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: sigPathway

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

Pathway Analysis
1 version
Latest release: about 1 year ago
44,854 downloads total

Papers Mentioning sigPathway 15

10.1371/journal.pone.0079217

A Comparison of Gene Set Analysis Methods in Terms of Sensitivity, Prioritization and Specificity
Cited by: 154
Author(s): Adi L. Tarca, Gaurav Bhatti, Roberto Romero
Software Mentions: 12
Published: about 11 years ago

10.1186/s13059-019-1790-4

Identifying significantly impacted pathways: a comprehensive review and assessment
Cited by: 113
Author(s): Tuan-Minh Nguyen, Adib Shafi, Tin Nguyen, Sorin Drăghici
Software Mentions: 12
Published: about 5 years ago

10.1186/s13040-018-0166-8

Gene set analysis methods: a systematic comparison
Cited by: 57
Author(s): Ravi Mathur, Daniel M. Rotroff, Ma Jun, Ali Shojaie, Alison A. Motsinger‐Reif
Software Mentions: 7
Published: over 6 years ago

10.1186/1471-2105-12-92

Statistical Test of Expression Pattern (STEPath): a new strategy to integrate gene expression data with genomic information in individual and meta-analysis studies
Cited by: 5
Author(s): Paolo Martini, Davide Risso, Gabriele Sales, Chiara Romualdi, Gerolamo Lanfranchi, Stefano Cagnin
Software Mentions: 6
Published: over 13 years ago

10.1186/s12859-015-0708-8

Automatically visualise and analyse data on pathways using PathVisioRPC from any programming environment
Cited by: 13
Author(s): Anwesha Bohler, Lars Eijssen, Martijn P. van Iersel, C. René Leemans, Egon Willighagen, Martina Kutmon, Magali Jaillard, Chris T. Evelo
Software Mentions: 5
Published: over 9 years ago

10.1186/1471-2105-10-300

RCMAT: a regularized covariance matrix approach to testing gene sets
Cited by: 8
Author(s): Phillip D. Yates, Mark Reimers
Software Mentions: 3
Published: about 15 years ago

10.1186/1471-2105-9-502

Microarray-based gene set analysis: a comparison of current methods
Cited by: 68
Author(s): Sarah Song, Michael A. Black
Software Mentions: 3
Published: almost 16 years ago

10.1371/journal.pone.0017118

Distinct Early Molecular Responses to Mutations Causing vLINCL and JNCL Presage ATP Synthase Subunit C Accumulation in Cerebellar Cells
Cited by: 52
Author(s): Yi Cao, John F. Staropoli, Sunita Biswas, Janice A. Espinola, Marcy E. MacDonald, Jongmin Lee, Susan L. Cotman
Software Mentions: 3
Published: almost 14 years ago

10.1186/gb-2007-8-10-r210

Perturbation of gene expression of the chromatin remodeling pathway in premature newborns at risk for bronchopulmonary dysplasia
Cited by: 38
Author(s): Jack Cohen, Linda J. Van Marter, Yanfang Sun, Elizabeth N. Allred, Alan Leviton, Isaac S. Kohane
Software Mentions: 3
Published: almost 18 years ago

10.1371/journal.pone.0003794

Comprehensive Dissection of PDGF-PDGFR Signaling Pathways in PDGFR Genetically Defined Cells
Cited by: 103
Author(s): Erxi Wu, Nathan Palmer, Ze Tian, Annie P. Moseman, Michal Galdzicki, Xuetao Wang, Bonnie Berger, Hongbing Zhang, Isaac S. Kohane
Software Mentions: 2
Published: almost 16 years ago

10.1186/1471-2105-10-264

GEOGLE: context mining tool for the correlation between gene expression and the phenotypic distinction
Cited by: 4
Author(s): Yao Yu, Kang Tu, Siyuan Zheng, Yun Li, Guohui Ding, Jie Ping, Pei Hao, Yixue Li
Software Mentions: 2
Published: about 15 years ago

10.1186/ar2541

Mapping similarities in mTOR pathway perturbations in mouse lupus nephritis models and human lupus nephritis
Cited by: 37
Author(s): Padmalatha S. Reddy, Holly Legault, Joseph P. Sypek, Mark J Collins, Elizabeth Goad, Samuel J. Goldman, Wei Liu, Stuart Murray, Andrew J. Dorner, Margot O’Toole
Software Mentions: 2
Published: almost 17 years ago

10.1186/1471-2474-12-86

Regulation of gene expression in human tendinopathy
Cited by: 84
Author(s): Scott A. Jelinsky, Scott A. Rodeo, Jian Li, Lawrence V. Gulotta, Joanne Archambault, Howard Seeherman
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0005436

Tissue and Process Specific microRNA–mRNA Co-Expression in Mammalian Development and Malignancy
Cited by: 66
Author(s): Hongye Liu, Isaac S. Kohane
Software Mentions: 1
Published: over 15 years ago

10.1371/journal.pgen.0030135

Unbiased Gene Expression Analysis Implicates the huntingtin Polyglutamine Tract in Extra-mitochondrial Energy Metabolism
Cited by: 71
Author(s): Jong Min Lee, Elena Ivanova, Ihn Sik Seong, Tanya Cashorali, Isaac S. Kohane, James F. Gusella, Marcy E. MacDonald
Software Mentions: 1
Published: over 17 years ago