Man pages for anilchalisey/parseR
Pipeline for Analysis of RNA-seq in R

aggregate_fqcAggregate and summarise FastQC reports for multiple samples
align_rnaAlignment of RNA-seq reads
annotationSAF file for human hg19 genome
count_readsCount reads in bam files using featureCounts
create_contrastDesign and contrast matrices
create_fqreportCreate a QC report
create_hmpHeatmap of most differential genes.
create_maplotCreate MA plot
create_mdsCreate multi-dimensional scaling plot from DGE object
create_pcaCreate principal component analysis plot from DDS object
create_seCreate Summarized Experiment
deseq2_normCount normalisation using DESeq2
deseq2_pipePipeline for DESeq2 analysis
edger_normCount normalisation using edgeR
edger_pipePipeline for edgeR analysis
homer_knownParse HOMER motif files
limma_pipePipeline for limma+voom analysis
load_samplesLoad sample metadata file
make_bigwigCreate bigwig files from BAM
make_vennMake venn diagrams showing overlapping gene lists
plot_fqcPlot FastQC Results
process_countsPre-processing of counts
read_fastqcRead a single FastQC data file
read_multifastqcRead a a directory of FastQC data files
run_deseq2Run DESeq2 analysis
run_diffRun the differential analysis pipeline
run_edgerRun edgeR-QLF
run_fastqcRun FastQC
run_goseqGene ontology and pathway analysis of DE genes
run_hisat2Wrapper script to run HISAT2.
run_homerRun HOMER for promoter motif enrichment
run_limmaRun limma+voom
run_sambambadupMark duplicates in BAM file
run_samsortWrapper scripts for SAMtools functions
anilchalisey/parseR documentation built on June 24, 2017, 12:22 a.m.