149 related articles for article (PubMed ID: 36384457)
1. Modeling and cleaning RNA-seq data significantly improve detection of differentially expressed genes.
Deyneko IV; Mustafaev ON; Tyurin AА; Zhukova KV; Varzari A; Goldenkova-Pavlova IV
BMC Bioinformatics; 2022 Nov; 23(1):488. PubMed ID: 36384457
[TBL] [Abstract][Full Text] [Related]
2. Gene dispersion is the key determinant of the read count bias in differential expression analysis of RNA-seq data.
Yoon S; Nam D
BMC Genomics; 2017 May; 18(1):408. PubMed ID: 28545404
[TBL] [Abstract][Full Text] [Related]
3. SPARTA: Simple Program for Automated reference-based bacterial RNA-seq Transcriptome Analysis.
Johnson BK; Scholz MB; Teal TK; Abramovitch RB
BMC Bioinformatics; 2016 Feb; 17():66. PubMed ID: 26847232
[TBL] [Abstract][Full Text] [Related]
4. Shiny-DEG: A Web Application to Analyze and Visualize Differentially Expressed Genes in RNA-seq.
Wang S; Zhang Y; Hu C; Zhang N; Gribskov M; Yang H
Interdiscip Sci; 2020 Sep; 12(3):349-354. PubMed ID: 32666343
[TBL] [Abstract][Full Text] [Related]
5. Optimal Gene Filtering for Single-Cell data (OGFSC)-a gene filtering algorithm for single-cell RNA-seq data.
Hao J; Cao W; Huang J; Zou X; Han ZG
Bioinformatics; 2019 Aug; 35(15):2602-2609. PubMed ID: 30535000
[TBL] [Abstract][Full Text] [Related]
6. Detrimental effects of duplicate reads and low complexity regions on RNA- and ChIP-seq data.
Dozmorov MG; Adrianto I; Giles CB; Glass E; Glenn SB; Montgomery C; Sivils KL; Olson LE; Iwayama T; Freeman WM; Lessard CJ; Wren JD
BMC Bioinformatics; 2015; 16 Suppl 13(Suppl 13):S10. PubMed ID: 26423047
[TBL] [Abstract][Full Text] [Related]
7. Next-generation sequencing facilitates quantitative analysis of wild-type and Nrl(-/-) retinal transcriptomes.
Brooks MJ; Rajasimha HK; Roger JE; Swaroop A
Mol Vis; 2011; 17():3034-54. PubMed ID: 22162623
[TBL] [Abstract][Full Text] [Related]
8. Evaluating gene expression in C57BL/6J and DBA/2J mouse striatum using RNA-Seq and microarrays.
Bottomly D; Walter NA; Hunter JE; Darakjian P; Kawane S; Buck KJ; Searles RP; Mooney M; McWeeney SK; Hitzemann R
PLoS One; 2011 Mar; 6(3):e17820. PubMed ID: 21455293
[TBL] [Abstract][Full Text] [Related]
9. A fuzzy method for RNA-Seq differential expression analysis in presence of multireads.
Consiglio A; Mencar C; Grillo G; Marzano F; Caratozzolo MF; Liuni S
BMC Bioinformatics; 2016 Nov; 17(Suppl 12):345. PubMed ID: 28185579
[TBL] [Abstract][Full Text] [Related]
10. OUTRIDER: A Statistical Method for Detecting Aberrantly Expressed Genes in RNA Sequencing Data.
Brechtmann F; Mertes C; Matusevičiūtė A; Yépez VA; Avsec Ž; Herzog M; Bader DM; Prokisch H; Gagneur J
Am J Hum Genet; 2018 Dec; 103(6):907-917. PubMed ID: 30503520
[TBL] [Abstract][Full Text] [Related]
11. Comparison of normalization and differential expression analyses using RNA-Seq data from 726 individual Drosophila melanogaster.
Lin Y; Golovnina K; Chen ZX; Lee HN; Negron YL; Sultana H; Oliver B; Harbison ST
BMC Genomics; 2016 Jan; 17():28. PubMed ID: 26732976
[TBL] [Abstract][Full Text] [Related]
12. Removal of redundant contigs from de novo RNA-Seq assemblies via homology search improves accurate detection of differentially expressed genes.
Ono H; Ishii K; Kozaki T; Ogiwara I; Kanekatsu M; Yamada T
BMC Genomics; 2015 Dec; 16():1031. PubMed ID: 26637306
[TBL] [Abstract][Full Text] [Related]
13. Analyzing Multifactorial RNA-Seq Experiments with DicoExpress.
Baudry K; Paysant-Le Roux C; Colella S; Castandet B; Martin ML
J Vis Exp; 2022 Jul; (185):. PubMed ID: 35969075
[TBL] [Abstract][Full Text] [Related]
14. Statistical detection of differentially expressed genes based on RNA-seq: from biological to phylogenetic replicates.
Gu X
Brief Bioinform; 2016 Mar; 17(2):243-8. PubMed ID: 26108230
[TBL] [Abstract][Full Text] [Related]
15. Powerful differential expression analysis incorporating network topology for next-generation sequencing data.
Dona MSI; Prendergast LA; Mathivanan S; Keerthikumar S; Salim A
Bioinformatics; 2017 May; 33(10):1505-1513. PubMed ID: 28172447
[TBL] [Abstract][Full Text] [Related]
16. CEDER: accurate detection of differentially expressed genes by combining significance of exons using RNA-Seq.
Wan L; Sun F
IEEE/ACM Trans Comput Biol Bioinform; 2012; 9(5):1281-92. PubMed ID: 22641709
[TBL] [Abstract][Full Text] [Related]
17. MustSeq, an alternative approach for multiplexible strand-specific 3' end sequencing of mRNA transcriptome confers high efficiency and practicality.
Mai L; Qiu Y; Lian Z; Chen C; Wang L; Yin Y; Wang S; Yang X; Li Y; Peng W; Luo C; Pan X
RNA Biol; 2021 Oct; 18(sup1):232-243. PubMed ID: 34586036
[TBL] [Abstract][Full Text] [Related]
18. BADGE: a novel Bayesian model for accurate abundance quantification and differential analysis of RNA-Seq data.
Gu J; Wang X; Halakivi-Clarke L; Clarke R; Xuan J
BMC Bioinformatics; 2014; 15 Suppl 9(Suppl 9):S6. PubMed ID: 25252852
[TBL] [Abstract][Full Text] [Related]
19. Evaluation of the coverage and depth of transcriptome by RNA-Seq in chickens.
Wang Y; Ghaffari N; Johnson CD; Braga-Neto UM; Wang H; Chen R; Zhou H
BMC Bioinformatics; 2011 Oct; 12 Suppl 10(Suppl 10):S5. PubMed ID: 22165852
[TBL] [Abstract][Full Text] [Related]
20. The Vacc-SeqQC project: Benchmarking RNA-Seq for clinical vaccine studies.
Goll JB; Bosinger SE; Jensen TL; Walum H; Grimes T; Tharp GK; Natrajan MS; Blazevic A; Head RD; Gelber CE; Steenbergen KJ; Patel NB; Sanz P; Rouphael NG; Anderson EJ; Mulligan MJ; Hoft DF
Front Immunol; 2022; 13():1093242. PubMed ID: 36741404
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]