HTSeqGenie              Package overview
TP53GenomicFeatures     Demo genomic features around the TP53 gene
analyzeVariants         Calculate and process Variants
annotateVariants        Annotate variants via vep
buildGenomicFeaturesFromTxDb
                        Build genomic features from a TxDb object
callVariantsGATK        Variant calling via GATK
checkGATKJar            Check for the GATK jar file
detectRRNA              Detect rRNA Contamination in Reads
excludeVariantsByRegions
                        Filter variants by regions
gatk                    gatk
generateSingleGeneDERs
                        generateSingleGeneDERs
getRRNAIds              Detect reads that look like rRNA
getTabDataFromFile      Load tabular data from the NGS pipeline result
                        directory
hashCoverage            Hashing function for coverage
hashVariants            Hashing function for variants
hashVector              Hashing function for vector
isSparse                isSparse
markDuplicates          markDuplicates
markDups                markDups
realignIndels           realignIndels
realignIndelsGATK       Realign indels via GATK
runPipeline             Run the NGS analysis pipeline
runPipelineConfig       Run the NGS analysis pipeline
setupTestFramework      setup test framework
vcfStat                 Compute stats on a VCF file
wrap.callVariants       Variant calling
writeVCF                writeVCF
