Man pages for anilchalisey/rseqR
RNA-seq data processing pipeline

annotate_dataAnnotate gene data
build_indexBuild index for mapping using Salmon
check_sampleCheck that targets file contains the necessary info in the...
deseq2_analysisRun DESeq2 analysis on RNA-seq count data
edger_analysisRun edgeR analysis on RNA-seq count data
exploratory_analysis_deseq2Exploratory analysis of DESeq2 data
exploratory_analysis_edgerExploratory analysis of edgeR data
limma_voom_analysisRun Limma-voom analysis on RNA-seq count data
make_heatmapCreate heatmap with clustering of samples and genes for DEGs
make_MACreate MA plot
make_PCACreate PCA plot for transformed data
make_screeCreate scree plot from prcomp data
make_upsetPlot intersections of list of DE genes
make_volcanoCreate Volcano Plot
pipePipe operator
read_salmonRead the run info from Salmon output
run_deaRun differential expression analysis
run_fastqcQC reports for fastq files using FastQC
run_multiqcGenerate MultiQC report for FastQC
run_salmonQuantify transcript abundances using Salmon
run_tximportWrapper function to run tximport
sanity_checkImport the metadata and check it is correct
trim_fastqAn R-based wrapper for Trim Galore!
anilchalisey/rseqR documentation built on May 25, 2019, 2:25 p.m.