RsubreadUsersGuide      View Rsubread Users Guide
align                   Align Sequence Reads to a Reference Genome via
                        Seed-and-Vote
atgcContent             Calculate Percentages of Nucleotides in Reads
buildindex              Build Index for a Reference Genome
cellCounts              Map and quantify single-cell RNA-seq data
                        generated by 10X Genomics
detectionCall           Determine Detection P Values for Each Gene in
                        an RNA-seq Dataset
detectionCallAnnotation
                        Generate Annotation Data Used for Calculating
                        Detection P Values
exactSNP                Accurately and Efficiently call SNPs
featureCounts           Count Reads by Genomic Features
findCommonVariants      Finding the Common Variants Among All Input VCF
                        Files
flattenGTF              Flatten Features in GTF or GFF Annotation Files
getInBuiltAnnotation    Retrieve inbuilt gene annotations
processExons            Obtain Chromosomal Coordiates of Each Exon
                        Using NCBI Annotation
promoterRegions         Generate Annotation for Promoter Regions of
                        Genes
propmapped              Calculate the Proportion of Mapped Reads or
                        Fragments in SAM/BAM Files
qualityScores           Extract Quality Score Data in a Sequencing Read
                        Dataset
removeDupReads          Remove Sequencing Reads Mapped to Identical
                        Locations
repair                  Re-Order Paired-End Reads to Place Reads
sam2bed                 Convert a SAM Format File to a BED 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