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Papers: 10.1186/s12859-019-3146-1

https://doi.org/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
Published: over 5 years ago

Software Mentions 10

bioconductor: CAMERA
Collection of annotation related methods for mass spectrometry data
Papers that mentioned: 429
Very Likely Science (75)
bioconductor: DEGraph
Two-sample tests on a graph
Papers that mentioned: 15
Very Likely Science (90)
bioconductor: graphite
GRAPH Interaction from pathway Topological Environment
Papers that mentioned: 30
Very Likely Science (100)
bioconductor: limma
Linear Models for Microarray Data
Papers that mentioned: 7,776
Very Likely Science (78)
bioconductor: PathNet
An R package for pathway analysis using topological information
Papers that mentioned: 13
Very Likely Science (100)
bioconductor: SPIA
Signaling Pathway Impact Analysis (SPIA) using combined evidence of pathway over-representation and unusual signaling perturbations
Papers that mentioned: 155
Very Likely Science (100)
cran: CePa
Centrality-Based Pathway Enrichment
Papers that mentioned: 22
Very Likely Science (87)
cran: topologyGSA
Gene Set Analysis Exploiting Pathway Topology
Papers that mentioned: 4
Very Likely Science (85)
pypi: analysis
Source code analysis of Python programs
Papers that mentioned: 2,036
Very Likely Science (90)
pypi: graphite
Papers that mentioned: 30
Very Likely Science (65)