Man pages for HowardChao/RNA-seq_pipeline
| BallgownPreprocess | Run ballgown analysis |
| CheckBallgownObject | Check ballgown object |
| CheckDirAll | Check sample gene and binary directory |
| CheckGffcompare | Check Gffcompare Check whether Gffcompare is installed on the... |
| CheckHisat2 | Check 'hisat2' Check whether 'hisat2' is installed on the... |
| CheckInputDirFiles | #' Choose the location where 'gene_data' and 'RNAseq_bin'... |
| CheckPrefixPath | Checking the absolute path |
| CheckSamtools | Check Samtools Check whether Samtools is installed on the... |
| CheckStringTie | Check s'tringtie' Check whether 'stringtie' is installed on... |
| CheckToolAll | Check whether programs are installed |
| CopyInputDir | Copy input files directory |
| CreateHisat2Index | Creating Hisat2 index Creat Hisat2 index for further use |
| DEDESeq2Plot | DEG analysis with DESeq2 |
| DEGCorrelationPlot | Plot correlation plo |
| DEGedgeRPlot | DEG analysis with edgeR |
| DEGFrequencyPlot | Frequency plot |
| DEGMAPlot | DEGMAPlot |
| DEGPCAPlot | DEGPCAPlot |
| DEGTranscriptRelatedPlot | DEGTranscriptRelatedPlot |
| DEGVolcanoPlot | DEG volcanplot |
| ExportPath | Add '~/RNAseq_bin/ to R environment "PATH" |
| get_os | get operating system |
| GffcompareRefSample | Examine how the transcripts compare with the reference... |
| Hisat2AlignmentDefault | hisat2 alignment default |
| Hisat2ReportAssemble | Report Hisat2 assemble rate |
| InstallAll | Install Hisat2, StringTie, Gffcompare, Samtools |
| InstallGffcompareBinary | Install Gffcompare binary |
| InstallHisat2Bianry | Install Hisat2 binay |
| InstallSamtoolsBinary | Install Samtools binary |
| InstallStringTieBinary | Install stringtie binary |
| InstallToolsCMD | install all the tools and create a binary library. |
| LoadBallgownObject | load ballgown object |
| MkdirAll | Create sample gene and binary directory |
| MkdirGeneDir | Create sample gene directory |
| MkdirRNAseq_bin | Make RNAseq_bin/ directory |
| MkdirRNAseq_results | Make RNAseq_results/ directory |
| PreDECountTable | converting stringtie ballogwn preprocessed data to count... |
| ProgressGenesFiles | check 'gene_data' and subdirectory files exit |
| QualityControl | Quality control |
| RNAseqPipeline | rna seq pipline |
| RNAseqPipelineCMD | Create 'RNAseqPipline.R' that user can |
| RNASeqWorkFlowParam-class | RNASeq An S4 class for storing RNA-Seq workflow parameters of... |
| SamtoolsToBam | use 'samtools' to sort and convert the SAM files to BAM |
| StringTieAssemble | stringtie assemble and quantify expressed genes and... |
| StringTieMergeTrans | stringtie merge transcripts from all samples |
| StringTieToBallgown | stringtie estimate transcript abundances and create table... |
