1262 related articles for article (PubMed ID: 30783653)
1. The R package Rsubread is easier, faster, cheaper and better for alignment and quantification of RNA sequencing reads.
Liao Y; Smyth GK; Shi W
Nucleic Acids Res; 2019 May; 47(8):e47. PubMed ID: 30783653
[TBL] [Abstract][Full Text] [Related]
2. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features.
Liao Y; Smyth GK; Shi W
Bioinformatics; 2014 Apr; 30(7):923-30. PubMed ID: 24227677
[TBL] [Abstract][Full Text] [Related]
3. From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline.
Chen Y; Lun AT; Smyth GK
F1000Res; 2016; 5():1438. PubMed ID: 27508061
[TBL] [Abstract][Full Text] [Related]
4. It's DE-licious: A Recipe for Differential Expression Analyses of RNA-seq Experiments Using Quasi-Likelihood Methods in edgeR.
Lun AT; Chen Y; Smyth GK
Methods Mol Biol; 2016; 1418():391-416. PubMed ID: 27008025
[TBL] [Abstract][Full Text] [Related]
5. ChimeRScope: a novel alignment-free algorithm for fusion transcript prediction using paired-end RNA-Seq data.
Li Y; Heavican TB; Vellichirammal NN; Iqbal J; Guda C
Nucleic Acids Res; 2017 Jul; 45(13):e120. PubMed ID: 28472320
[TBL] [Abstract][Full Text] [Related]
6. JAGuaR: junction alignments to genome for RNA-seq reads.
Butterfield YS; Kreitzman M; Thiessen N; Corbett RD; Li Y; Pang J; Ma YP; Jones SJ; Birol İ
PLoS One; 2014; 9(7):e102398. PubMed ID: 25062255
[TBL] [Abstract][Full Text] [Related]
7. scPipe: A flexible R/Bioconductor preprocessing pipeline for single-cell RNA-sequencing data.
Tian L; Su S; Dong X; Amann-Zalcenstein D; Biben C; Seidi A; Hilton DJ; Naik SH; Ritchie ME
PLoS Comput Biol; 2018 Aug; 14(8):e1006361. PubMed ID: 30096152
[TBL] [Abstract][Full Text] [Related]
8. scruff: an R/Bioconductor package for preprocessing single-cell RNA-sequencing data.
Wang Z; Hu J; Johnson WE; Campbell JD
BMC Bioinformatics; 2019 May; 20(1):222. PubMed ID: 31046658
[TBL] [Abstract][Full Text] [Related]
9. Mapping RNA-seq Reads with STAR.
Dobin A; Gingeras TR
Curr Protoc Bioinformatics; 2015 Sep; 51():11.14.1-11.14.19. PubMed ID: 26334920
[TBL] [Abstract][Full Text] [Related]
10. QuasR: quantification and annotation of short reads in R.
Gaidatzis D; Lerch A; Hahne F; Stadler MB
Bioinformatics; 2015 Apr; 31(7):1130-2. PubMed ID: 25417205
[TBL] [Abstract][Full Text] [Related]
11. RNASequel: accurate and repeat tolerant realignment of RNA-seq reads.
Wilson GW; Stein LD
Nucleic Acids Res; 2015 Oct; 43(18):e122. PubMed ID: 26082497
[TBL] [Abstract][Full Text] [Related]
12. Prediction and Quantification of Splice Events from RNA-Seq Data.
Goldstein LD; Cao Y; Pau G; Lawrence M; Wu TD; Seshagiri S; Gentleman R
PLoS One; 2016; 11(5):e0156132. PubMed ID: 27218464
[TBL] [Abstract][Full Text] [Related]
13. The exon quantification pipeline (EQP): a comprehensive approach to the quantification of gene, exon and junction expression from RNA-seq data.
Schuierer S; Roma G
Nucleic Acids Res; 2016 Sep; 44(16):e132. PubMed ID: 27302131
[TBL] [Abstract][Full Text] [Related]
14. Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM).
Grant GR; Farkas MH; Pizarro AD; Lahens NF; Schug J; Brunk BP; Stoeckert CJ; Hogenesch JB; Pierce EA
Bioinformatics; 2011 Sep; 27(18):2518-28. PubMed ID: 21775302
[TBL] [Abstract][Full Text] [Related]
15. SplicingCompass: differential splicing detection using RNA-seq data.
Aschoff M; Hotz-Wagenblatt A; Glatting KH; Fischer M; Eils R; König R
Bioinformatics; 2013 May; 29(9):1141-8. PubMed ID: 23449093
[TBL] [Abstract][Full Text] [Related]
16. RES-Scanner: a software package for genome-wide identification of RNA-editing sites.
Wang Z; Lian J; Li Q; Zhang P; Zhou Y; Zhan X; Zhang G
Gigascience; 2016 Aug; 5(1):37. PubMed ID: 27538485
[TBL] [Abstract][Full Text] [Related]
17. Rcount: simple and flexible RNA-Seq read counting.
Schmid MW; Grossniklaus U
Bioinformatics; 2015 Feb; 31(3):436-7. PubMed ID: 25322836
[TBL] [Abstract][Full Text] [Related]
18. The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote.
Liao Y; Smyth GK; Shi W
Nucleic Acids Res; 2013 May; 41(10):e108. PubMed ID: 23558742
[TBL] [Abstract][Full Text] [Related]
19. AllelicImbalance: an R/bioconductor package for detecting, managing, and visualizing allele expression imbalance data from RNA sequencing.
Gådin JR; van't Hooft FM; Eriksson P; Folkersen L
BMC Bioinformatics; 2015 Jun; 16(1):194. PubMed ID: 26066318
[TBL] [Abstract][Full Text] [Related]
20. SplicingTypesAnno: annotating and quantifying alternative splicing events for RNA-Seq data.
Sun X; Zuo F; Ru Y; Guo J; Yan X; Sablok G
Comput Methods Programs Biomed; 2015 Apr; 119(1):53-62. PubMed ID: 25720307
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]