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.

Papers: 10.1093/bib/bbz158

https://doi.org/10.1093/bib/bbz158

Toward a gold standard for benchmarking gene set enrichment analysis

Cited by: 74
Author(s): Ludwig Geistlinger, Gergely Csaba, Mara Santarelli, Marcel Ramos, Lucas Schiffer, Nitesh Turaga, Charity W. Law, Sean Davis, Vincent J. Carey, Martin Morgan, Ralf Zimmer, Levi Waldron
Published: over 4 years ago

Software Mentions 13

bioconductor: CAMERA
Collection of annotation related methods for mass spectrometry data
Papers that mentioned: 429
bioconductor: clusterProfiler
A universal enrichment tool for interpreting omics data
Papers that mentioned: 2,223
bioconductor: DESeq2
Differential gene expression analysis based on the negative binomial distribution
Papers that mentioned: 9,583
bioconductor: edgeR
Empirical Analysis of Digital Gene Expression Data in R
Papers that mentioned: 6,568
bioconductor: EnrichmentBrowser
Seamless navigation through combined results of set-based and network-based enrichment analysis
Papers that mentioned: 12
bioconductor: GSEABenchmarkeR
Reproducible GSEA Benchmarking
Papers that mentioned: 2
bioconductor: GSVA
Gene Set Variation Analysis for microarray and RNA-seq data
Papers that mentioned: 893
bioconductor: limma
Linear Models for Microarray Data
Papers that mentioned: 7,776
bioconductor: PADOG
Pathway Analysis with Down-weighting of Overlapping Genes (PADOG)
Papers that mentioned: 19
bioconductor: vsn
Variance stabilization and calibration for microarray data
Papers that mentioned: 91
cran: GSA
Gene Set Analysis
Papers that mentioned: 285
pypi: GSA
Python Package to implement Gravitational Search Algorithm. Documentation at:https://github.com/deepanshu1999/GSA
Papers that mentioned: 285
pypi: GSVA
Python CLI and module for running the GSVA R bioconductor package with Python Pandas inputs and outputs.
Papers that mentioned: 893