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: pypi: graphite
https://packages.ecosyste.ms/registries/pypi.org/packages/graphite
2 versions
Latest release: almost 16 years ago
93 downloads last month
Papers Mentioning graphite 30
10.3390/metabo9100200
The metaRbolomics Toolbox in Bioconductor and beyondCited 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 AlgorithmsCited by: 17
Author(s): Frank Krämer, Michaela Bayerlová, Tim Beißbarth
Software Mentions: 28
Published: over 10 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: about 9 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: over 3 years ago
10.1186/s12920-020-00754-5
Identification of potential crucial genes in atrial fibrillation: a bioinformatic analysisCited 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 methodsCited 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 dataCited by: 48
Author(s): Sebastian Canzler, Jörg Hackermüller
Software Mentions: 9
Published: almost 4 years ago
10.3390/cancers12051122
The Role of lncRNAs TAPIR-1 and -2 as Diagnostic Markers and Potential Therapeutic Targets in Prostate CancerCited 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 StudyCited 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 modelsCited 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 networkCited 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 NeuropsychiatryCited 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 methodsCited 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 dementiaCited 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 ModelingCited by: 67
Author(s): Sarah Mubeen, Charles Tapley Hoyt, André Gemünd, Martin Hofmann‐Apitius, Holger Fröhlich, Daniel Domingo‐Fernándéz
Software Mentions: 6
Published: almost 5 years ago
10.7717/peerj.4571
Pathways of topological rank analysis (PoTRA): a novel method to detect pathways involved in hepatocellular carcinomaCited 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 muscleCited 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 AnalysisCited 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: about 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 diseaseCited 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 networksCited 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 linkagesCited by: 15
Author(s): Yulong Niu, Chengcheng Liu, Shayan Moghimyfiroozabad, Yi Yang, Kambiz N. Alavian
Software Mentions: 5
Published: about 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-2Cited 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 EngineeringCited 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 PathwayCited 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 pathwaysCited by: 6
Author(s): Sree Krishna Chanumolu, Mustafa Albahrani, Handan Can, Hasan H. Otu
Software Mentions: 3
Published: over 3 years ago
10.1371/journal.pone.0175844
Transcriptional networks are associated with resistance to Mycobacterium tuberculosis infectionCited 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 signaturesCited by: 11
Author(s): Mohammad Asif Emon, Daniel Domingo‐Fernándéz, Charles Tapley Hoyt, Martin Hofmann‐Apitius
Software Mentions: 3
Published: over 4 years ago
10.1371/journal.pone.0197595
Beyond degree and betweenness centrality: Alternative topological measures to predict viral targetsCited by: 7
Author(s): Prajwal Devkota, Matt C. Danzi, Stefan Wuchty
Software Mentions: 3
Published: over 6 years ago
10.1186/s12859-019-2863-9
PathMe: merging and exploring mechanistic pathway knowledgeCited by: 38
Author(s): Daniel Domingo‐Fernándéz, Sarah Mubeen, Josep Marín-Llaó, Charles Tapley Hoyt, Martin Hofmann‐Apitius
Software Mentions: 3
Published: over 5 years ago
10.1186/1471-2105-15-S5-S3
timeClip: pathway analysis for time course data without replicatesCited by: 14
Author(s): Paolo Martini, Gabriele Sales, Enrica Calura, Stefano Cagnin, Monica Chiogna, Chiara Romualdi
Software Mentions: 2
Published: over 10 years ago