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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://sourceforge.net/projects/chipotle-perl/
A peak-finding algorithm used to analyze ChIP-chip microarray data.
Proper citation: ChIPOTle Peak Finder (RRID:SCR_012991) Copy
http://www.bioconductor.org/packages/2.12/bioc/html/BiSeq.html
Software package that provides useful classes and functions to handle and analyze targeted bisulfite sequencing (BS) data such as reduced-representation bisulfite sequencing (RRBS) data.
Proper citation: BiSeq (RRID:SCR_012993) 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
http://sourceforge.net/projects/ngspeanalysis/
A pipeline using open-source tools which can implement a set of pair ended Next-generation sequencing analysis, include short reads alignment, high-quality variation genotype calling and variants annotation.
Proper citation: NGSpeAnalysis (RRID:SCR_013040) Copy
http://www.bioconductor.org/packages/2.12/bioc/html/MEDME.html
Software that allows the prediction of absolute and relative methylation levels based on measures obtained by MeDIP-microarray experiments.
Proper citation: MEDME (RRID:SCR_012995) 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/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/rnacompass/
A web-based GUI distributed computational pipeline, provides all-in-one functionality including human transcriptome quantification and the typical endogenous RNA-Sequencing analysis along with the investigation of exogenous sequences.
Proper citation: RNA CoMPASS (RRID:SCR_013058) Copy
http://compbio.bccrc.ca/software/conan-snv/
Software for a probabilistic framework for the discovery of single nucleotide variants in WGSS data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: CoNAn-SNV (RRID:SCR_013059) Copy
http://sourceforge.net/projects/snptools/
A suite of software tools that enables integrative SNP analysis in next generation sequencing data with large cohorts.
Proper citation: SNPTools (RRID:SCR_013052) Copy
http://sourceforge.net/projects/swiftng/
An open source package for primary data analysis on next-gen sequence data from images to basecalls. Currently Swift is targeted toward Solexa/Illumina sequencing, but is designed to be platform agnostic.
Proper citation: Swift (RRID:SCR_013018) 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://www.bioconductor.org/packages/2.12/bioc/html/Rolexa.html
Software that provides probabilistic base calling, quality checks and diagnostic plots for Solexa sequencing data.
Proper citation: Rolexa (RRID:SCR_013017) Copy
http://www.ra.cs.uni-tuebingen.de/software/InCroMAP/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 5,2023. Integrated analysis of cross-platform microarray and pathway data.
Proper citation: InCroMAP (RRID:SCR_012964) 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://sourceforge.net/projects/mireap/
A software tool which can be used to identify both known and novel microRNAs from small RNA libraries deeply sequenced by Solexa/454/Solid technology.
Proper citation: MIREAP (RRID:SCR_013025) Copy
http://www.lgm.upmc.fr/mirena/index.html
A software tool to find microRNAs with high accuracy and no learning at genome scale and from deep sequencing data.
Proper citation: MIReNA (RRID:SCR_013024) Copy
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