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Table 1 Selected functions. The table lists a subset of over 50 methods and functions defined by systemPipeR. Usage instructions are provided in the corresponding help pages and vignettes of the package

From: systemPipeR: NGS workflow and report generation environment

Function name Description
genWorkenvir Generates workflow templates provided by systemPipeRdata helper package
systemArgs Constructs SYSargs workflow control module (S4 object) fromtargets and param files
runCommandline Executes command-line software on samples and parameters specified in SYSargs
clusterRun Runs command-line software in parallel mode on a computer cluster
preprocessReads Filtering and/or trimming of short reads using predefined or custom parameters
seeFASTQ/seeFASTQplot Generates quality reports for any number of FASTQ files
alignStats Generates alignment statistics, such as total number of reads and alignment frequency
run_edgeR/run_DESeq2 Runs edgeR or DESeq2 for any number of pairwise sample comparisons
filterDEGs Filters and plots DEG results based on user-defined parameters
overLapper/vennPlot Computation of Venn intersects for 2-20 or more samples and 2-5 way Venn diagrams
GOCluster_Report GO term enrichment analysis for large numbers of gene sets
variantReport Generates a variant report containing genomic annotations and confidence statistics
predORF Prediction of short open reading frames in DNA sequences
featuretypeCounts Computes and plots read distribution for many feature types at once
featureCoverage Computes and plots read depth coverage from many transcripts