# Subread Sequence Alignment and Counting for R

## Documentation for package ‘Rsubread’ version 1.34.7

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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
cellCounts | Map and count single-cell RNA data sets
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/GFF 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
scanFasta | Generate simulated reads from a set of transcripts
simReads | Generate simulated reads from a set of transcripts
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