bioconductor: graphite | Projects

10.3390/metabo9100200

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: over 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

10.1186/s12859-015-0763-1

ToPASeq: an R package for topology-based pathway analysis of microarray and RNA-Seq data
Cited by: 29
Author(s): Ivana Ihnatová, Eva Budínská
Software Mentions: 12
Published: about 9 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/s12920-020-00754-5

Identification of potential crucial genes in atrial fibrillation: a bioinformatic analysis
Cited by: 15
Author(s): Junguo Zhang, Xin Huang, Xiaojie Wang, Yanhui Gao, Li Liu, Ziyi Li, Xuejiao Chen, Jie Zeng, Zebing Ye, Guowei Li
Software Mentions: 10
Published: over 4 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

10.1186/s12859-020-03910-x

multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data
Cited by: 48
Author(s): Sebastian Canzler, Jörg Hackermüller
Software Mentions: 9
Published: about 4 years ago

10.3390/cancers12051122

The Role of lncRNAs TAPIR-1 and -2 as Diagnostic Markers and Potential Therapeutic Targets in Prostate Cancer
Cited by: 11
Author(s): M. Friedrich, Karolin Wiedemann, Kristin Reiche, Sven-Holger Puppel, Gabriele Pfeifer, Ivonne Zipfel, Stefanie Petrou Binder, Ulrike Köhl, G Müller, Kurt Engeland, Achim Aigner, S. Füssel, M. Fröhner, Claudia Peitzsch, Anna Dubrovska, Michael Rade, Sabina Christ, S Schreiber, Jörg Hackermüller, Jörg Lehmann, Marieta Toma, Michael H. Muders, Ulrich Sommer, Gustavo Baretton, Manfred P. Wirth, Friedemann Horn
Software Mentions: 9
Published: over 4 years ago

10.2196/16084

A User-Friendly, Web-Based Integrative Tool (ESurv) for Survival Analysis: Development and Validation Study
Cited by: 32
Author(s): Kyoungjune Pak, Sae‐Ock Oh, Tae Sik Goh, Hye Jin Heo, Myoung‐Eun Han, Dae Cheon Jeong, Chi‐Seung Lee, Hokeun Sun, Junmo Kang, Suji Choi, Soo‐Hwan Lee, Eun Jung Kwon, Ji Wan Kang, Yun Hak Kim
Software Mentions: 9
Published: over 4 years ago

10.1186/1471-2105-15-132

Investigating perturbed pathway modules from gene expression data via structural equation models
Cited by: 19
Author(s): Daniele Pepe, Mario Grassi
Software Mentions: 7
Published: over 10 years ago

10.1186/1471-2105-13-20

graphite - a Bioconductor package to convert pathway topology to gene network
Cited by: 157
Author(s): Gabriele Sales, Enrica Calura, Duccio Cavalieri, Chiara Romualdi
Software Mentions: 7
Published: almost 13 years ago

10.3389/fnins.2012.00187

Systems Biology, Bioinformatics, and Biomarkers in Neuropsychiatry
Cited by: 43
Author(s): Ali Alawieh, Fadi A. Zaraket, Jianliang Li, Stefania Mondello, Amaly Nokkari, Mahdi Razafsha, Bilal H. Fadlallah, Rose‐Mary Boustany, Firas Kobeissy
Software Mentions: 7
Published: almost 13 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.pone.0185797

A novel network analysis approach reveals DNA damage, oxidative stress and calcium/cAMP homeostasis-associated biomarkers in frontotemporal dementia
Cited by: 21
Author(s): Fernando Palluzzi, Raffaele Ferrari, Francesca Graziano, Valeria Novelli, Giacomina Rossi, Daniela Galimberti, Innocenzo Rainero, Luisa Benussi, Benedetta Nacmias, Amalia C. Bruni, Daniele Cusi, Erika Salvi, Barbara Borroni, Mario Grassi
Software Mentions: 6
Published: about 7 years ago

10.3389/fgene.2019.01203

The Impact of Pathway Database Choice on Statistical Enrichment Analysis and Predictive Modeling
Cited by: 67
Author(s): Sarah Mubeen, Charles Tapley Hoyt, André Gemünd, Martin Hofmann‐Apitius, Holger Fröhlich, Daniel Domingo‐Fernándéz
Software Mentions: 6
Published: about 5 years ago

10.7717/peerj.4571

Pathways of topological rank analysis (PoTRA): a novel method to detect pathways involved in hepatocellular carcinoma
Cited by: 5
Author(s): Chaoxing Li, Li Liu, Valentin Dinu
Software Mentions: 5
Published: over 6 years ago

10.1016/j.csbj.2021.07.020

MyoData: An expression knowledgebase at single cell/nucleus level for the discovery of coding-noncoding RNA functional interactions in skeletal muscle
Cited by: 3
Author(s): Davide Corso, Francesco Chemello, Enrico Alessio, Ilenia Urso, Giulia Ferrarese, Martina Bazzega, Chiara Romualdi, Gerolamo Lanfranchi, Gabriele Sales, Stefano Cagnin
Software Mentions: 5
Published: almost 4 years ago

10.1038/srep13044

ESEA: Discovering the Dysregulated Pathways based on Edge Set Enrichment Analysis
Cited by: 24
Author(s): Junwei Han, Xinrui Shi, Yunpeng Zhang, Yanjun Xu, Ying Jiang, Chunlong Zhang, Feng Li, Haixiu Yang, Desi Shang, Zeguo Sun, Fei Su, Chunquan Li, Xia Li
Software Mentions: 5
Published: over 9 years ago

10.1186/s12859-019-2872-8

Integration of probabilistic regulatory networks into constraint-based models of metabolism with applications to Alzheimer’s disease
Cited by: 12
Author(s): Han Yu, Rachael Hageman Blair
Software Mentions: 5
Published: over 5 years ago

10.1186/s12859-017-1673-1

NFPscanner: a webtool for knowledge-based deciphering of biomedical networks
Cited by: 0
Author(s): Wenjian Xu, Yang Cao, Ziwei Xie, Haochen He, Song He, Hong Hao, Xiaochen Bo, Fēi Li
Software Mentions: 5
Published: over 7 years ago

10.7717/peerj.3712

PrePhyloPro: phylogenetic profile-based prediction of whole proteome linkages
Cited by: 15
Author(s): Yulong Niu, Chengcheng Liu, Shayan Moghimyfiroozabad, Yi Yang, Kambiz N. Alavian
Software Mentions: 5
Published: over 7 years ago

10.1186/s12911-020-01373-x

Computational analysis to repurpose drugs for COVID-19 based on transcriptional response of host cells to SARS-CoV-2
Cited by: 18
Author(s): Fuhai Li, Andrew P. Michelson, Randi E. Foraker, Ming Zhan, Philip R. O. Payne
Software Mentions: 4
Published: almost 4 years ago

10.3390/s17102321

Design of a Low-Cost Air Levitation System for Teaching Control Engineering
Cited by: 31
Author(s): Jesús Chacón, Jacobo Sáenz, Luís de la Torre, José Quintanal Díaz, Francisco Esquembre
Software Mentions: 4
Published: about 7 years ago

10.1371/journal.pone.0132813

Subpathway Analysis based on Signaling-Pathway Impact Analysis of Signaling Pathway
Cited by: 39
Author(s): Xianbin Li, Liangzhong Shen, Xuequn Shang, Wenbin Liu
Software Mentions: 3
Published: over 9 years ago

10.14806/ej.26.0.949

KEGG2Net: Deducing gene interaction networks and acyclic graphs from KEGG pathways
Cited by: 6
Author(s): Sree Krishna Chanumolu, Mustafa Albahrani, Handan Can, Hasan H. Otu
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pone.0175844

Transcriptional networks are associated with resistance to Mycobacterium tuberculosis infection
Cited by: 55
Author(s): Chetan Seshadri, Nafiseh Sedaghat, Monica Campo, Glenna J. Peterson, Richard D. Wells, Gregory S. Olson, David R. Sherman, Catherine M. Stein, Harriet Mayanja‐Kizza, Ali Shojaie, W. Henry Boom, Thomas R. Hawn
Software Mentions: 3
Published: over 7 years ago

10.1186/s12859-020-03568-5

PS4DR: a multimodal workflow for identification and prioritization of drugs based on pathway signatures
Cited by: 11
Author(s): Mohammad Asif Emon, Daniel Domingo‐Fernándéz, Charles Tapley Hoyt, Martin Hofmann‐Apitius
Software Mentions: 3
Published: over 4 years ago

Ecosyste.ms: Papers

Projects: bioconductor: graphite

Papers Mentioning graphite 30