Repositories list

• ATACseeker

  Public
  ATACseq tools for Bioconductor

  atac-seqbioconductor

  R

  •7•7•0•0•Updated Apr 14, 2018Apr 14, 2018

• atacseeker_app

  Public
  Illumina BaseSpace ATACseq pipeline.

  dockergenomicsatac-seq+ 1basespace

  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

  •24•0•0•0•Updated Jan 6, 2016Jan 6, 2016

• ramsinghlab.github.io

  Public
  The lab website prototype

  HTML

  •

  MIT License

  •16k•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 Homepage: http://bioconductor.org/packages/devel/bioc/html/EnrichmentBrowser

  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 Homepage: http://bioconductor.org/packages/devel/bioc/html/SummarizedExperiment

  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: http://bioconductor.org/packages/devel/bioc/html/GenomicRanges

  R

  •4•0•0•0•Updated Jun 29, 2015Jun 29, 2015

• PileOMeth

  Public
  A (mostly) universal methylation extractor for BS-seq experiments.

  C

  •45•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

  •12•0•0•0•Updated May 6, 2015May 6, 2015

• VarDict

  Public
  VarDict

  Perl

  •

  MIT License

  •62•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

  •54•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