Rsubread: an R package for the alignment, summarization and analyses of next-generation sequencing data


[Up] [Top]

Documentation for package ‘Rsubread’ version 1.10.5

Help Pages

align The Subread aligner - mapping next-generation sequencing reads 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
callSNPs Finding Single Nucleotide Polymorphisms (SNPs) from next-gen sequencing data
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
featureCounts featureCounts: a general-purpose read summarization function
processExons Obtain chromosomal coordiates of each exon using NCBI annotation
propmapped Obtain the proportion of mapped reads
qualityScores Extract quality score infromation from a sequencing read dataset
removeDupReads Remove sequencing reads which are mapped to identical locations
RsubreadUsersGuide View Rsubread Users Guide
sam2bed Convert a SAM format file to a BED format file
subjunc Discovering exon-exon junctions from using RNA-seq data
write.Rsubread Create an annotation file from a GRanges object, suitable for featureCounts()