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: DEGraph
https://packages.ecosyste.ms/registries/bioconductor.org/packages/DEGraph
Two-sample tests on a graph
1 version
Latest release: 10 months ago
1 dependent package
25,493 downloads total
Papers Mentioning DEGraph 15
10.3390/biology3010085
R-Based Software for the Integration of Pathway Data into Bioinformatic AlgorithmsCited by: 17
Author(s): Frank Krämer, Michaela Bayerlová, Tim Beißbarth
Software Mentions: 28
Published: over 10 years ago
10.1371/journal.pcbi.1008979
netgsa: Fast computation and interactive visualization for topology-based pathway enrichment analysisCited by: 4
Author(s): Michael Hellstern, Jing Ma, Kun Yue, Ali Shojaie
Software Mentions: 12
Published: about 3 years ago
10.1186/s12859-015-0763-1
ToPASeq: an R package for topology-based pathway analysis of microarray and RNA-Seq dataCited by: 29
Author(s): Ivana Ihnatová, Eva Budínská
Software Mentions: 12
Published: over 8 years ago
10.1186/s12859-019-3146-1
A comparative study of topology-based pathway enrichment analysis methodsCited by: 51
Author(s): Jing Ma, Ali Shojaie, George Michailidis
Software Mentions: 10
Published: over 4 years ago
10.3389/fphys.2013.00278
Methods and approaches in the topology-based analysis of biological pathwaysCited 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: over 11 years ago
10.3390/metabo10050202
Metabolomics and Multi-Omics Integration: A Survey of Computational Methods and ResourcesCited by: 59
Author(s): Tara Eicher, Garrett Kinnebrew, Andrew Patt, Kyle Spencer, Kevin L. Ying, Qin Ma, Raghu Machiraju, Ewy A. Mathé
Software Mentions: 8
Published: about 4 years ago
10.1186/1471-2105-13-20
graphite - a Bioconductor package to convert pathway topology to gene networkCited by: 157
Author(s): Gabriele Sales, Enrica Calura, Duccio Cavalieri, Chiara Romualdi
Software Mentions: 7
Published: over 12 years ago
10.1371/journal.pone.0191154
A critical comparison of topology-based pathway analysis methodsCited by: 51
Author(s): Ivana Ihnatová, Vlad Popovici, Eva Budínská
Software Mentions: 6
Published: over 6 years ago
10.18632/oncotarget.14107
High throughput estimation of functional cell activities reveals disease mechanisms and predicts relevant clinical outcomesCited by: 59
Author(s): Marta R. Hidalgo, Cankut Çubuk, Alicia Amadoz, Francisco Salavert, José Carbonell-Caballero, Joaquín Dopazo
Software Mentions: 5
Published: over 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 modelsCited by: 9
Author(s): Lillian R Thistlethwaite, Varduhi Petrosyan, Xiqi Li, Marcus J. Miller, Sarah H. Elsea, Aleksandar Milosavljevic
Software Mentions: 5
Published: over 3 years ago
10.1186/1471-2164-16-S8-S6
NET-GE: a novel NETwork-based Gene Enrichment for detecting biological processes associated to Mendelian diseasesCited by: 15
Author(s): Pietro Di Lena, Pier Luigi Martelli, Piero Fariselli, Rita Casadio
Software Mentions: 4
Published: about 9 years ago
10.1186/s12859-014-0358-2
A MATLAB tool for pathway enrichment using a topology-based pathway regulation scoreCited by: 10
Author(s): M Ibrahim, Sabah Jassim, Michael A. Cawthorne, Kenneth Langlands
Software Mentions: 3
Published: over 9 years ago
10.14814/phy2.13871
A transcriptomics model of estrogen action in the ovine fetal hypothalamus: evidence for estrogenic effects of ICI 182,780Cited by: 4
Author(s): María Belén Rabaglino, Maureen Keller‐Wood, Charles E. Wood
Software Mentions: 2
Published: almost 6 years ago
10.3389/fphys.2017.00947
Identification of Biomarkers Correlated with the TNM Staging and Overall Survival of Patients with Bladder CancerCited by: 78
Author(s): Sheng Li, Xiaoping Li, Tongzu Liu, Xiangyu Meng, Xiaohong Yin, Cheng Fang, Di Huang, Yue Cao, Hong Weng, Xian‐Tao Zeng, Xinghuan Wang
Software Mentions: 2
Published: over 6 years ago
10.3390/genes9070323
DynSig: Modelling Dynamic Signaling Alterations along Gene Pathways for Identifying Differential PathwaysCited by: 0
Author(s): Ming Shi, Yanwen Chong, Weiming Shen, Xueping Xie, Hongqiang Wang
Software Mentions: 2
Published: about 6 years ago