Man pages for robertdouglasmorrison/DuffyNGS
Duffy Lab NGS Analysis Pipeline for RNA-seq, ChIP-seq, and DNA-seq

alignToWigAdd BAM Alignments to Wiggle Track data objects.
bamAlign-classClass '"bamAlign"'
BAM_FilesUtilities for Manipulating BAM Files.
bamRangebamRange(bamReader, coordinates,complex=FALSE)
bamRange-classClass '"bamRange"'
bamReader-classClass '"bamReader"'
bamReadStatsQuality Control Statistics of Raw Sequencing Reads
bowtie2ParSet or Query Bowtie2 Parameters
buildAllAnnotationFilesCreate All Annotation-dependant Files for a DuffyNGS Target...
buildBowtie2BuildCommandLineBuild a Bowtie2-build Command Line
buildBowtie2CommandLineBuild a Bowtie2 Command Line
buildRiboClearingFilesBuild Ribo Clearing Index and Map
buildSpliceJunctionFilesBuild Splice Junction Index and Maps
callBowtie2Call the Bowtie Alignment Tool
checkBowtie2VersionCheck the Bowtie2 executable
compressSpliceMapsCompress Splice Maps
DuffyNGSDuffy Lab Next Gen Sequencing "NGS" package Overview
DuffyNGS_AnnotationAnnotation File of Sample-Specific Settings
DuffyNGS_OptionsOptions File of Processing Settings
fastqToBAMConvert FASTQ file(s) into a BAM file, by calling Bowtie2.
getBowtie2AlignMetricsGet Bowtie2 Alignment Metrics
MPU.callBasesMPILEUP Base Call Utility Functions
pipe.AlignmentAlignment Stage of DuffyNGS Pipeline workflow.
pipe.AlignStatsGenerate Alignment Success Stats Images.
pipe.AlignToWigTurn BAM Alignments into Wiggle Tracks.
pipe.BAMpileupExtract Pileup Details from BAM file.
pipe.ChIPpeaksTurn Alignments into Wiggle Tracks and ChIP Peaks.
pipe.DEtoolsPipes for Group-wise Differential Expression Tools like...
pipe.DiffExpressionTurn Pairs of Transcriptomes into Differential Gene...
pipe.ExtractPipelineSummaryDetailsSummarize Alignment Metrics
pipe.GenomicAlignGenomic Alignment Pileline Step for NGS Data
pipe.MetaResultsDispatch Multiple Differential Expression Tools and then...
pipe.PlotGenePlot Gene Expression as Wiggle Track Pileups
pipe.PlotSNPPlot Single Nucleotide Polymorphism (SNP) Sites at Nucleotide...
pipe.PostAlignTasksPost-Alignment Tasks
pipe.PreAlignTasksPre-Alignment Tasks
pipe.QuickQCQuick Quality Control 'A to Z' Alignment & Transcriptome.
pipe.RiboClearRibo Clearing Pileline Step for NGS Data
pipe.RIPpeaksTurn RIP-seq Data Alignments into Wiggle Tracks and RIP...
pipe.RIPpeaksToAltGeneMapCombine RIP Peaks into an Alternate Gene Map
pipe.RNAseqDuffyNGS Pipelines
pipe.SpliceAlignSplice Alignment Pileline Step for NGS Data
pipe.TranscriptClusterHierarchical Clustering of Transcriptomes.
pipe.TranscriptomeTurn Alignments into Wiggle Tracks and Transcriptomes.
pipe.TranscriptToHTMLTurn transcriptome into HTML table with gene plot hyperlinks.
pipe.VariantCallsFind Variant Alleles (aka SNPs) in Alignment Data
pipe.VariantSummarySummarize all Chromosomes of SNP Calls into one File
robertdouglasmorrison/DuffyNGS documentation built on Jan. 11, 2019, 5:37 p.m.