Ecosyste.ms: Papers

An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.

Projects: bioconductor: SeqGSEA

https://packages.ecosyste.ms/registries/bioconductor.org/packages/SeqGSEA

Gene Set Enrichment Analysis (GSEA) of RNA-Seq Data: integrating differential expression and splicing
1 version
Latest release: 10 months ago
36,877 downloads total

Papers Mentioning SeqGSEA 18

10.1186/s13059-016-0881-8

A survey of best practices for RNA-seq data analysis
Cited by: 1,691
Author(s): Ana Conesa, Pedro Madrigal, Sonia Tarazona, David Gomez-Cabrero, Alejandra Cervera, Andrew McPherson, Michał Wojciech Szcześniak, Daniel J. Gaffney, Laura L. Elo, Xuegong Zhang, A Mortazavi
Software Mentions: 21
Published: over 8 years ago

10.1186/s13040-017-0125-9

Gene set analysis controlling for length bias in RNA-seq experiments
Cited by: 7
Author(s): Xing Ren, Qiang Hu, Song Liu, Jianmin Wang, Jeffrey C. Miecznikowski
Software Mentions: 9
Published: over 7 years ago

10.1093/bib/bbv069

Gene set analysis approaches for RNA-seq data: performance evaluation and application guideline
Cited by: 45
Author(s): Yasir Rahmatallah, Frank Emmert‐Streib, Galina Glazko
Software Mentions: 8
Published: almost 9 years ago

10.3390/e22040427

Fifteen Years of Gene Set Analysis for High-Throughput Genomic Data: A Review of Statistical Approaches and Future Challenges
Cited by: 30
Author(s): Das S, Craig J. McClain, N. Shesh
Software Mentions: 7
Published: over 4 years ago

10.1371/journal.pcbi.1004393

Informatics for RNA Sequencing: A Web Resource for Analysis on the Cloud
Cited by: 73
Author(s): Malachi Griffith, Jason Walker, Nicholas C. Spies, Benjamin J. Ainscough, Obi L. Griffith
Software Mentions: 6
Published: almost 9 years ago

10.1186/s12859-015-0729-3

htsint: a Python library for sequencing pipelines that combines data through gene set generation
Cited by: 1
Author(s): Adam Richards, Anthony Herrel, Camille Bonneaud
Software Mentions: 6
Published: almost 9 years ago

10.1186/s12859-017-1674-0

Ranking metrics in gene set enrichment analysis: do they matter?
Cited by: 47
Author(s): Joanna Żyła, Michał Marczyk, January Weiner, Joanna Polańska
Software Mentions: 5
Published: about 7 years ago

10.1186/s12859-019-2697-5

GSEPD: a Bioconductor package for RNA-seq gene set enrichment and projection display
Cited by: 5
Author(s): Karl Stamm, Aoy Tomita‐Mitchell, Serdar Bozdag
Software Mentions: 5
Published: over 5 years ago

10.1155/2018/2439527

RNA-seq Reveals the Overexpression of IGSF9 in Endometrial Cancer
Cited by: 11
Author(s): Zonggao Shi, Chunyan Li, Laura Tarwater, Jun Li, Yang Li, William Kaliney, Darshan S. Chandrashekar, M. Sharon Stack
Software Mentions: 5
Published: over 6 years ago

10.18632/oncotarget.9370

Practical aspects of NGS-based pathways analysis for personalized cancer science and medicine
Cited by: 13
Author(s): Ekaterina Kotelnikova, Mikhail A. Pyatnitskiy, A. G. Paleeva, O. S. Kremenetskaya, D. V. Vinogradov
Software Mentions: 4
Published: about 8 years ago

10.1038/srep06347

GSAASeqSP: A Toolset for Gene Set Association Analysis of RNA-Seq Data
Cited by: 52
Author(s): Qing Xiong, Sayan Mukherjee, Terrence S. Furey
Software Mentions: 4
Published: almost 10 years ago

10.1186/s12859-014-0397-8

Comparative evaluation of gene set analysis approaches for RNA-Seq data
Cited by: 26
Author(s): Yasir Rahmatallah, Frank Emmert‐Streib, Galina Glazko
Software Mentions: 3
Published: over 9 years ago

10.3389/fnins.2019.00376

Medullary Respiratory Circuit Is Reorganized by a Seasonally-Induced Program in Preparation for Hibernation
Cited by: 3
Author(s): Tom Russell, Jichang Zhang, Michał Okoniewski, Felix Franke, Sandrine Bichet, Andreas Hierlemann
Software Mentions: 3
Published: over 5 years ago

10.3389/fphys.2015.00383

Pathway Analysis: State of the Art
Cited by: 170
Author(s): Miguel Angel García-Campos, Jesús Espinal-Enríquez, Enrique Hernández‐Lemus
Software Mentions: 3
Published: over 8 years ago

10.1186/1471-2105-14-S5-S16

Gene set enrichment analysis of RNA-Seq data: integrating differential expression and splicing
Cited by: 41
Author(s): Xi Wang, Murray J. Cairns
Software Mentions: 3
Published: over 11 years ago

10.1186/s12859-014-0364-4

Comparisons of computational methods for differential alternative splicing detection using RNA-seq in plant systems
Cited by: 85
Author(s): Ruolin Liu, Ann E. Loraine, Julie A. Dickerson
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0165919

Improving Gene-Set Enrichment Analysis of RNA-Seq Data with Small Replicates
Cited by: 18
Author(s): Susan A. Yoon, Seon‐Young Kim, Dougu Nam
Software Mentions: 2
Published: over 7 years ago

10.1186/s40478-019-0820-5

Improved risk-stratification for posterior fossa ependymoma of childhood considering clinical, histological and genetic features – a retrospective analysis of the HIT ependymoma trial cohort
Cited by: 20
Author(s): Stephanie T. Jünger, Martin Mynarek, Inken Wohlers, Evelyn Dörner, Anja zur Mühlen, Natalia Velez-Char, Katja von Hoff, Stefan Rutkowski, Monika Warmuth‐Metz, Rolf‐Dieter Kortmann, Beate Timmermann, Sven Rahmann, Ludger Klein‐Hitpass, André O. von Bueren, Torsten Pietsch
Software Mentions: 1
Published: over 4 years ago