# Mapping, quantification and variant analysis of sequencing data

## Documentation for package ‘Rsubread’ version 2.4.3

- 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 in Reads
buildindex | Build Index for a Reference Genome
cellCounts | Map and quantify single cell RNA-seq data generated by 10X Genomics
detectionCall | Determine Detection P Values for Each Gene in an RNA-seq Dataset
detectionCallAnnotation | Generate Annotation Data Used for Calculating Detection P Values
exactSNP | Accurately and Efficiently call SNPs
featureCounts | Count Reads by Genomic Features
findCommonVariants | Finding the Common Variants Among All Input VCF Files
flattenGTF | Flatten Features in GTF or GFF Annotation Files
getInBuiltAnnotation | Retrieve In-Built Annotations
processExons | Obtain Chromosomal Coordiates of Each Exon Using NCBI Annotation
promoterRegions | Generate Annotation for Promoter Regions of Genes
propmapped | Calculate the Proportion of Mapped Reads or Fragments in SAM/BAM Files
qualityScores | Extract Quality Score Data in a Sequencing Read Dataset
removeDupReads | Remove Sequencing Reads Mapped to Identical Locations
repair | Re-Order Paired-End Reads to Place Reads
RsubreadUsersGuide | View Rsubread Users Guide
sam2bed | Convert a SAM Format File to a BED 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