Man pages for robertdouglasmorrison/DuffyNGS
Duffy Lab NGS Analysis Pipeline for RNA-seq, DNA-seq, ChIP-seq, and RIP-seq
| alignToWig | Add BAM Alignments to Wiggle Track data objects. |
| bamAlign-class | Class '"bamAlign"' |
| BAM_Files | Utilities for Manipulating BAM Files. |
| bamRange | bamRange(bamReader, coordinates,complex=FALSE) |
| bamRange-class | Class '"bamRange"' |
| bamReader | bamReader |
| bamReader-class | Class '"bamReader"' |
| bamReadStats | Quality Control Statistics of Raw Sequencing Reads |
| bowtie2Par | Set or Query Bowtie2 Parameters |
| buildAllAnnotationFiles | Create All Annotation-dependant Files for a DuffyNGS Target... |
| buildBowtie2BuildCommandLine | Build a Bowtie2-build Command Line |
| buildBowtie2CommandLine | Build a Bowtie2 Command Line |
| buildRiboClearingFiles | Build Ribo Clearing Index and Map |
| buildSpliceJunctionFiles | Build Splice Junction Index and Maps |
| callBowtie2 | Call the Bowtie Alignment Tool |
| checkBowtie2Version | Check the Bowtie2 executable |
| compressSpliceMaps | Compress Splice Maps |
| DuffyNGS | Duffy Lab Next Gen Sequencing "NGS" package Overview |
| DuffyNGS_Annotation | Annotation File of Sample-Specific Settings |
| DuffyNGS_Options | Options File of Processing Settings |
| fastqToBAM | Convert FASTQ file(s) into a BAM file, by calling Bowtie2. |
| getBowtie2AlignMetrics | Get Bowtie2 Alignment Metrics |
| MPU.callBases | MPILEUP Base Call Utility Functions |
| pipe.Alignment | Alignment Stage of DuffyNGS Pipeline workflow. |
| pipe.AlignStats | Generate Alignment Success Stats Images. |
| pipe.AlignToWig | Turn BAM Alignments into Wiggle Tracks. |
| pipe.BAMpileup | Extract Pileup Details from BAM file. |
| pipe.ChIPpeaks | Turn Alignments into Wiggle Tracks and ChIP Peaks. |
| pipe.DEtools | Pipes for Group-wise Differential Expression Tools like... |
| pipe.DiffExpression | Turn Pairs of Transcriptomes into Differential Gene... |
| pipe.ExtractPipelineSummaryDetails | Summarize Alignment Metrics |
| pipe.GenomicAlign | Genomic Alignment Pileline Step for NGS Data |
| pipe.MetaResults | Dispatch Multiple Differential Expression Tools and then... |
| pipe.PlotGene | Plot Gene Expression as Wiggle Track Pileups |
| pipe.PlotSNP | Plot Single Nucleotide Polymorphism (SNP) Sites at Nucleotide... |
| pipe.PostAlignTasks | Post-Alignment Tasks |
| pipe.PreAlignTasks | Pre-Alignment Tasks |
| pipe.QuickQC | Quick Quality Control 'A to Z' Alignment & Transcriptome. |
| pipe.RiboClear | Ribo Clearing Pileline Step for NGS Data |
| pipe.RIPpeaks | Turn RIP-seq Data Alignments into Wiggle Tracks and RIP... |
| pipe.RIPpeaksToAltGeneMap | Combine RIP Peaks into an Alternate Gene Map |
| pipe.RNAseq | DuffyNGS Pipelines |
| pipe.SpliceAlign | Splice Alignment Pileline Step for NGS Data |
| pipe.TranscriptCluster | Hierarchical Clustering of Transcriptomes. |
| pipe.Transcriptome | Turn Alignments into Wiggle Tracks and Transcriptomes. |
| pipe.TranscriptToHTML | Turn transcriptome into HTML table with gene plot hyperlinks. |
| pipe.VariantCalls | Find Variant Alleles (aka SNPs) in Alignment Data |
| pipe.VariantSummary | Summarize all Chromosomes of SNP Calls into one File |
