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http://sourceforge.net/projects/samcomp/

A simple arithmetic coding based compressor for the SAM and BAM (DNA sequence alignment) file format.

Proper citation: sam comp (RRID:SCR_013179) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/heuraa/

Software for accurate and fast detection of genetic variations with a novel heuristic amplicon aligner program for next generation sequencing.

Proper citation: HeurAA (RRID:SCR_013212) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/bisreadmapper/

Fast and lightweight package for mapping bisulfite converted DNA sequencing reads from the Illumina platform.

Proper citation: bisReadMapper (RRID:SCR_013171) Copy   

•   Source: SciCrunch Registry

http://bioinfo.eie.polyu.edu.hk/mGoaSvmServer/mGOASVM.html

Data analysis service for the prediction of multi-label protein subcellular localization based on gene ontology and support vector machines. Web services are also available.

Proper citation: mGOASVM (RRID:SCR_013098) Copy   

•   Source: SciCrunch Registry

http://www-rcf.usc.edu/~fsun/Programs/CEDER/CEDERmain.html

R package intended to implement a program for detecting differentially expressed genes (DEG) using RNA-Seq by combining significance of exons within a gene.

Proper citation: CEDER (RRID:SCR_013255) Copy   

•   Source: SciCrunch Registry

https://sites.google.com/site/quantisnp/

THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone.Software to detect rare or de novo copy number alterations in normal DNA samples. Please note that QuantiSNP is no longer under active development.

Proper citation: QuantiSNP (RRID:SCR_013091) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/celeragb/

Software developed at Celera Genomics as part of Celera''s sequencing and annotation of the human genome, and released as open source in 2006.

Proper citation: Celera Genome Browser (RRID:SCR_013093) Copy   

•   Source: SciCrunch Registry

http://www-rcf.usc.edu/~liangche/software.html

A software tool to analyze RNA-seq data to estimate gene and exon expression, identify differentially expressed genes, and differentially spliced exons., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: GPSeq (RRID:SCR_013250) Copy   

•   Source: SciCrunch Registry

http://bioinfo.ctb.pku.edu.cn/MAP/

This resource is out of service. Documented on February 23,2021. Software for de novo metagenomic assembly program for shotgun DNA reads., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: MAP (RRID:SCR_013216) Copy   

•   Source: SciCrunch Registry

http://www.netlab.uky.edu/p/bioinfo/DiffSplice

The Genome-Wide Detection of Differential Splicing Events with RNA-seq.

Proper citation: DiffSplice (RRID:SCR_013215) Copy   

•   Source: SciCrunch Registry

https://code.google.com/p/gencat/

Software designed as an open platform that allows users to incorporate as many datasets (concepts) as possible to annotate the input gene list, as long as these datasets are prepared in bigwig, BED, BAM/SAM formats.

Proper citation: genCAT (RRID:SCR_013220) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/socs/

Performs ungapped alignment of SOLiD (color space) sequencing reads against reference sequences.

Proper citation: SOCS (RRID:SCR_013223) Copy   

•   Source: SciCrunch Registry

http://genetics.bwh.harvard.edu/pph2/

Software tool which predicts possible impact of amino acid substitution on structure and function of human protein using straightforward physical and comparative considerations. PolyPhen-2 is new development of PolyPhen tool for annotating coding nonsynonymous SNPs.

Proper citation: PolyPhen: Polymorphism Phenotyping (RRID:SCR_013189) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages//2.10/bioc/html/aCGH.html

Software functions for reading aCGH data from image analysis output files and clone information files, creation of aCGH S3 objects for storing these data. Basic methods for accessing/replacing, subsetting, printing and plotting aCGH objects.

Proper citation: aCGH (RRID:SCR_013232) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/denovosolid/

Pipeline for small genome assembly using SOLiD sequencing technology.

Proper citation: DSP (RRID:SCR_013114) Copy   

•   Source: SciCrunch Registry

https://github.com/adaptivegenome/repeatseq

Software that determines genotypes for microsatellite repeats in high-throughput sequencing data.

Proper citation: RepeatSeq (RRID:SCR_013235) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/tuxe/

Software that manages the RNA-sequencing pipeline based on the TopHat suite of software automatically.

Proper citation: Tuxedo (RRID:SCR_013194) Copy   

•   Source: SciCrunch Registry

http://www.seqan.de/projects/microrazers/

A software tool optimized for mapping short RNAs onto a reference genome.

Proper citation: MicroRazerS (RRID:SCR_013316) Copy   

•   Source: SciCrunch Registry

http://archive.gersteinlab.org/proj/rnaseq/fusionseq/

A modular framework for finding gene fusions by analyzing Paired-End RNA-Sequencing data.

Proper citation: FusionSeq (RRID:SCR_013329) Copy   

•   Source: SciCrunch Registry

https://github.com/macs3-project/MACS

Software Python package for identifying transcript factor binding sites. Used to evaluate significance of enriched ChIP regions. Improves spatial resolution of binding sites through combining information of both sequencing tag position and orientation. Can be used for ChIP-Seq data alone, or with control sample with increase of specificity.

Proper citation: MACS (RRID:SCR_013291) Copy   

•   Source: SciCrunch Registry