Tag: reactome.db
Handling NA’s in Deseq2
Hi everyone First of all thank you for making rna-seq data much more accessible to an average clinical doctor through the DEseq2 packages and vignettes. I am though running into some trouble: I have a dataset of Nanostring mRNA-data from clinical study, which later was followed up. I therefore have…
Bioconductor – methylGSA
DOI: 10.18129/B9.bioc.methylGSA This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see methylGSA. Gene Set Analysis Using the Outcome of Differential Methylation Bioconductor version: 3.13 The main functions for methylGSA are methylglm and methylRRA. methylGSA implements logistic regression adjusting number of probes as…
Obtaining directionality of pathways
Obtaining directionality of pathways 0 I am attempting to use R to extract biological pathway information from several different online databases (specifically KEGG, Wikipathways and Reactome) and use that information in a larger project I am working on where I am attempting to gauge levels of pathway functionality. An important…
Bioconductor – neaGUI
This package is for version 2.13 of Bioconductor; for the stable, up-to-date release version, see neaGUI. An R package to perform the network enrichment analysis (NEA). Bioconductor version: 2.13 neaGUI is an easy to use R package developed to perform the network enrichment analysis (NEA) proposed by Alexeyenko…
Bioconductor – reactome.db
This package is for version 2.14 of Bioconductor; for the stable, up-to-date release version, see reactome.db. A set of annotation maps for reactome Bioconductor version: 2.14 A set of annotation maps for reactome assembled using data from reactome Author: Willem Ligtenberg Maintainer: Willem Ligtenberg <willem.ligtenberg at openanalytics.eu> Citation…
