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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://soap.genomics.org.cn/soapsnp.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software providng a method based on Bayes? theorem (the reverse probability model) to call consensus genotype by carefully considering the data quality, alignment, and recurring experimental errors., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: SOAPsnp (RRID:SCR_010602) Copy   

•   Source: SciCrunch Registry
  

http://www.isical.ac.in/~bioinfo_miu/targetminer20.htm

A robust tool for microRNA target prediction with systematic identification of negative examples.

Proper citation: TargetMiner (RRID:SCR_010573) Copy   

•   Source: SciCrunch Registry
  

http://sourceforge.net/p/mira-assembler/wiki/Home/

Sequence assembler and mapper for whole genome shotgun and EST/RNASeq sequencing data.

Proper citation: MIRA (RRID:SCR_010731) Copy   

•   Source: SciCrunch Registry
  

http://www.comp.nus.edu.sg/~bioinfo/peasm/PE_manual.htm

Software providing a method that eschews the traditional graph-based approach in favor of a simple 3'' extension approach that has potential to be massively parallelized.

Proper citation: PE-Assembler (RRID:SCR_010732) Copy   

•   Source: SciCrunch Registry
  

http://jr-assembler.iis.sinica.edu.tw/

An assembler for the de novo assembly of large genomes using short sequence reads via jumping extension and read remapping.

Proper citation: JR-Assembler (RRID:SCR_010681) Copy   

•   Source: SciCrunch Registry
  

http://cseweb.ucsd.edu/~ppevzner/software.html#EULER-short

Assembly package that contains a suite of software programs for correcting errors in short reads and assembling them. The assembler may take as input classical Sanger reads, 454 sequences, and Illumina reads.

Proper citation: EULER-SR (RRID:SCR_010485) Copy   

•   Source: SciCrunch Registry
  

http://sourceforge.net/projects/openadam/

A web-based database management system for the large amount of genotype data generated from the Affymetrix GeneChip Mapping Array and Genome-Wide Human SNP Array platforms.

Proper citation: openADAM (RRID:SCR_002018) Copy   

•   Source: SciCrunch Registry
  

http://www.bioconductor.org/packages/release/bioc/html/flowTrans.html

Software for profile maximum likelihood estimation of parameters for flow cytometry data transformations.

Proper citation: flowTrans (RRID:SCR_002093) Copy   

•   Source: SciCrunch Registry
  

http://www.broadinstitute.org/mpg/snap/

A computer program and web-based service for the rapid retrieval of linkage disequilibrium proxy single nucleotide polymorphism (SNP) results given input of one or more query SNPs and based on empirical observations from the International HapMap Project and the 1000 Genomes Project. A series of filters allow users to optionally retrieve results that are limited to specific combinations of genotyping platforms, above specified pairwise r2 thresholds, or up to a maximum distance between query and proxy SNPs. SNAP can also generate linkage disequilibrium plots

Proper citation: SNAP - SNP Annotation and Proxy Search (RRID:SCR_002127) Copy   

•   Source: SciCrunch Registry
  

https://github.com/nicolazzie/AffyPipe

An open-source software pipeline for Affymetrix Axiom genotyping workflow.

Proper citation: AffyPipe (RRID:SCR_002032) Copy   

•   Source: SciCrunch Registry
  

https://github.com/adrlar/CanSNPer

Software that is a hierarchical genotype classifier of clonal pathogens.

Proper citation: CanSNPer (RRID:SCR_001980) Copy   

•   Source: SciCrunch Registry
  

http://sourceforge.net/projects/dmetanalyzer/

Software tool for the automatic association analysis among the variation of the patient genomes and the clinical conditions of patients, i.e. the different response to drugs. The system allows: (i) to automatize the workflow of analysis of DMET (drug metabolism enzymes and transporters)-SNP (Single Nucleotide Polymorphism) data avoiding the use of multiple tools; (ii) the automatic annotation of DMET-SNP data and the search in existing databases of SNPs (e.g. dbSNP), (iii) the association of SNP with pathway through the search in PharmaKGB, a major knowledge base for pharmacogenomic studies. It has a simple graphical user interface that allows users (doctors/biologists) to upload and analyze DMET files produced by Affymetrix DMET-Console in an interactive way.

Proper citation: DMET-Analyzer (RRID:SCR_002030) Copy   

•   Source: SciCrunch Registry
  

http://snver.sourceforge.net/

Statistical software tool for calling common and rare variants in analysis of pool or individual next-generation sequencing data. This software is optimized for analysis of whole-exome sequencing data and whole-genome sequencing data.

Proper citation: SNVer (RRID:SCR_002061) Copy   

•   Source: SciCrunch Registry
  

http://cmb.gis.a-star.edu.sg/ChIPSeq/paperChIPSeq.htm

THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 12, 2017. A software tool to find peaks from ChIPSeq data generated from the Solexa/Illumina platform., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: ChIPSeq Peak Finder (RRID:SCR_002081) Copy   

•   Source: SciCrunch Registry
  

https://github.com/homopolymer/PyroTools/

A software program to call short indels and SNPs for Ion Torrent and 454 data.

Proper citation: PyroHMMvar (RRID:SCR_002073) Copy   

•   Source: SciCrunch Registry
  

http://www.bioconductor.org/packages/release/bioc/html/flowMap.html

Software package that quantifies the similarity of cell populations across multiple flow cytometry samples using a nonparametric multivariate statistical test. The algorithm allows the users to specify a reference sample for comparison or to construct a reference sample from the available data. The output of the algorithm is a set of text files where the cell population labels are replaced by a metaset of population labels, generated from the matching process.

Proper citation: flowMap (RRID:SCR_002269) Copy   

•   Source: SciCrunch Registry
  

http://cakesomatic.sourceforge.net/

A bioinformatics software pipeline that integrates four publicly available somatic variant-calling algorithms to identify single nucleotide variants with higher sensitivity and accuracy than any one algorithm alone.

Proper citation: Cake (RRID:SCR_002133) Copy   

•   Source: SciCrunch Registry