Mapping, quantification and variant analysis of sequencing data

Documentation for package ‘Rsubread’ version 2.4.3

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