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Papers: 10.1371/journal.pone.0079217

https://doi.org/10.1371/journal.pone.0079217

A Comparison of Gene Set Analysis Methods in Terms of Sensitivity, Prioritization and Specificity

Cited by: 154
Author(s): Adi L. Tarca, Gaurav Bhatti, Roberto Romero
Published: almost 13 years ago

Software Mentions 12

bioconductor: CAMERA
Collection of annotation related methods for mass spectrometry data
Papers that mentioned: 429
Very Likely Science (75)
bioconductor: gage
Generally Applicable Gene-set Enrichment for Pathway Analysis
Papers that mentioned: 45
Very Likely Science (100)
bioconductor: GOstats
Tools for manipulating GO and microarrays
Papers that mentioned: 368
Very Likely Science (100)
bioconductor: GSVA
Gene Set Variation Analysis for microarray and RNA-seq data
Papers that mentioned: 893
Very Likely Science (100)
bioconductor: KEGGREST
Client-side REST access to the Kyoto Encyclopedia of Genes and Genomes (KEGG)
Papers that mentioned: 75
Very Likely Science (90)
bioconductor: limma
Linear Models for Microarray Data
Papers that mentioned: 7,776
Very Likely Science (78)
bioconductor: PADOG
Pathway Analysis with Down-weighting of Overlapping Genes (PADOG)
Papers that mentioned: 19
Very Likely Science (100)
bioconductor: safe
Significance Analysis of Function and Expression
Papers that mentioned: 4
Very Likely Science (100)
bioconductor: sigPathway
Pathway Analysis
Papers that mentioned: 15
Very Likely Science (100)
cran: GSA
Gene Set Analysis
Papers that mentioned: 285
Very Likely Science (93)
pypi: GSA
Python Package to implement Gravitational Search Algorithm. Documentation at:https://github.com/deepanshu1999/GSA
Papers that mentioned: 285
Very Likely Science (90)
pypi: GSVA
Python CLI and module for running the GSVA R bioconductor package with Python Pandas inputs and outputs.
Papers that mentioned: 893
Very Likely Science (100)