255 related articles for article (PubMed ID: 34844637)
1. recount3: summaries and queries for large-scale RNA-seq expression and splicing.
Wilks C; Zheng SC; Chen FY; Charles R; Solomon B; Ling JP; Imada EL; Zhang D; Joseph L; Leek JT; Jaffe AE; Nellore A; Collado-Torres L; Hansen KD; Langmead B
Genome Biol; 2021 Nov; 22(1):323. PubMed ID: 34844637
[TBL] [Abstract][Full Text] [Related]
2. OneStopRNAseq: A Web Application for Comprehensive and Efficient Analyses of RNA-Seq Data.
Li R; Hu K; Liu H; Green MR; Zhu LJ
Genes (Basel); 2020 Oct; 11(10):. PubMed ID: 33023248
[TBL] [Abstract][Full Text] [Related]
3. 3D RNA-seq: a powerful and flexible tool for rapid and accurate differential expression and alternative splicing analysis of RNA-seq data for biologists.
Guo W; Tzioutziou NA; Stephen G; Milne I; Calixto CP; Waugh R; Brown JWS; Zhang R
RNA Biol; 2021 Nov; 18(11):1574-1587. PubMed ID: 33345702
[TBL] [Abstract][Full Text] [Related]
4. Human splicing diversity and the extent of unannotated splice junctions across human RNA-seq samples on the Sequence Read Archive.
Nellore A; Jaffe AE; Fortin JP; Alquicira-Hernández J; Collado-Torres L; Wang S; Phillips RA; Karbhari N; Hansen KD; Langmead B; Leek JT
Genome Biol; 2016 Dec; 17(1):266. PubMed ID: 28038678
[TBL] [Abstract][Full Text] [Related]
5. Using RNentropy to Detect Significant Variation in Gene Expression Across Multiple RNA-Seq or Single-Cell RNA-Seq Samples.
Zambelli F; Pavesi G
Methods Mol Biol; 2021; 2284():77-96. PubMed ID: 33835439
[TBL] [Abstract][Full Text] [Related]
6. PASSion: a pattern growth algorithm-based pipeline for splice junction detection in paired-end RNA-Seq data.
Zhang Y; Lameijer EW; 't Hoen PA; Ning Z; Slagboom PE; Ye K
Bioinformatics; 2012 Feb; 28(4):479-86. PubMed ID: 22219203
[TBL] [Abstract][Full Text] [Related]
7. rSeqNP: a non-parametric approach for detecting differential expression and splicing from RNA-Seq data.
Shi Y; Chinnaiyan AM; Jiang H
Bioinformatics; 2015 Jul; 31(13):2222-4. PubMed ID: 25717189
[TBL] [Abstract][Full Text] [Related]
8. 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]
9. Snaptron: querying splicing patterns across tens of thousands of RNA-seq samples.
Wilks C; Gaddipati P; Nellore A; Langmead B
Bioinformatics; 2018 Jan; 34(1):114-116. PubMed ID: 28968689
[TBL] [Abstract][Full Text] [Related]
10. 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]
11. RNA-Seq Data Analysis in Galaxy.
Batut B; van den Beek M; Doyle MA; Soranzo N
Methods Mol Biol; 2021; 2284():367-392. PubMed ID: 33835453
[TBL] [Abstract][Full Text] [Related]
12. RAP: A Web Tool for RNA-Seq Data Analysis.
D'Antonio M; Libro P; Picardi E; Pesole G; Castrignanò T
Methods Mol Biol; 2021; 2284():393-415. PubMed ID: 33835454
[TBL] [Abstract][Full Text] [Related]
13. ReCount: a multi-experiment resource of analysis-ready RNA-seq gene count datasets.
Frazee AC; Langmead B; Leek JT
BMC Bioinformatics; 2011 Nov; 12():449. PubMed ID: 22087737
[TBL] [Abstract][Full Text] [Related]
14. Systematic evaluation of spliced alignment programs for RNA-seq data.
Engström PG; Steijger T; Sipos B; Grant GR; Kahles A; Rätsch G; Goldman N; Hubbard TJ; Harrow J; Guigó R; Bertone P;
Nat Methods; 2013 Dec; 10(12):1185-91. PubMed ID: 24185836
[TBL] [Abstract][Full Text] [Related]
15. 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]
16. Read-Split-Run: an improved bioinformatics pipeline for identification of genome-wide non-canonical spliced regions using RNA-Seq data.
Bai Y; Kinne J; Donham B; Jiang F; Ding L; Hassler JR; Kaufman RJ
BMC Genomics; 2016 Aug; 17 Suppl 7(Suppl 7):503. PubMed ID: 27556805
[TBL] [Abstract][Full Text] [Related]
17. Nanopore RNA Sequencing Analysis.
Leonardi T; Leger A
Methods Mol Biol; 2021; 2284():569-578. PubMed ID: 33835464
[TBL] [Abstract][Full Text] [Related]
18. RNASeqR: An R Package for Automated Two-Group RNA-Seq Analysis Workflow.
Chao KH; Hsiao YW; Lee YF; Lee CY; Lai LC; Tsai MH; Lu TP; Chuang EY
IEEE/ACM Trans Comput Biol Bioinform; 2021; 18(5):2023-2031. PubMed ID: 31796413
[TBL] [Abstract][Full Text] [Related]
19. Methods to study splicing from high-throughput RNA sequencing data.
Alamancos GP; Agirre E; Eyras E
Methods Mol Biol; 2014; 1126():357-97. PubMed ID: 24549677
[TBL] [Abstract][Full Text] [Related]
20. iDEP: an integrated web application for differential expression and pathway analysis of RNA-Seq data.
Ge SX; Son EW; Yao R
BMC Bioinformatics; 2018 Dec; 19(1):534. PubMed ID: 30567491
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
