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() |