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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
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 | 2026-08-08 11:59:50 | 68 | ||||||||
|
Multivariate Analysis of Transcript Splicing Resource Report Resource Website 100+ mentions |
Multivariate Analysis of Transcript Splicing (RRID:SCR_013049) | MATS | software resource, software application, data analysis software, data processing software | Software tool to detect differential alternative splicing events from RNA-Seq data. Calculates P value and false discovery rate that difference in isoform ratio of gene between two conditions exceeds given user defined threshold. Can automatically detect and analyze alternative splicing events corresponding to all major types of alternative splicing patterns. Handles replicate RNA-Seq data from both paired and unpaired study design. | Differential alternative splicing events, splicing events calculation, RNA-Seq data, gene isoform ratio, alternative splicing patterns, patterns detection, patterns analysis, replicate RNA-Seq data |
is listed by: OMICtools is listed by: SourceForge has parent organization: Childrens Hospital of Philadelphia - Research Institute; Pennsylvania; USA |
Free, Available for download, Freely available | OMICS_01336, SCR_020941 | SCR_013049 | RNAseq MATS, RMATS, rMATS, MATS, RNA MATS | 2026-08-08 12:00:07 | 203 | |||||||
|
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 | 2026-08-08 12:00:06 | 30 | ||||||||||
|
Trinity Resource Report Resource Website 10000+ 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 | 2026-08-08 11:59:51 | 10043 | |||||||
|
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 | 2026-08-08 11:59:50 | 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 | 2026-08-08 12:00:18 | 4 | |||||||
|
GRASSIUS Resource Report Resource Website 10+ mentions |
GRASSIUS (RRID:SCR_012999) | GRASSIUS | data or information resource, production service resource, data analysis service, database, analysis service resource, service resource, storage service resource, data repository | A public resource composed of a collection of databases, computational and experimental resources that relate to the control of gene expression in the grasses, and their relationship with agronomic traits. As knowledge on the interactions of transcription factors (TFs) and cis-regulatory elements in the promoters of the genes that they regulate continues to accumulate, the information is acquired by GRASSIUS, either through contributions by the community, or by literature analysis. The overarching objective of GRASSIUS is to provide a one-stop resource that will facilitate research and communication within the plant community with regards to genome-wide regulation of gene expression processes. | transcription factor, coregulator, promoter sequence, transcription factor orf clone, blast, genome browser |
is listed by: OMICtools has parent organization: Ohio State University; Ohio; USA |
NSF | PMID:18987217 | Free | OMICS_00555 | SCR_012999 | Grass Regulatory Information Server | 2026-08-08 12:00:06 | 32 | |||||
|
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 | 2026-08-08 12:00:19 | 553 | ||||||
|
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 | 2026-08-08 12:00:07 | 7 | |||||||
|
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 | 2026-08-08 11:59:51 | 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 | 2026-08-08 11:59:50 | 76 | |||||||||
|
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 | 2026-08-08 12:00:05 | 4 | ||||||
|
Rolexa Resource Report Resource Website 1+ mentions |
Rolexa (RRID:SCR_013017) | Rolexa | software resource | Software that provides probabilistic base calling, quality checks and diagnostic plots for Solexa sequencing data. |
is listed by: OMICtools has parent organization: Bioconductor |
OMICS_01156 | SCR_013017 | 2026-08-08 12:00:18 | 1 | ||||||||||
|
InCroMAP Resource Report Resource Website 10+ mentions |
InCroMAP (RRID:SCR_012964) | InCroMAP | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 5,2023. Integrated analysis of cross-platform microarray and pathway data. | is listed by: OMICtools | PMID:23257199 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00855 | SCR_012964 | 2026-08-08 11:59:49 | 11 | ||||||||
|
TraceTuner Resource Report Resource Website 10+ mentions |
TraceTuner (RRID:SCR_013019) | TraceTuner | software resource | Software tool for base and quality calling of trace files from DNA sequencing instruments. |
is listed by: OMICtools is listed by: Debian has parent organization: SourceForge |
Free | OMICS_01158 | https://sources.debian.org/src/tracetuner/ | SCR_013019 | TraceTuner - DNA sequencing quality values base calling and trace processing | 2026-08-08 12:00:06 | 14 | |||||||
|
GenomeView Resource Report Resource Website 10+ mentions |
GenomeView (RRID:SCR_012968) | GenomeView | database, data or information resource, software resource | A next-generation stand-alone genome browser and editor initiated in the BSB group at VIB and currently developed at Broad Institute. | is listed by: OMICtools | PMID:22102585 | OMICS_00913 | SCR_012968 | 2026-08-08 12:00:18 | 36 | |||||||||
|
seqMINER Resource Report Resource Website 100+ mentions |
seqMINER (RRID:SCR_013020) | seqMINER | software resource | Software for a genome wide mapping data interpretation platform for NGS (ChIPSeq). | java, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:21177645 | GNU General Public License, v3 | biotools:seqminer, OMICS_00460 | https://bio.tools/seqminer | SCR_013020 | 2026-08-08 12:00:18 | 190 | ||||||
|
MIREAP Resource Report Resource Website 100+ mentions |
MIREAP (RRID:SCR_013025) | MIREAP | software resource | A software tool which can be used to identify both known and novel microRNAs from small RNA libraries deeply sequenced by Solexa/454/Solid technology. |
is listed by: OMICtools has parent organization: SourceForge |
GNU General Public License, v2 | OMICS_00376 | SCR_013025 | 2026-08-08 12:00:18 | 389 | |||||||||
|
MIReNA Resource Report Resource Website 1+ mentions |
MIReNA (RRID:SCR_013024) | MIReNA | software resource | A software tool to find microRNAs with high accuracy and no learning at genome scale and from deep sequencing data. | is listed by: OMICtools | PMID:20591903 | Acknowledgement requested, CeCILL license | OMICS_00377 | SCR_013024 | 2026-08-08 12:00:06 | 8 | ||||||||
|
MIG Resource Report Resource Website 1+ mentions |
MIG (RRID:SCR_012972) | MIG | software resource | Allows the user to conveniently compare data from many loci., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | is listed by: OMICtools | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00942 | SCR_012972 | Multi-Image Genome | 2026-08-08 11:59:49 | 1 |
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