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http://bioconductor.org/packages/release/bioc/html/DEXSeq.html
Software package focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results.
Proper citation: DEXSeq (RRID:SCR_012823) Copy
http://bioconductor.org/packages/release/bioc/html/DNaseR.html
A R package that enables the identification of protein binding footprints in DNase I hypersensitive sites sequencing (DNase-seq) data.
Proper citation: DNaseR (RRID:SCR_012819) Copy
http://www.bioconductor.org/packages/2.12/bioc/html/charm.html
Software package that implements analysis tools for DNA methylation data generated using Nimblegen microarrays and the McrBC protocol.
Proper citation: charm (RRID:SCR_012992) Copy
http://trinityrnaseq.sourceforge.net/
Software for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data.
Proper citation: Trinity (RRID:SCR_013048) Copy
https://github.com/brentp/methylcode
A single program that takes of bisulfite-treated reads and outputs per-base methylation data.
Proper citation: MethylCoder (RRID:SCR_012997) Copy
http://sourceforge.net/projects/genecounter/
A computational pipeline for analyzing RNA-Sequencing (RNA-Seq) data for differential gene expression of eukaryotes, prokaryotes, as well as organisms with no available genome reference sequence.
Proper citation: GENE-counter (RRID:SCR_013056) Copy
http://sourceforge.net/projects/cloudaligner/
A map/reduce based application for mapping short reads generated by the next-generation sequencing machines.
Proper citation: CloudAligner (RRID:SCR_012962) Copy
http://sourceforge.net/projects/seqminer/
Software for a genome wide mapping data interpretation platform for NGS (ChIPSeq).
Proper citation: seqMINER (RRID:SCR_013020) Copy
http://bioconductor.org/packages/2.12/bioc/html/cn.mops.html
A data processing pipeline for copy number variations and aberrations (CNVs and CNAs) from next generation sequencing (NGS) data.
Proper citation: cn.mops (RRID:SCR_013036) Copy
http://sammate.sourceforge.net/
An open source GUI software suite to process RNA-Seq data. It is composed of two modules: assemblySAM and SAMMate.
Proper citation: SAMMate (RRID:SCR_013037) Copy
http://sourceforge.net/projects/flexbar/
Flexible barcode and adapter removal for sequencing platforms.
Proper citation: Flexbar (RRID:SCR_013001) Copy
http://sourceforge.net/projects/locas/
A software to assemble short reads of next generation sequencing technologies at low coverage.
Proper citation: LOCAS (RRID:SCR_013064) Copy
http://derisilab.ucsf.edu/software/price/index.html
Software for a de novo genome assembler implemented in C++.
Proper citation: PRICE (RRID:SCR_013063) Copy
https://confluence.crbs.ucsd.edu/display/NIF/OntoQuestMain
An ontology management module to perform ontology-based search over data sources. This management system permits a user to store, search and navigate any number of OWL-structured ontologies. Ontoquest may also be accessed through a variety of web services via the Neuroscience Information Framework.
Proper citation: OntoQuest (RRID:SCR_013281) Copy
http://rdxplorer.sourceforge.net/
A computational tool for copy number variants (CNV) detection in whole human genome sequence data using read depth (RD) coverage.
Proper citation: RDXplorer (RRID:SCR_013290) Copy
http://alumni.cs.ucr.edu/~liw/cem.html
An algorithm to assemble transcripts and estimate their expression levels from RNA-Seq reads.
Proper citation: CEM (RRID:SCR_013241) Copy
Software for a normalization scheme that corrects nucleotide composition bias, mappability variations and differential local DNA structural effects in deep sequencing data.
Proper citation: BEADS (RRID:SCR_013229) Copy
http://www.bcgsc.ca/platform/bioinfo/software/trans-abyss
A software pipeline for analyzing ABySS-assembled contigs from shotgun transcriptome data.
Proper citation: Trans-ABySS (RRID:SCR_013322) Copy
http://code.google.com/p/chimerascan/
Software package that detects gene fusions in paired-end RNA sequencing (RNA-Seq) datasets. Used for detection of chimeric transcripts in high-throughput sequencing data.
Proper citation: chimerascan (RRID:SCR_013298) Copy
http://bioinfo.au.tsinghua.edu.cn/software/pcs/
A stand-alone package to identify and analyze conserved k-mers in pairwise alignment. This program shows high performance for identifying miRNA seed binding sites in 3''-UTRs.
Proper citation: Pairwise Conservation Scores - An Algorithm to Identify Conserved K-mers (RRID:SCR_013409) Copy
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