About: The R package Rsubread is easier, faster, cheaper and better for alignment and quantification of RNA sequencing reads

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article by Yang Liao et al published 20 February 2019 in Nucleic Acids Research

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description	wetenschappelijk artikel (nl) im Februar 2019 veröffentlichter wissenschaftlicher Artikel (de) наукова стаття, опублікована в лютому 2019 (uk) article by Yang Liao et al published 20 February 2019 in Nucleic Acids Research (en)
publication date	wds:Q62817473-4751D2C6-0D2F-4C87-8416-534385FFA32F
publication date	2019-02-20 00:00:00Z (xsd:dateTime)
language of work or name	wds:Q62817473-4E633DF8-43B0-4CA0-96F5-60640E6EB522
language of work or name	English
cites work	wds:Q62817473-00741042-0654-4FDF-B7EE-46F1E09C0CB7 wds:Q62817473-05E63F07-C1EC-4CB6-8135-EDB5015A9D01 wds:Q62817473-07079C2F-8160-47E4-B8D1-8523CE010606 wds:Q62817473-1610C13B-31F6-4949-BE9F-01E675221E0F wds:Q62817473-1CFF4E88-D56E-4ADA-AC52-5E9067B7C97C wds:Q62817473-205FA4E7-5285-46F8-903B-5981C68AAB86 wds:Q62817473-32DFDFDD-5386-4D70-A49B-437F475312BC wds:Q62817473-3A407A17-E95E-470F-98BC-BF231A4BB9DE wds:Q62817473-4B4A565C-8744-4AFF-B92F-050D26F24C31 wds:Q62817473-4C2BA021-C396-4595-89F1-AF541D8B9DD1 wds:Q62817473-6D11F0F3-EE3A-432E-B260-458507BC89A8 wds:Q62817473-784A4C73-2091-436E-B7B9-60C23D559AB4 wds:Q62817473-79B91D38-9F79-464D-8B61-03851A6BD4E8 wds:Q62817473-8497FEDB-0BCD-447E-8246-C0708DC13CFB wds:Q62817473-86ED46A5-9EB4-41D0-9904-FBE1B19E4380 wds:Q62817473-97CF82FC-2BA4-4D60-8F89-0B42E2B166D8 wds:Q62817473-A2F92FA9-F307-4040-890A-B83A021C682F wds:Q62817473-B3DFF83F-E2F2-4FAB-A8EB-AFC0AF9B0DC4 wds:Q62817473-B4389D86-3FF2-4AE8-BF9D-F200B02476F5 wds:Q62817473-B9DD1DEB-2C1C-484C-AF39-D7C37ECA0A47 wds:Q62817473-C1EDD9C9-DD27-4CA1-AC2B-C6EF20E6A71B wds:Q62817473-C9D53BD5-9398-44BE-9FA7-7A894E943B84 wds:Q62817473-D31A8171-72E5-4140-A125-A1646C6AB59B wds:Q62817473-D36790AC-AFF1-4F04-940E-743CE082B97B wds:Q62817473-EA0FE89D-89DA-4AD1-A1D7-44DDA38AA60D wds:Q62817473-EA136CAE-B61D-4503-AC4D-5F55D60D1364 wds:Q62817473-FC0D8FE0-C20D-40AD-B8CF-745CA8C9D52B
cites work	BEDTools: a flexible suite of utilities for comparing genomic features Rcount: simple and flexible RNA-Seq read counting. QuasR: quantification and annotation of short reads in R. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data TopHat: discovering splice junctions with RNA-Seq TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions Ultrafast and memory-efficient alignment of short DNA sequences to the human genome The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote Global changes in the mammary epigenome are induced by hormonal cues and coordinated by Ezh2. Detecting differential usage of exons from RNA-seq data Orchestrating high-throughput genomic analysis with Bioconductor SeqAn an efficient, generic C++ library for sequence analysis HISAT: a fast spliced aligner with low memory requirements BET inhibitor resistance emerges from leukaemia stem cells voom: Precision weights unlock linear model analysis tools for RNA-seq read counts Systematic evaluation of spliced alignment programs for RNA-seq data featureCounts: an efficient general purpose program for assigning sequence reads to genomic features A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium limma powers differential expression analyses for RNA-sequencing and microarray studies Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 HTSeq--a Python framework to work with high-throughput sequencing data STAR: ultrafast universal RNA-seq aligner Detection of splice junctions from paired-end RNA-seq data by SpliceMap. From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline Simulation-based comprehensive benchmarking of RNA-seq aligners. RNA-Seq Data Analysis Protocol: Combining In-House and Publicly Available Data Analysis of ChIP-seq Data in R/Bioconductor
author name string	wds:Q62817473-72D96034-F4D2-418B-A6B7-BA75EF7A2F71 wds:Q62817473-B2A433E1-0307-408A-911B-D77A15F7382E
author name string	Wei Shi Yang Liao
rdfs:label	The R package Rsubread is easier, faster, cheaper and better for alignment and quantification of RNA sequencing reads (en) The R package Rsubread is easier, faster, cheaper and better for alignment and quantification of RNA sequencing reads (nl)
skos:prefLabel	The R package Rsubread is easier, faster, cheaper and better for alignment and quantification of RNA sequencing reads (en) The R package Rsubread is easier, faster, cheaper and better for alignment and quantification of RNA sequencing reads (nl)
name	The R package Rsubread is easier, faster, cheaper and better for alignment and quantification of RNA sequencing reads (en) The R package Rsubread is easier, faster, cheaper and better for alignment and quantification of RNA sequencing reads (nl)
author	wds:Q62817473-62704BC3-2944-464B-A446-3D986CA7C047
author	Gordon K Smyth
title	wds:Q62817473-B0C315C0-DA52-4173-9959-F6FE867B9906
title	The R package Rsubread is easier, faster, cheaper and better for alignment and quantification of RNA sequencing reads (en)
page(s)	wds:Q62817473-2BD21D42-972A-407E-BBE0-A9ED85D0A851
page(s)	e47-e47
instance of	wds:Q62817473-E97ED6E2-9F04-43F8-9F7D-2BEAB90A44E2
instance of	scholarly article
main subject	wds:Q62817473-1CDC36B0-60AB-478A-BE75-D777FEB796BF wds:Q62817473-2B97A786-988E-4DAE-ADF7-027611F9A524
main subject	sequence alignment R package
PubMed ID	wds:Q62817473-3B2C2609-8DA4-4109-8E87-450659BB3E28
PubMed ID	http://rdf.ncbi.nlm.nih.gov/pubchem/reference/30783653
PubMed ID	30783653
published in	wds:Q62817473-F16BDE24-1E9B-4627-B7CA-5FB861F7A895
published in	Nucleic Acids Research
issue	wds:Q62817473-B1576516-0083-446C-B7A3-752A4172FA8C
volume	wds:Q62817473-302E81BB-4775-420A-BF8C-1B878FED3977
issue	8
volume	47
DOI	wds:Q62817473-2CCF1929-5F27-4752-A213-D9529C77E90F
DOI	http://dx.doi.org/10.1093/NAR/GKZ114
DOI	10.1093/NAR/GKZ114
copyright license	wds:Q62817473-5b9ad1af-ce77-4d45-bae3-6ea71c11e6cf
copyright status	wds:Q62817473-e37c955f-776b-4d1e-b7b8-90ea2dba4300
copyright license	Creative Commons Attribution-NonCommercial 4.0 International

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