Tools   Select Another Resource Report Type

http://osprey.ucalgary.ca/

Oligonucleotide design software that calculates optimal oligonucleotides for a range of tasks: sequence assembly, differential expression, and microarrays (cDNA and spotted oligos)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Osprey (RRID:SCR_003627) Copy   

•   Source: SciCrunch Registry

http://srna-tools.cmp.uea.ac.uk/

Software tools for the analysis of high-throughput small RNA data.

Proper citation: UEA sRNA toolkit (RRID:SCR_003620) Copy   

•   Source: SciCrunch Registry

http://khavarilab.stanford.edu/resources.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 6, 2023. An intersection-based pathogen detection workflow that utilizes a user-provided custom reference genome set for identification of nonhuman sequences in deep sequencing datasets. This is a package recommended for advanced users only.

Proper citation: RINS (RRID:SCR_003652) Copy   

•   Source: SciCrunch Registry

http://jexpress.bioinfo.no/site/

Gene expression analysis software using Java.

Proper citation: J-Express (RRID:SCR_003609) Copy   

•   Source: SciCrunch Registry

https://github.com/armintoepfer/QuasiRecomb/releases

A jumping hidden Markov model that describes the generation of the viral quasispecies and a method to infer its parameters by analysing next generation sequencing data.

Proper citation: QuasiRecomb (RRID:SCR_008812) Copy   

•   Source: SciCrunch Registry

http://cran.r-project.org/web/packages/isva/

An algorithm for feature selection in the presence of potential confounding factors.

Proper citation: isva (RRID:SCR_008772) Copy   

•   Source: SciCrunch Registry

http://cran.r-project.org/web/packages/svd/

Interfaces to various state-of-art SVD and eigensolvers.

Proper citation: svd (RRID:SCR_008805) Copy   

•   Source: SciCrunch Registry

https://genome.unc.edu/xpn/

Merging Two Gene Expression Studies via Cross Platform Normalization.

Proper citation: XPN (RRID:SCR_008845) Copy   

•   Source: SciCrunch Registry

http://tvap.genome.wustl.edu/tools/music/

A set of tools aimed at determining the significance of somatic mutations discovered within a given cohort of cancer samples, incorporating the cohort''s alignment data, variant lists and any relevant clinical data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: MuSiC (RRID:SCR_008792) Copy   

•   Source: SciCrunch Registry

http://roadmapepigenomics.org/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 11, 2022. Project for human epigenomic data from experimental pipelines built around next-generation sequencing technologies to map DNA methylation, histone modifications, chromatin accessibility and small RNA transcripts in stem cells and primary ex vivo tissues selected to represent normal counterparts of tissues and organ systems frequently involved in human disease. Consortium expects to deliver collection of normal epigenomes that will provide framework or reference for comparison and integration within broad array of future studies. Consortium is also committed to development, standardization and dissemination of protocols, reagents and analytical tools to enable research community to utilize, integrate and expand upon this body of data.

Proper citation: Roadmap Epigenomics Project (RRID:SCR_008924) Copy   

•   Source: SciCrunch Registry

http://www.gzip.org/

A compression utility designed to be a replacement for compress.

Proper citation: Gzip (RRID:SCR_009291) Copy   

•   Source: SciCrunch Registry

http://bioinfo.au.tsinghua.edu.cn/software/seqsaw/

A package for mapping of spliced reads and unbiased detection of novel splice junctions from RNA-seq data.

Proper citation: SeqSaw (RRID:SCR_009185) Copy   

•   Source: SciCrunch Registry

http://www.medinfopoli.polimi.it/GAAS/

An integrated software framework for efficient management, analysis and visualization of large amounts of gene expression data across replicated experiments., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: GAAS (RRID:SCR_008967) Copy   

•   Source: SciCrunch Registry

http://metagenomics.atc.tcs.com/compression/DELIMINATE/

A practical implementation of a novel compression approach that can rapidly compress FASTA files containing genomic sequence data in a loss-less fashion.

Proper citation: DELIMINATE (RRID:SCR_008956) Copy   

•   Source: SciCrunch Registry

https://gmod.org/wiki/CMap.1

Web-based tool that allows users to view comparisons of genetic and physical maps. The package also includes tools for curating map data. (entry from Genetic Analysis Software)

Proper citation: CMAP (RRID:SCR_009034) Copy   

•   Source: SciCrunch Registry

http://www.ics.uci.edu/~dnazip/

DNA sequence compression using a reference genome.

Proper citation: DNAzip (RRID:SCR_009032) Copy   

•   Source: SciCrunch Registry

http://cliiq.sourceforge.net/Home

An algorithm to simultaneously identify and quantify expressed isoforms based on RNA-Seq data from multiple sample(s) in a population.

Proper citation: CLIIQ (RRID:SCR_009972) Copy   

•   Source: SciCrunch Registry

http://kks.inf.kcl.ac.uk/MSbind.html

Software tool that calculates features of meta-stable RNA secondary structure target sites.

Proper citation: MSbind (RRID:SCR_009910) Copy   

•   Source: SciCrunch Registry

http://hood.systemsbiology.net/rnaseqr.php

A streamlined and accurate RNA-seq sequence analysis program.

Proper citation: RNASEQR (RRID:SCR_009871) Copy   

•   Source: SciCrunch Registry

http://www.ufrgs.br/RNAi/isomiRID/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on 4/1/14. Software providing a framework to find isomiRNAs, templated and non-templated modifications in microRNAs.

Proper citation: isomiRID (RRID:SCR_009809) Copy   

•   Source: SciCrunch Registry