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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
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 | 2026-09-05 06:27:15 | 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 | 2026-09-05 06:27:15 | 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 | 2026-09-05 06:27:16 | 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 | 2026-09-05 06:27:15 | 3 | ||||||||
|
SeqPipe Resource Report Resource Website |
SeqPipe (RRID:SCR_011862) | SeqPipe | software resource | A command line-based pipeline framework for bioinformatics research. |
is listed by: OMICtools has parent organization: Google Code |
OMICS_01135 | SCR_011862 | 2026-09-05 06:27:14 | 0 | ||||||||||
|
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 | 2026-09-05 06:27:14 | 157 | ||||||||||
|
Stack Overflow Resource Report Resource Website 10+ mentions |
Stack Overflow (RRID:SCR_011984) | Stack Overflow | community building portal, data or information resource, portal | A question and answer site for professional and enthusiast programmers. | programmer | is listed by: OMICtools | Free | OMICS_01711 | SCR_011984 | 2026-09-05 06:27:17 | 23 | ||||||||
|
Bioinformaticsweb Resource Report Resource Website |
Bioinformaticsweb (RRID:SCR_011988) | BIW | data or information resource, portal, topical portal | Open Access Bioinformatics resource portal. | bioinformatics | is listed by: OMICtools | Free | OMICS_01729 | SCR_011988 | 2026-09-05 06:27:17 | 0 | ||||||||
|
HTS Mappers Resource Report Resource Website 1+ mentions |
HTS Mappers (RRID:SCR_011991) | HTS Mappers | data or information resource, data set, software repository, software resource | 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 | 2026-09-05 06:27:17 | 2 | ||||||||
|
Next Generation Sequencing WikiBook Resource Report Resource Website |
Next Generation Sequencing WikiBook (RRID:SCR_011993) | NGS WikiBook | book, data or information resource, narrative resource, wiki | The Need for an Up-To-Date Synthesis of Next Generation Sequencing Know-How. |
is listed by: OMICtools has parent organization: Wikibooks |
OMICS_01744 | SCR_011993 | The NGS WikiBook | 2026-09-05 06:27:17 | 0 | |||||||||
|
GeneTack Resource Report Resource Website 1+ mentions |
GeneTack (RRID:SCR_011953) | GeneTack | analysis service resource, data analysis service, data or information resource, database, production 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 | 2026-09-05 06:27:16 | 1 | ||||||||
|
JiffyNet Resource Report Resource Website 1+ mentions |
JiffyNet (RRID:SCR_011954) | analysis service resource, data analysis service, production service resource, service resource, simulation software, software application, software 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 | 2026-09-05 06:27:16 | 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 | 2026-09-05 06:27:17 | 2 | ||||||||
|
INSDC Resource Report Resource Website 100+ mentions |
INSDC (RRID:SCR_011967) | INSDC | community building portal, data or information resource, 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 | 2026-09-05 06:27:17 | 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 | 2026-09-05 06:27:20 | 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 | 2026-09-05 06:27:20 | 3 | ||||||||||
|
Simulate PCR Resource Report Resource Website 1+ mentions |
Simulate PCR (RRID:SCR_012106) | software resource | Software that can be run from the command line for high throughput applications which can calculate all products from large lists of primers and probes compared to a large sequence database such as nt. | standalone software, perl |
is listed by: OMICtools has parent organization: SourceForge |
PMID:25005023 | Free, Public | OMICS_05372 | SCR_012106 | 2026-09-05 06:27:20 | 2 | ||||||||
|
CONDEX Resource Report Resource Website |
CONDEX (RRID:SCR_012109) | software resource | Software that implements a HMM Model to detect copy number variants in exome sequence data. | standalone software, java |
is listed by: OMICtools has parent organization: Google Code |
GNU General Public License | OMICS_05442 | SCR_012109 | 2026-09-05 06:27:21 | 0 | |||||||||
|
SAT-Assembler Resource Report Resource Website 1+ mentions |
SAT-Assembler (RRID:SCR_012108) | software resource | A targeted gene assembly software program which aims to recover gene families of particular interest to biologists. | standalone software, python |
is listed by: OMICtools has parent organization: SourceForge |
PMID:25122209 | Creative Commons License | OMICS_05397 | SCR_012108 | 2026-09-05 06:27:20 | 3 | ||||||||
|
ProteoCloud Resource Report Resource Website |
ProteoCloud (RRID:SCR_012075) | software resource | A Java-based proteomics cloud computing pipeline system for peptide and protein identifications. |
is listed by: OMICtools has parent organization: Google Code |
PMID:23305951 | Apache License | OMICS_04549 | SCR_012075 | 2026-09-05 06:27:19 | 0 |
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