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    29 repositories

    • ATACseeker

      Public
      ATACseq tools for Bioconductor
      bioconductoratac-seq
      R
      •7•7•0•0•Updated Apr 14, 2018Apr 14, 2018

    • atacseeker_app

      Public
      Illumina BaseSpace ATACseq pipeline.
      dockergenomicsatac-seqbasespace
      HTML
      •0•3•6•0•Updated Oct 24, 2017Oct 24, 2017

    • arkas

      Public
      This is the kallisto package
      R
      •0•0•1•1•Updated May 25, 2017May 25, 2017

    • Arkas-RNASeq

      Public
      Source Code related to Arkas BaseSpace on Illumina BaseSpace
      HTML
      •0•0•0•0•Updated Apr 11, 2017Apr 11, 2017

    • arkasData

      Public
      staging area for building arkasData
      R
      •0•0•1•0•Updated Aug 25, 2016Aug 25, 2016

    • TxDbLite

      Public
      This is TxDbLite with respect arkas arcolombo branch (staging area)
      R
      •0•0•2•0•Updated Aug 21, 2016Aug 21, 2016

    • WGBS

      Public
      Packages for the WGBS Pipeline, localized and basespace nativeApp
      Shell
      •2•2•0•0•Updated Jan 21, 2016Jan 21, 2016

    • biscuit

      Public
      a little tool for bisulfite data
      C
      •26•0•0•0•Updated Jan 6, 2016Jan 6, 2016

    • ramsinghlab.github.io

      Public
      The lab website prototype
      HTML
      •
      MIT License
      •17k•0•0•0•Updated Jan 5, 2016Jan 5, 2016

    • USCBigWigGenerator

      Public
      BaseSpace App for USC BigWig Generator.
      Shell
      •1•0•0•0•Updated Nov 11, 2015Nov 11, 2015

    • ozymandias

      Public
      Look on my works, ye Mighty, and despair... just kidding, it's a slightly better meth lab
      R
      •
      Other
      •1•2•0•0•Updated Nov 5, 2015Nov 5, 2015

    • nanocorr

      Public
      Error correction for Oxford Nanopore data
      Python
      •
      GNU Lesser General Public License v3.0
      •9•0•0•0•Updated Aug 24, 2015Aug 24, 2015

    • USC-BedGraph-Converter-License

      Public
      This repo holds the end user license agreement for Illumina's Basespace platform that hosts USC BedGraph Converter
      1•0•0•0•Updated Jul 29, 2015Jul 29, 2015

    • EnrichmentBrowser

      Public
      This is a read-only mirror of the Bioconductor SVN repository. Bug Reports: https://support.bioconductor.org/p/new/post/?tag_val=EnrichmentBrowser. Package Home…
      R
      •0•0•0•0•Updated Jul 15, 2015Jul 15, 2015

    • SummarizedExperiment

      Public
      This is a read-only mirror of the Bioconductor SVN repository. Bug Reports: https://support.bioconductor.org/p/new/post/?tag_val=SummarizedExperiment. Package H…
      R
      •5•0•0•0•Updated Jun 30, 2015Jun 30, 2015

    • GenomicRanges

      Public
      This is a read-only mirror of the Bioconductor SVN repository. Bug Reports: https://support.bioconductor.org/p/new/post/?tag_val=GenomicRanges. Package Homepage…
      R
      •4•0•0•0•Updated Jun 29, 2015Jun 29, 2015

    • PileOMeth

      Public
      A (mostly) universal methylation extractor for BS-seq experiments.
      C
      •46•0•0•0•Updated Jun 24, 2015Jun 24, 2015

    • curriculum

      Public
      Recommended background for new lab members.
      1•2•0•0•Updated Jun 8, 2015Jun 8, 2015

    • motifBreakR

      Public
      A Package For Predicting The Disruptiveness Of Single Nucleotide Polymorphisms On Transcription Factor Binding Sites.
      R
      •14•0•0•0•Updated May 6, 2015May 6, 2015

    • VarDict

      Public
      VarDict
      Perl
      •
      MIT License
      •65•0•0•0•Updated May 1, 2015May 1, 2015

    • rasqual

      Public
      Robust Allele Specific Quantification and quality controL
      C
      •20•0•0•0•Updated Apr 23, 2015Apr 23, 2015

    • basespace-python-sdk

      Public
      BaseSpace Python SDK
      Python
      •
      Apache License 2.0
      •30•0•0•0•Updated Feb 23, 2015Feb 23, 2015

    • derfinder

      Public
      Fast differential expression analysis of RNA-seq data at base-pair resolution
      R
      •15•0•0•0•Updated Feb 13, 2015Feb 13, 2015

    • Bisulfighter

      Public
      a pipeline for accurate detection of methylated cytosine and differentially methylated regions
      C++
      •6•0•0•0•Updated Dec 24, 2014Dec 24, 2014

    • crystal

      Public
      find clusters and model correlated data from DNA methylation and other genomic sources.
      Python
      •
      MIT License
      •2•0•0•0•Updated Nov 14, 2014Nov 14, 2014

    • bwa-meth

      Public
      align BS-Seq reads and extract methylation without intermediate temp files
      PostScript
      •
      MIT License
      •57•0•0•0•Updated Oct 27, 2014Oct 27, 2014

    • docker-rstudio-server

      Public
      Docker container that runs rstudio server
      ApacheConf
      •8•0•0•0•Updated Oct 27, 2014Oct 27, 2014

    • BCPeakR

      Public
      Xing et al's BayesianChangePoint peak caller. Currently requires patching to install as an R package.
      C++
      •1•0•0•0•Updated Aug 16, 2013Aug 16, 2013

    • basespace-r-sdk

      Public
      R
      •1•0•0•0•Updated Mar 15, 2013Mar 15, 2013