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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
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 | 2026-09-12 12:57:56 | 0 | ||||||||||
|
Multivariate Analysis of Transcript Splicing Resource Report Resource Website 100+ mentions |
Multivariate Analysis of Transcript Splicing (RRID:SCR_013049) | MATS | data analysis software, data processing software, software application, software resource | 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 | 2026-09-12 12:57:58 | 203 | |||||||
|
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 | 2026-09-12 12:57:58 | 10043 | |||||||
|
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 | 2026-09-12 12:57:58 | 0 | |||||||||
|
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 | 2026-09-12 12:57:58 | 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 | 2026-09-12 12:57:58 | 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 | 2026-09-12 12:57:58 | 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 | 2026-09-12 12:57:58 | 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 | 2026-09-12 12:57:57 | 76 | |||||||||
|
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 | 2026-09-12 12:57:57 | 14 | |||||||
|
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 | 2026-09-12 12:57:57 | 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 | 2026-09-12 12:57:57 | 389 | |||||||||
|
EDNA Resource Report Resource Website 10+ mentions |
EDNA (RRID:SCR_012981) | EDNA | software resource | Software for Multiple Sequence Alignment for Transcription Factor Binding Sites using Di nucleotides dependencies and relying on Free Interaction energies between neighbouring DNA bases to stabilise substitution energy of the alignment. | matlab |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23990411 | Creative Commons Attribution NonCommercial License, v2 | OMICS_00974 | SCR_012981 | EDNA - Energy Based Multiple Sequence Alignment (MSA) for Binding Sites | 2026-09-12 12:57:56 | 34 | ||||||
|
SAMZIP Resource Report Resource Website |
SAMZIP (RRID:SCR_012980) | SAMZIP | software resource | An encoding and decoding tool for Sequence Alignment/Map (SAM) files. |
is listed by: OMICtools has parent organization: SourceForge |
PMID:22164252 | OMICS_00967 | SCR_012980 | 2026-09-12 12:57:56 | 0 | |||||||||
|
SAMMate Resource Report Resource Website 10+ mentions |
SAMMate (RRID:SCR_013037) | SAMMate | software resource | An open source GUI software suite to process RNA-Seq data. It is composed of two modules: assemblySAM and SAMMate. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
biotools:sammate, OMICS_01264 | https://bio.tools/sammate | SCR_013037 | 2026-09-12 12:57:57 | 11 | ||||||||
|
Flexbar Resource Report Resource Website 100+ mentions |
Flexbar (RRID:SCR_013001) | Flexbar | software resource | Flexible barcode and adapter removal for sequencing platforms. | bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
DOI:10.3390/biology1030895 | biotools:flexbar | https://bio.tools/flexbar, https://sources.debian.org/src/flexbar/ | SCR_013001 | 2026-09-12 12:57:57 | 307 | |||||||
|
SHREC Resource Report Resource Website 10+ mentions |
SHREC (RRID:SCR_013009) | SHREC | software resource | A bioinformatics tool for error correction of HTS read data. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_01110 | SCR_013009 | 2026-09-12 12:57:57 | 14 | ||||||||||
|
hiCtools Resource Report Resource Website |
hiCtools (RRID:SCR_013010) | hiCtools | software resource | This collection of tools stream-lines the processing of HiC data from raw sequence to contact matrices and beyond. |
is listed by: OMICtools has parent organization: SourceForge |
GNU General Public License, v3 | OMICS_00522 | SCR_013010 | 2026-09-12 12:57:57 | 0 | |||||||||
|
AutoMap Resource Report Resource Website 100+ mentions |
AutoMap (RRID:SCR_013095) | AutoMap | software resource | A tool for structural biology and drug design. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_01596 | SCR_013095 | 2026-09-12 12:57:59 | 100 | ||||||||||
|
LOCAS Resource Report Resource Website 1+ mentions |
LOCAS (RRID:SCR_013064) | LOCAS | software resource | A software to assemble short reads of next generation sequencing technologies at low coverage. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:21858125 | OMICS_00019, biotools:locas | https://bio.tools/locas | SCR_013064 | 2026-09-12 12:57:58 | 2 |
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