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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/lofreq/
A fast and sensitive variant-caller for inferring single-nucleotide variants (SNVs) from high-throughput sequencing data.
Proper citation: LoFreq (RRID:SCR_013054) 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/tracetuner/
Software tool for base and quality calling of trace files from DNA sequencing instruments.
Proper citation: TraceTuner (RRID:SCR_013019) 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
http://www.eisenlab.org/eisen/?page_id=42
Software to graphically browse results of clustering and other analyses from Cluster.
Proper citation: TreeView (RRID:SCR_013503) Copy
http://tiger.dbs.nus.edu.sg/cnv-seq/
A method for detecting DNA copy number variation (CNV) using high-throughput sequencing., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: CNV-seq (RRID:SCR_013357) Copy
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