Subread sequence alignment for R


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Documentation for package ‘Rsubread’ version 1.20.6

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align Read mapping for genomic DNA-seq and RNA-seq data via seed-and-vote (Subread and Subjunc)
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
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 Read mapping for genomic DNA-seq and RNA-seq data via seed-and-vote (Subread and Subjunc)
write.Rsubread Create an annotation file from a GRanges object, suitable for featureCounts()