Package: Rsubread 2.19.0

Wei Shi

Rsubread: Mapping, quantification and variant analysis of sequencing data

Alignment, quantification and analysis of RNA sequencing data (including both bulk RNA-seq and scRNA-seq) and DNA sequenicng data (including ATAC-seq, ChIP-seq, WGS, WES etc). Includes functionality for read mapping, read counting, SNP calling, structural variant detection and gene fusion discovery. Can be applied to all major sequencing techologies and to both short and long sequence reads.

Authors:Wei Shi, Yang Liao and Gordon K Smyth with contributions from Jenny Dai

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Rsubread.pdf |Rsubread.html✨
Rsubread/json (API)
NEWS

# Install 'Rsubread' in R:

install.packages('Rsubread', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Uses libs:

zlib– Compression library

On BioConductor:Rsubread-2.19.0(bioc 3.20)Rsubread-2.18.0(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

bioconductor-package

24 exports 6.48 score 2 dependencies 9 dependents 331 mentions

Last updated 2 months agofrom:ff207530e9

Exports:align atgcContent buildindex cellCounts detectionCall detectionCallAnnotation exactSNP featureCounts findCommonVariants flattenGTF getInBuiltAnnotation processExons promoterRegions propmapped qualityScores removeDupReads repair RsubreadUsersGuide sam2bed scanFasta simReads subjunc sublong txUnique

Dependencies:lattice Matrix

Vignettes and/or manual for this package failed to build, some documents may be unavailable. Please inspect thebuild logs for more information.

Rsubread Vignette

Rendered fromRsubread.Rnwusingutils::Sweaveon Jul 02 2024.

Last update: 2023-07-06
Started: 2013-10-25

Help page	Topics
Align Sequence Reads to a Reference Genome via Seed-and-Vote	align subjunc
Calculate Percentages of Nucleotides in Reads	atgcContent
Build Index for a Reference Genome	buildindex
Map and quantify single-cell RNA-seq data generated by 10X Genomics	cellCounts
Determine Detection P Values for Each Gene in an RNA-seq Dataset	detectionCall
Generate Annotation Data Used for Calculating Detection P Values	detectionCallAnnotation
Accurately and Efficiently call SNPs	exactSNP
Count Reads by Genomic Features	featureCounts
Finding the Common Variants Among All Input VCF Files	findCommonVariants
Flatten Features in GTF or GFF Annotation Files	flattenGTF
Retrieve inbuilt gene annotations	getInBuiltAnnotation
Obtain Chromosomal Coordiates of Each Exon Using NCBI Annotation	processExons
Generate Annotation for Promoter Regions of Genes	promoterRegions
Calculate the Proportion of Mapped Reads or Fragments in SAM/BAM Files	propmapped
Extract Quality Score Data in a Sequencing Read Dataset	qualityScores
Remove Sequencing Reads Mapped to Identical Locations	removeDupReads
Re-Order Paired-End Reads to Place Reads	repair
View Rsubread Users Guide	RsubreadUsersGuide
Convert a SAM Format File to a BED File	sam2bed
Generate Simulated Reads from a Set of Transcripts	scanFasta simReads
Align Long Sequence Reads to a Reference Genome via Seed-and-Vote	sublong
Count Number of Bases Unique to Each Transcript	txUnique

Package: Rsubread 2.19.0

Rsubread: Mapping, quantification and variant analysis of sequencing data

Rsubread Vignette

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Help Manual

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