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arkas

This is the kallisto package

arkas-rnaseq

Source Code related to Arkas BaseSpace on Illumina BaseSpace

arkasdata

staging area for building arkasData

atacseeker

ATACseq tools for Bioconductor

atacseeker_app

Illumina BaseSpace ATACseq pipeline.

basespace-python-sdk

BaseSpace Python SDK

basespace-r-sdk

bcpeakr

Xing et al's BayesianChangePoint peak caller. Currently requires patching to install as an R package.

biscuit

a little tool for bisulfite data

bisulfighter

a pipeline for accurate detection of methylated cytosine and differentially methylated regions

bwa-meth

align BS-Seq reads and extract methylation without intermediate temp files

crystal

find clusters and model correlated data from DNA methylation and other genomic sources.

curriculum

Recommended background for new lab members.

derfinder

Fast differential expression analysis of RNA-seq data at base-pair resolution

docker-rstudio-server

Docker container that runs rstudio server

enrichmentbrowser

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

genomicranges

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

motifbreakr

A Package For Predicting The Disruptiveness Of Single Nucleotide Polymorphisms On Transcription Factor Binding Sites.

nanocorr

Error correction for Oxford Nanopore data

ozymandias

Look on my works, ye Mighty, and despair... just kidding, it's a slightly better meth lab

pileometh

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

ramsinghlab.github.io

The lab website prototype

rasqual

Robust Allele Specific Quantification and quality controL

summarizedexperiment

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

txdblite

This is TxDbLite with respect arkas arcolombo branch (staging area)

usc-bedgraph-converter-license

This repo holds the end user license agreement for Illumina's Basespace platform that hosts USC BedGraph Converter

uscbigwiggenerator

BaseSpace App for USC BigWig Generator.

vardict

VarDict

wgbs

Packages for the WGBS Pipeline, localized and basespace nativeApp