Man pages for HowardChao/RNA-seq_pipeline

BallgownPreprocessRun ballgown analysis
CheckBallgownObjectCheck ballgown object
CheckDirAllCheck sample gene and binary directory
CheckGffcompareCheck Gffcompare Check whether Gffcompare is installed on the...
CheckHisat2Check 'hisat2' Check whether 'hisat2' is installed on the...
CheckInputDirFiles#' Choose the location where 'gene_data' and 'RNAseq_bin'...
CheckPrefixPathChecking the absolute path
CheckSamtoolsCheck Samtools Check whether Samtools is installed on the...
CheckStringTieCheck s'tringtie' Check whether 'stringtie' is installed on...
CheckToolAllCheck whether programs are installed
CopyInputDirCopy input files directory
CreateHisat2IndexCreating Hisat2 index Creat Hisat2 index for further use
DEDESeq2PlotDEG analysis with DESeq2
DEGCorrelationPlotPlot correlation plo
DEGedgeRPlotDEG analysis with edgeR
DEGFrequencyPlotFrequency plot
DEGMAPlotDEGMAPlot
DEGPCAPlotDEGPCAPlot
DEGTranscriptRelatedPlotDEGTranscriptRelatedPlot
DEGVolcanoPlotDEG volcanplot
ExportPathAdd '~/RNAseq_bin/ to R environment "PATH"
get_osget operating system
GffcompareRefSampleExamine how the transcripts compare with the reference...
Hisat2AlignmentDefaulthisat2 alignment default
Hisat2ReportAssembleReport Hisat2 assemble rate
InstallAllInstall Hisat2, StringTie, Gffcompare, Samtools
InstallGffcompareBinaryInstall Gffcompare binary
InstallHisat2BianryInstall Hisat2 binay
InstallSamtoolsBinaryInstall Samtools binary
InstallStringTieBinaryInstall stringtie binary
InstallToolsCMDinstall all the tools and create a binary library.
LoadBallgownObjectload ballgown object
MkdirAllCreate sample gene and binary directory
MkdirGeneDirCreate sample gene directory
MkdirRNAseq_binMake RNAseq_bin/ directory
MkdirRNAseq_resultsMake RNAseq_results/ directory
PreDECountTableconverting stringtie ballogwn preprocessed data to count...
ProgressGenesFilescheck 'gene_data' and subdirectory files exit
QualityControlQuality control
RNAseqPipelinerna seq pipline
RNAseqPipelineCMDCreate 'RNAseqPipline.R' that user can
RNASeqWorkFlowParam-classRNASeq An S4 class for storing RNA-Seq workflow parameters of...
SamtoolsToBamuse 'samtools' to sort and convert the SAM files to BAM
StringTieAssemblestringtie assemble and quantify expressed genes and...
StringTieMergeTransstringtie merge transcripts from all samples
StringTieToBallgownstringtie estimate transcript abundances and create table...
HowardChao/RNA-seq_pipeline documentation built on July 12, 2018, 10:57 a.m.