Subread sequence alignment and counting for R

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Documentation for package ‘Rsubread’ version 1.32.4

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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
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
flattenGTF Flatten features provided in a GTF 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
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
sublong Align long 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()