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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
KisSplice Resource Report Resource Website 10+ mentions |
KisSplice (RRID:SCR_011893) | KisSplice | software resource, software application, data analysis software, data processing software | Software tool that enables analysis of RNA-seq data with or without reference genome. Local transcriptome assembler for SNPs, indels and AS events. | RNA-seq data analysis, with reference genome, without reference genome, local transcriptome assembler, SNPs, indels, AS events., bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
DOI:10.1186/1471-2105-13-S6-S5 | Free, Available for download, Freely available | biotools:KisSplice, OMICS_01321 | https://bio.tools/KisSplice, https://sources.debian.org/src/kissplice/ | SCR_011893 | 2026-08-08 12:00:01 | 21 | ||||||
|
FusionFinder Resource Report Resource Website 1+ mentions |
FusionFinder (RRID:SCR_011894) | FusionFinder | software resource | A perl-based software package, which can be used to find fusion transcript candidates in RNA-Seq data. | is listed by: OMICtools | OMICS_01349 | SCR_011894 | FusionHunter: identifying fusion transcripts using paired-end RNA-seq | 2026-08-08 11:59:37 | 4 | |||||||||
|
ECHO Resource Report Resource Website 100+ mentions |
ECHO (RRID:SCR_011851) | ECHO | sequence analysis software, software resource, software application, algorithm resource, data analysis software, data processing software | Error correction algorithm designed for short-reads from next-generation sequencing platforms such as Illumina''s Genome Analyzer II. | error correction, rnaseq, rna sequence, short-read, next-generation sequencing, ngs, illumina, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:21482625 DOI:10.1101/gr.111351.110 |
Free, Available for download | biotools:echo, OMICS_01102 | https://bio.tools/echo, https://sources.debian.org/src/uc-echo/ | SCR_011851 | ECHO: A reference-free short-read error correction algorithm | 2026-08-08 11:59:36 | 312 | |||||
|
CaMPDB Resource Report Resource Website 1+ mentions |
CaMPDB (RRID:SCR_011976) | CaMPDB | data or information resource, production service resource, data analysis service, database, analysis service resource, service resource | Calpain cleavage prediction using multiple kernel learning. | is listed by: OMICtools | PMID:21559271 | OMICS_01669 | SCR_011976 | Calpain for Modulatory Proteolysis Database | 2026-08-08 11:59:38 | 7 | ||||||||
|
Guide Resource Report Resource Website 50+ mentions |
Guide (RRID:SCR_011903) | Guide | software resource | A desktop application for the bench biologists to analyse RNA-Seq and microarray expression data. It performs gene-centric analyses such as differential expression and pathways using well-established R modules, integrates data from multiple sources, and enables editing of R commands., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | is listed by: OMICtools | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01405 | SCR_011903 | Guide: Application for gene expression analysis | 2026-08-08 12:00:02 | 63 | ||||||||
|
Oncofuse Resource Report Resource Website 10+ mentions |
Oncofuse (RRID:SCR_011904) | Oncofuse | software resource | Software tool designed to predict the oncogenic potential of fusion genes found by Next-Generation Sequencing in cancer cells. |
is listed by: OMICtools is listed by: Debian |
DOI:10.1093/bioinformatics/btt445 | OMICS_01406 | https://sources.debian.org/src/oncofuse/ | SCR_011904 | 2026-08-08 11:59:37 | 15 | ||||||||
|
PRADA Resource Report Resource Website 50+ mentions |
PRADA (RRID:SCR_011906) | PRADA | software resource | A pipeline to analyze paired end RNA-Seq data to generate gene expression values (RPKM) and gene-fusion candidates. | unix/linux, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
OMICS_01408, biotools:prada-rnaseq | https://bio.tools/prada-rnaseq | SCR_011906 | Pipeline for RNA-Sequencing Data Analysis | 2026-08-08 12:00:02 | 51 | |||||||
|
R-SAP Resource Report Resource Website 1+ mentions |
R-SAP (RRID:SCR_011907) | R-SAP | software resource | An automated bioinformatics pipeline that analyzes and quantitates high-throughput RNA-Seq datasets. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Georgia Institute of Technology; Georgia; USA |
OMICS_01409, biotools:r-sap | https://bio.tools/r-sap | http://www.mcdonaldlab.biology.gatech.edu/r-sap.htm | SCR_011907 | 2026-08-08 11:59:37 | 3 | |||||||
|
RobiNA Resource Report Resource Website 10+ mentions |
RobiNA (RRID:SCR_011908) | RobiNA | software resource | Software package for RNA-Seq-based transcriptomics. Used to analyse Illumina/Solexa-based RNA-Seq data, Affymetrix data and generic tabular two color or single channel array data. Offers variety of quality control methods that can be used to gain overview of experimental data technical quality and structure. | analyse Illumina/Solexa-based RNA-Seq data, data quality control, |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:22684630 | OMICS_01411 | SCR_011908 | 2026-08-08 11:59:55 | 19 | ||||||||
|
RseqFlow Resource Report Resource Website 1+ mentions |
RseqFlow (RRID:SCR_011909) | RseqFlow | software resource | An RNA-Seq analysis pipeline which offers an express implementation of analysis steps for RNA sequencing datasets. |
is listed by: OMICtools has parent organization: Google Code |
PMID:21795323 | OMICS_01412 | SCR_011909 | RseqFlow - An RNA-Seq analysis pipeline for Quality Control Expression Level Estimation Differentially Expressed Gene | 2026-08-08 12:00:02 | 3 | ||||||||
|
SHORE Resource Report Resource Website 100+ mentions |
SHORE (RRID:SCR_011863) | SHORE | software resource | A mapping and analysis pipeline for short read data produced on the Illumina platform. | is listed by: OMICtools | OMICS_01136 | SCR_011863 | 2026-08-08 11:59:36 | 157 | ||||||||||
|
Stack Overflow Resource Report Resource Website 10+ mentions |
Stack Overflow (RRID:SCR_011984) | Stack Overflow | data or information resource, portal, community building portal | A question and answer site for professional and enthusiast programmers. | programmer | is listed by: OMICtools | Free | OMICS_01711 | SCR_011984 | 2026-08-08 12:00:03 | 23 | ||||||||
|
HTS Mappers Resource Report Resource Website 1+ mentions |
HTS Mappers (RRID:SCR_011991) | HTS Mappers | software repository, data or information resource, software resource, data set | Data set providing an up-to-date compendium of HTS mappers initially provided in the article Tools for mapping high-throughput sequencing data. Please let fill out the provided form if you are a developer and your mapper is not listed or you want to update the data for your mapper. | mapping, high-throughput sequencing, dna, rna, mirna, bisulfite, mapper |
is listed by: OMICtools has parent organization: European Bioinformatics Institute |
PMID:23060614 | OMICS_01733 | SCR_011991 | 2026-08-08 12:00:03 | 2 | ||||||||
|
GeneTack Resource Report Resource Website 1+ mentions |
GeneTack (RRID:SCR_011953) | GeneTack | data or information resource, production service resource, data analysis service, database, analysis service resource, service resource | Tools for frameshift prediction and a frameshift database. | genomic sequence, transcript sequence, sequence, metagenomic sequence, frameshift |
is listed by: OMICtools has parent organization: Georgia Institute of Technology; Georgia; USA |
OMICS_01540 | SCR_011953 | GeneTack: tools for frameshift prediction | 2026-08-08 12:00:03 | 1 | ||||||||
|
JiffyNet Resource Report Resource Website 1+ mentions |
JiffyNet (RRID:SCR_011954) | production service resource, software resource, data analysis service, software application, simulation software, analysis service resource, service resource | Web based instant protein network modeler for newly sequenced species. Web server designed to instantly construct genome scale protein networks using protein sequence data. Provides network visualization, analysis pages and solution for instant network modeling of newly sequenced species. | protein network, protein, network, genome, sequence, pathway annotation, network visualization, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Yonsei University; Seoul; South Korea |
National Research Foundation of Korea ; Next-Generation BioGreen 21 Program |
PMID:23685435 | Free, Freely available | OMICS_01548, biotools:jiffynet | https://bio.tools/jiffynet | SCR_011954 | 2026-08-08 11:59:38 | 1 | ||||||
|
ArrayMiner Resource Report Resource Website 1+ mentions |
ArrayMiner (RRID:SCR_011955) | ArrayMiner | software resource | A set of analysis tools using advanced algorithms to reveal the true structure of your gene expression data. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
OMICS_01570, biotools:arrayminer | https://bio.tools/arrayminer | SCR_011955 | 2026-08-08 11:59:55 | 2 | ||||||||
|
TagCleaner Resource Report Resource Website 50+ mentions |
TagCleaner (RRID:SCR_011846) | web application, standalone software, software resource, software application | A software tool which can automatically detect and efficiently remove tag sequences from genomic and metagenomic datasets. | tag sequence, standalone software, web application, microbiome, genomic, metagenomic, datasets |
is listed by: OMICtools is listed by: Human Microbiome Project has parent organization: SourceForge |
Available for download | OMICS_01094 | SCR_011846 | 2026-08-08 11:59:54 | 65 | |||||||||
|
INSDC Resource Report Resource Website 100+ mentions |
INSDC (RRID:SCR_011967) | INSDC | data or information resource, portal, community building portal | International collaboration of the International Nucleotide Sequence Databases (INSD), DDBJ, ENA, and GenBank, maintained for over 18 years. Individuals submitting data to the international sequence databases should be aware of INSDC policy. | nucleotide sequence, FASEB list |
is listed by: OMICtools is affiliated with: DDBJ Sequence Read Archive is related to: DNA DataBank of Japan (DDBJ) is related to: RefSeq is related to: NCBI BioProject is related to: DNA DataBank of Japan (DDBJ) is related to: GenBank is related to: European Nucleotide Archive (ENA) is related to: GenBank is related to: European Nucleotide Archive (ENA) is related to: RefSeq is related to: UniProt Proteomes |
OMICS_01653 | SCR_011967 | International Nucleotide Sequence Database Collaboration | 2026-08-08 11:59:55 | 240 | ||||||||
|
miRPlant Resource Report Resource Website 10+ mentions |
miRPlant (RRID:SCR_012105) | software resource | A user-friendly plant miRNA prediction tool. | applet, unix/linux, mac os x, windows, java, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:25117656 | GNU General Public License | OMICS_05325, biotools:mirplant | https://bio.tools/mirplant | SCR_012105 | 2026-08-08 11:59:40 | 14 | |||||||
|
PyPedal Resource Report Resource Website 1+ mentions |
PyPedal (RRID:SCR_012104) | software resource | A pedigree analysis software package that provides tools for error checking, mathematical analysis, report generation, pedigree simulation, and data visualization. | standalone software |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_05311 | SCR_012104 | 2026-08-08 12:00:07 | 3 |
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