_01327 | https://bio.tools/trinity https://sources.debian.org/src/trinityrnaseq/ |
SCR_013048 | 2026-02-14 02:02:49 | 9576 | |||||||
|
NGSpeAnalysis Resource Report Resource Website |
NGSpeAnalysis (RRID:SCR_013040) | NGSpeAnalysis | software resource | A pipeline using open-source tools which can implement a set of pair ended Next-generation sequencing analysis, include short reads alignment, high-quality variation genotype calling and variants annotation. |
is listed by: OMICtools has parent organization: SourceForge |
GNU General Public License, v2 | OMICS_00291 | SCR_013040 | 2026-02-14 02:02:21 | 0 | |||||||||
|
MEDME Resource Report Resource Website 10+ mentions |
MEDME (RRID:SCR_012995) | MEDME | software resource | Software that allows the prediction of absolute and relative methylation levels based on measures obtained by MeDIP-microarray experiments. |
is listed by: OMICtools has parent organization: Bioconductor |
OMICS_00614 | SCR_012995 | 2026-02-14 02:02:45 | 18 | ||||||||||
|
MethylCoder Resource Report Resource Website 1+ mentions |
MethylCoder (RRID:SCR_012997) | MethylCoder | software resource | A single program that takes of bisulfite-treated reads and outputs per-base methylation data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:21724594 | biotools:methylcoder, OMICS_00585 | https://bio.tools/methylcoder | SCR_012997 | 2026-02-14 02:02:49 | 4 | |||||||
|
LoFreq Resource Report Resource Website 500+ mentions |
LoFreq (RRID:SCR_013054) | LoFreq | software resource | A fast and sensitive variant-caller for inferring single-nucleotide variants (SNVs) from high-throughput sequencing data. |
is listed by: OMICtools is listed by: Debian has parent organization: SourceForge |
PMID:23066108 DOI:10.1093/nar/gks918 |
Free, Freely available | OMICS_00063 | https://sources.debian.org/src/lofreq/ | SCR_013054 | LoFreq - Sensitive variant-calling from sequencing data | 2026-02-14 02:02:21 | 523 | ||||||
|
GENE-counter Resource Report Resource Website 1+ mentions |
GENE-counter (RRID:SCR_013056) | GENE-counter | software resource | A computational pipeline for analyzing RNA-Sequencing (RNA-Seq) data for differential gene expression of eukaryotes, prokaryotes, as well as organisms with no available genome reference sequence. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:21998647 | OMICS_01404, biotools:gene-counter | https://bio.tools/gene-counter | SCR_013056 | 2026-02-14 02:02:26 | 7 | |||||||
|
RNA CoMPASS Resource Report Resource Website |
RNA CoMPASS (RRID:SCR_013058) | RNA CoMPASS | software resource | A web-based GUI distributed computational pipeline, provides all-in-one functionality including human transcriptome quantification and the typical endogenous RNA-Sequencing analysis along with the investigation of exogenous sequences. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_01410 | SCR_013058 | 2026-02-14 02:02:49 | 0 | ||||||||||
|
CoNAn-SNV Resource Report Resource Website |
CoNAn-SNV (RRID:SCR_013059) | CoNAn-SNV | software resource | Software for a probabilistic framework for the discovery of single nucleotide variants in WGSS data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. |
is listed by: OMICtools has parent organization: University of British Columbia; British Columbia; Canada |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00054 | SCR_013059 | 2026-02-14 02:02:21 | 0 | |||||||||
|
SNPTools Resource Report Resource Website 10+ mentions |
SNPTools (RRID:SCR_013052) | SNPTools | software resource | A suite of software tools that enables integrative SNP analysis in next generation sequencing data with large cohorts. | c++ |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00075 | SCR_013052 | 2026-02-14 02:02:26 | 19 | |||||||||
|
Swift Resource Report Resource Website 50+ mentions |
Swift (RRID:SCR_013018) | Swift | software resource | An open source package for primary data analysis on next-gen sequence data from images to basecalls. Currently Swift is targeted toward Solexa/Illumina sequencing, but is designed to be platform agnostic. |
is listed by: OMICtools has parent organization: SourceForge |
Open unspecified license | OMICS_01157 | SCR_013018 | 2026-02-14 02:02:49 | 74 | |||||||||
|
CloudAligner Resource Report Resource Website 1+ mentions |
CloudAligner (RRID:SCR_012962) | CloudAligner | software resource | A map/reduce based application for mapping short reads generated by the next-generation sequencing machines. | matlab, mapreduce/hadoop, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:21645377 | GNU General Public License, v3 | OMICS_00656, biotools:cloudaligner | https://bio.tools/cloudaligner | SCR_012962 | 2026-02-14 02:02:19 | 4 |
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