RsubreadUsersGuide      View Rsubread Users Guide
align                   Align sequence reads to a reference genome via
                        seed-and-vote
atgcContent             Calculate percentages of nucleotides A, T, G
                        and C in a sequencing read datafile
buildindex              Build index for a reference genome
cellCounts              Map and count single-cell RNA data sets
detectionCall           Determine detection p values for each gene in
                        an RNA-seq dataset
detectionCallAnnotation
                        Generate annotation data used for calculating
                        detection p values
exactSNP                exactSNP - an accurate and efficient SNP caller
featureCounts           featureCounts: a general-purpose read
                        summarization function
findCommonVariants      Finding the common variants among all input VCF
                        files
flattenGTF              Flatten features provided in a GTF/GFF
                        annotation
getInBuiltAnnotation    Retrieve in-built annotations provided by
                        featureCounts function
processExons            Obtain chromosomal coordiates of each exon
                        using NCBI annotation
promoterRegions         Generate annotation for promoter region of
                        genes
propmapped              Calculate the proportion of mapped
                        reads/fragments in SAM/BAM files
qualityScores           Extract quality score data in a sequencing read
                        dataset
removeDupReads          Remove sequencing reads which are mapped to
                        identical locations
repair                  Re-order paired-end reads to place reads from
                        the same pair next to each other
sam2bed                 Convert a SAM format file to a BED format file
simReads                Generate simulated reads from a set of
                        transcripts
sublong                 Align long sequence reads to a reference genome
                        via seed-and-vote
txUnique                Count number of bases unique to each transcript
