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: cran: CePa

https://packages.ecosyste.ms/registries/cran.r-project.org/packages/CePa

Centrality-Based Pathway Enrichment
8 versions
Latest release: over 2 years ago
1 dependent package
317 downloads last month

Papers Mentioning CePa 22

The metaRbolomics Toolbox in Bioconductor and beyond
Cited by: 61
Author(s): Jan Stanstrup, Corey D. Broeckling, Rick Helmus, Nils Hoffmann, Ewy A. Mathé, Thomas Naake, Luca Nicolotti, Kristian Peters, Johannes Michael Rainer, Reza M. Salek, Tobias Schulze, Emma L. Schymanski, Michael A. Stravs, Etienne Thévenot, Hendrik Treutler, Ralf Weber, Egon Willighagen, Michael Witting, Steffen Neumann
Software Mentions: 92
Published: about 5 years ago

10.3390/biology3010085

R-Based Software for the Integration of Pathway Data into Bioinformatic Algorithms
Cited by: 17
Author(s): Frank Krämer, Michaela Bayerlová, Tim Beißbarth
Software Mentions: 28
Published: almost 11 years ago

10.1371/journal.pcbi.1008979

netgsa: Fast computation and interactive visualization for topology-based pathway enrichment analysis
Cited by: 4
Author(s): Michael Hellstern, Jing Ma, Kun Yue, Ali Shojaie
Software Mentions: 12
Published: over 3 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

10.1038/srep18871

LEGO: a novel method for gene set over-representation analysis by incorporating network-based gene weights
Cited by: 37
Author(s): Xinran Dong, Yun Huang, Xiao Wang, Weidong Tian
Software Mentions: 12
Published: almost 9 years ago

10.1186/s12859-019-3146-1

A comparative study of topology-based pathway enrichment analysis methods
Cited by: 51
Author(s): Jing Ma, Ali Shojaie, George Michailidis
Software Mentions: 10
Published: about 5 years ago

10.3389/fphys.2013.00278

Methods and approaches in the topology-based analysis of biological pathways
Cited by: 162
Author(s): Cristina Mitrea, Zeinab Taghavi, Behzad Bokanizad, Samer Najeeb Hanoudi, Rebecca Tagett, Michèle Donato, Călin Voichiţa, Sorin Drăghici
Software Mentions: 9
Published: almost 12 years ago

10.1186/s12859-015-0751-5

Comparative study on gene set and pathway topology-based enrichment methods
Cited by: 61
Author(s): Michaela Bayerlová, Klaus Jung, Frank Krämer, Florian Klemm, Annalen Bleckmann, Tim Beißbarth
Software Mentions: 6
Published: about 9 years ago

10.1186/1752-0509-6-56

Centrality-based pathway enrichment: a systematic approach for finding significant pathways dominated by key genes
Cited by: 62
Author(s): Zuguang Gu, Jialin Liu, Kun-Ming Cao, Junfeng Zhang, Jin Wang
Software Mentions: 6
Published: over 12 years ago

10.1371/journal.pone.0191154

A critical comparison of topology-based pathway analysis methods
Cited by: 51
Author(s): Ivana Ihnatová, Vlad Popovici, Eva Budínská
Software Mentions: 6
Published: almost 7 years ago

10.1371/journal.pcbi.1008550

CTD: An information-theoretic algorithm to interpret sets of metabolomic and transcriptomic perturbations in the context of graphical models
Cited by: 9
Author(s): Lillian R Thistlethwaite, Varduhi Petrosyan, Xiqi Li, Marcus J. Miller, Sarah H. Elsea, Aleksandar Milosavljevic
Software Mentions: 5
Published: almost 4 years ago

10.3389/fgene.2020.00654

Gene Set Analysis: Challenges, Opportunities, and Future Research
Cited by: 98
Author(s): Farhad Maleki, Katie Ovens, Daniel J. Hogan, Anthony Kusalik
Software Mentions: 5
Published: over 4 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: over 7 years ago

10.1126/scisignal.abf8483

Kynurenic acid may underlie sex-specific immune responses to COVID-19
Cited by: 55
Author(s): Yuping Cai, Daniel Kim, Takehiro Takahashi, David Broadhurst, Yan Hong, Shuanagge Ma, Nicholas J. W. Rattray, Arnau Casanovas‐Massana, Benjamin Israelow, Jonathan Klein, Carolina Lucas, Tianyang Mao, Adam J. Moore, M. Catherine Muenker, Ji Eun Oh, Julio Silva, Patrick Wong, Albert Icksang Ko, Sajid Khan, Akiko Iwasaki, Caroline H. Johnson
Software Mentions: 4
Published: over 3 years ago

10.1186/s12864-020-07148-y

Analysing the meta-interaction between pathways by gene set topological impact analysis
Cited by: 2
Author(s): Yan Shu, Xu Chi, Xiao Chang, Mengliang Tian
Software Mentions: 4
Published: about 4 years ago

10.1186/s12864-019-6390-x

High-level integration of murine intestinal transcriptomics data highlights the importance of the complement system in mucosal homeostasis
Cited by: 8
Author(s): Nirupama Benis, Jerry M. Wells, M.A. Smits, Soumya K. Kar, Bart van der Hee, Vítor A. P. Martins dos Santos, María Suárez-Diez, Dirkjan Schokker
Software Mentions: 4
Published: almost 5 years ago

10.1093/bib/bbv049

Empirical comparison of structure-based pathway methods
Cited by: 24
Author(s): Maria K. Jaakkola, Laura L. Elo
Software Mentions: 4
Published: over 9 years ago

10.1016/j.celrep.2019.03.044

Transcriptomics-Based Screening Identifies Pharmacological Inhibition of Hsp90 as a Means to Defer Aging
Cited by: 56
Author(s): Georges E. Janssens, Xin-Xuan Lin, Lluís Millán-Ariño, Alan Kavšek, Ilke Sen, Renée I. Seinstra, Nicholas Stroustrup, Ellen A. A. Nollen, Christian G. Riedel
Software Mentions: 3
Published: over 5 years ago

10.1155/2015/746970

Identification of Novel Breast Cancer Subtype-Specific Biomarkers by Integrating Genomics Analysis of DNA Copy Number Aberrations and miRNA-mRNA Dual Expression Profiling
Cited by: 15
Author(s): Dongguo Li, Hong Xia, Zhen‐Ya Li, Lin Hua, Lin Li
Software Mentions: 3
Published: almost 10 years ago