Warning: Undefined array key "mm" in /www/wwwroot/www.ai-bt.com/si.php on line 10 Deprecated: trim(): Passing null to parameter #1 ($string) of type string is deprecated in /www/wwwroot/www.ai-bt.com/si.php on line 10 Differential analysis of RNA-seq incorporating quantification uncertainty.

Literature DB >> 28581496

Differential analysis of RNA-seq incorporating quantification uncertainty.

Harold Pimentel¹, Nicolas L Bray², Suzette Puente³, Páll Melsted⁴, Lior Pachter⁵.

Abstract

We describe sleuth (http://pachterlab.github.io/sleuth), a method for the differential analysis of gene expression data that utilizes bootstrapping in conjunction with response error linear modeling to decouple biological variance from inferential variance. sleuth is implemented in an interactive shiny app that utilizes kallisto quantifications and bootstraps for fast and accurate analysis of data from RNA-seq experiments.

Mesh：

Substances：
RNA

Year: 2017 PMID： 28581496 DOI： 10.1038/nmeth.4324

Source DB: PubMed Journal: Nat Methods ISSN： 1548-7091 Impact factor: 28.547

Keyword Cloud
Cited

489 in total

1. Altered RNA Splicing by Mutant p53 Activates Oncogenic RAS Signaling in Pancreatic Cancer.

Authors: Luisa F Escobar-Hoyos; Alex Penson; Ram Kannan; Hana Cho; Chun-Hao Pan; Rohit K Singh; Lisa H Apken; G Aaron Hobbs; Renhe Luo; Nicolas Lecomte; Sruthi Babu; Fong Cheng Pan; Direna Alonso-Curbelo; John P Morris; Gokce Askan; Olivera Grbovic-Huezo; Paul Ogrodowski; Jonathan Bermeo; Joseph Saglimbeni; Cristian D Cruz; Yu-Jui Ho; Sharon A Lawrence; Jerry P Melchor; Grant A Goda; Karen Bai; Alessandro Pastore; Simon J Hogg; Srivatsan Raghavan; Peter Bailey; David K Chang; Andrew Biankin; Kenneth R Shroyer; Brian M Wolpin; Andrew J Aguirre; Andrea Ventura; Barry Taylor; Channing J Der; Daniel Dominguez; Daniel Kümmel; Andrea Oeckinghaus; Scott W Lowe; Robert K Bradley; Omar Abdel-Wahab; Steven D Leach
Journal: Cancer Cell Date: 2020-06-18 Impact factor: 31.743

10. Neural progenitors derived from Tuberous Sclerosis Complex patients exhibit attenuated PI3K/AKT signaling and delayed neuronal differentiation.

Authors: Avery J Zucco; Valentina Dal Pozzo; Alina Afinogenova; Ronald P Hart; Orrin Devinsky; Gabriella D'Arcangelo
Journal: Mol Cell Neurosci Date: 2018-08-23 Impact factor: 4.314

Differential analysis of RNA-seq incorporating quantification uncertainty.

1. Altered RNA Splicing by Mutant p53 Activates Oncogenic RAS Signaling in Pancreatic Cancer.

2. Prey sensing and response in a nematode-trapping fungus is governed by the MAPK pheromone response pathway.

3. Tissue-Specific cis-Regulatory Divergence Implicates eloF in Inhibiting Interspecies Mating in Drosophila.

4. Cell-type specific polysome profiling from mammalian tissues.

5. Programmable RNA-Guided RNA Effector Proteins Built from Human Parts.

6. Atlas of Subcellular RNA Localization Revealed by APEX-Seq.

7. HSP90 inhibitor geldanamycin reverts IL-13- and IL-17-induced airway goblet cell metaplasia.

8. Nonparametric expression analysis using inferential replicate counts.

9. Swimming downstream: statistical analysis of differential transcript usage following Salmon quantification.

10. Neural progenitors derived from Tuberous Sclerosis Complex patients exhibit attenuated PI3K/AKT signaling and delayed neuronal differentiation.