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 |