Subread sequence alignment for R

Documentation for package ‘Rsubread’ version 1.28.1

align	Align sequence reads to a reference genome via seed-and-vote
atgcContent	Calculate percentages of nucletodies A, T, G and C in a sequencing read datafile
buildindex	Build index for a reference genome
createAnnotationFile	Create an annotation file from a GRanges object, suitable for featureCounts()
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
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
RsubreadUsersGuide	View Rsubread Users Guide
sam2bed	Convert a SAM format file to a BED format file
subjunc	Align sequence reads to a reference genome via seed-and-vote
txUnique	Count number of bases unique to each transcript
write.Rsubread	Create an annotation file from a GRanges object, suitable for featureCounts()