PennDiff: Detecting Differential Alternative Splicing and Transcription by RNA Sequencing (Q50104538)

25 February 2018

title

PennDiff: Detecting Differential Alternative Splicing and Transcription by RNA Sequencing (English)

1 reference

25 February 2018

alternative mRNA splicing, via spliceosome

main subject

1 reference

Yu Hu

1

1 reference

25 February 2018

Jennie Lin

2

1 reference

25 February 2018

Jian Hu

3

1 reference

25 February 2018

Gang Hu

4

1 reference

25 February 2018

Kui Wang

5

1 reference

25 February 2018

Hanrui Zhang

6

1 reference

25 February 2018

Muredach P Reilly

7

1 reference

25 February 2018

Mingyao Li

8

1 reference

25 February 2018

language of work or name

English

0 references

publication date

20 February 2018

1 reference

25 February 2018

published in

Bioinformatics

1 reference

25 February 2018

describes a project that uses

ImageJ

1 reference

11 June 2022

https://www.ebi.ac.uk/europepmc/webservices/rest/PMC6041879/fullTextXML

based on heuristic

inferred from PubMed Central ID database lookup

cites work

RNA mis-splicing in disease

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6041879

Functional analysis and transcriptomic profiling of iPSC-derived macrophages and their application in modeling Mendelian disease

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6041879

rMATS: robust and flexible detection of differential alternative splicing from replicate RNA-Seq data

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6041879

IUTA: a tool for effectively detecting differential isoform usage from RNA-Seq data.

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6041879

Identification of genetic variants associated with alternative splicing using sQTLseekeR.

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6041879

Comprehensive analysis of gene expression in human retina and supporting tissues.

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6041879

A survey of software for genome-wide discovery of differential splicing in RNA-Seq data

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6041879

PennSeq: accurate isoform-specific gene expression quantification in RNA-Seq by modeling non-uniform read distribution

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6041879

rSeqDiff: detecting differential isoform expression from RNA-Seq data using hierarchical likelihood ratio test

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6041879

SplicingCompass: differential splicing detection using RNA-seq data

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6041879

DiffSplice: the genome-wide detection of differential splicing events with RNA-seq.

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6041879

Modelling and simulating generic RNA-Seq experiments with the flux simulator

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6041879

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6041879

MATS: a Bayesian framework for flexible detection of differential alternative splicing from RNA-Seq data

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6041879

A Gaussian copula approach for the analysis of secondary phenotypes in case-control genetic association studies

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6041879

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6041879

Alternative transcription exceeds alternative splicing in generating the transcriptome diversity of cerebellar development

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6041879

Pre-mRNA splicing: where and when in the nucleus

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6041879

Analysis and design of RNA sequencing experiments for identifying isoform regulation

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6041879

Differential expression analysis for sequence count data

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6041879

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6041879

TopHat: discovering splice junctions with RNA-Seq

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6041879

Statistical inferences for isoform expression in RNA-Seq

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6041879

Alternative isoform regulation in human tissue transcriptomes

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6041879

Joint regression analysis of correlated data using Gaussian copulas

26 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6041879

Identifying differentially spliced genes from two groups of RNA-seq samples

26 August 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/29474557

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

The devil in the details of RNA-seq

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/29474557

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/BIOINFORMATICS/BTY097

1 reference

25 February 2018

journals/bioinformatics/HuLHHWZRL18

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

28 January 2021

PMC publication ID

6041879

0 references

1 reference

25 February 2018