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Rsubread (version 1.22.2)

Subread sequence alignment for R

Description

Provides powerful and easy-to-use tools for analyzing next-gen sequencing read data. Includes quality assessment of sequence reads, read alignment, read summarization, exon-exon junction detection, fusion detection, detection of short and long indels, absolute expression calling and SNP calling. Can be used with reads generated from any of the major sequencing platforms including Illumina GA/HiSeq/MiSeq, Roche GS-FLX, ABI SOLiD and LifeTech Ion PGM/Proton sequencers.

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Version

Version

1.22.2

License

GPL-3

Maintainer

Wei Shi

Last Published

February 15th, 2017

Functions in Rsubread (1.22.2)

detectionCallAnnotation

Generate annotation data used for calculating detection p values

getInBuiltAnnotation

Retrieve in-built annotations provided by featureCounts function

Determine detection p values for each gene in an RNA-seq dataset

Build index for a reference genome

exactSNP - an accurate and efficient SNP caller

findCommonVariants

Finding the common variants among all input VCF files

createAnnotationFile

Create an annotation file from a GRanges object, suitable for featureCounts()

Read mapping for genomic DNA-seq and RNA-seq data via seed-and-vote (Subread and Subjunc)

featureCounts: a general-purpose read summarization function

Calculate percentages of nucletodies A, T, G and C in a sequencing read datafile

Convert a SAM format file to a BED format file

Re-order paired-end reads to place reads from the same pair next to each other

RsubreadUsersGuide

View Rsubread Users Guide

Remove sequencing reads which are mapped to identical locations

Obtain chromosomal coordiates of each exon using NCBI annotation

Extract quality score data in a sequencing read dataset

Calculate the proportion of mapped reads/fragments in SAM/BAM files