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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
Software tool that enables analysis of RNA-seq data with or without reference genome. Local transcriptome assembler for SNPs, indels and AS events.
Proper citation: KisSplice (RRID:SCR_011893) Copy
http://bioinformatics.childhealthresearch.org.au/software/fusionfinder/
A perl-based software package, which can be used to find fusion transcript candidates in RNA-Seq data.
Proper citation: FusionFinder (RRID:SCR_011894) Copy
http://uc-echo.sourceforge.net/
Error correction algorithm designed for short-reads from next-generation sequencing platforms such as Illumina''s Genome Analyzer II.
Proper citation: ECHO (RRID:SCR_011851) Copy
http://calpain.org/predict.rb?cls=substrate
Calpain cleavage prediction using multiple kernel learning.
Proper citation: CaMPDB (RRID:SCR_011976) Copy
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.
Proper citation: Guide (RRID:SCR_011903) Copy
http://www.unav.es/genetica/oncofuse.html
Software tool designed to predict the oncogenic potential of fusion genes found by Next-Generation Sequencing in cancer cells.
Proper citation: Oncofuse (RRID:SCR_011904) Copy
http://bioinformatics.mdanderson.org/main/PRADA:Overview
A pipeline to analyze paired end RNA-Seq data to generate gene expression values (RPKM) and gene-fusion candidates.
Proper citation: PRADA (RRID:SCR_011906) Copy
https://mcdonaldlab.biology.gatech.edu/r-sap/
An automated bioinformatics pipeline that analyzes and quantitates high-throughput RNA-Seq datasets.
Proper citation: R-SAP (RRID:SCR_011907) Copy
http://mapman.gabipd.org/web/guest/robin
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.
Proper citation: RobiNA (RRID:SCR_011908) Copy
https://code.google.com/p/rseqflow/
An RNA-Seq analysis pipeline which offers an express implementation of analysis steps for RNA sequencing datasets.
Proper citation: RseqFlow (RRID:SCR_011909) Copy
http://1001genomes.org/software/shore.html
A mapping and analysis pipeline for short read data produced on the Illumina platform.
Proper citation: SHORE (RRID:SCR_011863) Copy
A question and answer site for professional and enthusiast programmers.
Proper citation: Stack Overflow (RRID:SCR_011984) Copy
http://wwwdev.ebi.ac.uk/fg/hts_mappers/
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.
Proper citation: HTS Mappers (RRID:SCR_011991) Copy
http://topaz.gatech.edu/GeneTack/cgi/print_page.cgi?fn=db_home.html&title=Frameshift%20Database
Tools for frameshift prediction and a frameshift database.
Proper citation: GeneTack (RRID:SCR_011953) Copy
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.
Proper citation: JiffyNet (RRID:SCR_011954) Copy
http://www.optimaldesign.com/ArrayMiner/ArrayMiner.htm
A set of analysis tools using advanced algorithms to reveal the true structure of your gene expression data.
Proper citation: ArrayMiner (RRID:SCR_011955) Copy
http://tagcleaner.sourceforge.net/
A software tool which can automatically detect and efficiently remove tag sequences from genomic and metagenomic datasets.
Proper citation: TagCleaner (RRID:SCR_011846) Copy
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.
Proper citation: INSDC (RRID:SCR_011967) Copy
http://sourceforge.net/projects/mirplant/
A user-friendly plant miRNA prediction tool.
Proper citation: miRPlant (RRID:SCR_012105) Copy
http://pypedal.sourceforge.net/
A pedigree analysis software package that provides tools for error checking, mathematical analysis, report generation, pedigree simulation, and data visualization.
Proper citation: PyPedal (RRID:SCR_012104) Copy
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