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Papers: 10.1186/s40246-019-0226-2

https://doi.org/10.1186/s40246-019-0226-2

Size matters: how sample size affects the reproducibility and specificity of gene set analysis

Cited by: 28
Author(s): Farhad Maleki, Katie Ovens, Ian McQuillan, Anthony Kusalik
Published: almost 6 years ago

Software Mentions 10

bioconductor: affy
Methods for Affymetrix Oligonucleotide Arrays
Papers that mentioned: 989
Very Likely Science (98)
bioconductor: ArrayExpress
Access the ArrayExpress Collection at EMBL-EBI Biostudies and build Bioconductor data structures: ExpressionSet, AffyBatch, NChannelSet
Papers that mentioned: 1,962
Very Likely Science (83)
bioconductor: gage
Generally Applicable Gene-set Enrichment for Pathway Analysis
Papers that mentioned: 45
Very Likely Science (100)
bioconductor: GEOquery
Get data from NCBI Gene Expression Omnibus (GEO)
Papers that mentioned: 328
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: 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)
cran: WGCNA
Weighted Correlation Network Analysis
Papers that mentioned: 3,479
Very Likely Science (85)
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)
pypi: stats
Calculator-style statistical functions
Papers that mentioned: 3,105
Very Likely Science (90)