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Tag: pathfindR
Myristoylated, alanine-rich C-kinase substrate (MARCKS) regulates toll-like receptor 4 signaling in macrophages
Cell line and LPS stimulation conditions Immortalized mouse macrophages (IMM), including the IMMs from TLR4 -/- mouse (generated by Bruce Beutler’s laboratory47) and available from Jackson Laboratory) were a generous gift from Dr. Eicke Latz48,49. The cells were cultured in complete DMEM (Gibco, Grand Island, NY, USA) complemented with 10%…
Enrichment Analysis, Clustering and Scoring with pathfindR
In this tutorial, I’ll try to provide a brief overview of the capabilities of our enrichment analysis R package pathfindR. The tool is in CRAN and its introductory vignette can be found here. We also have a detailed wiki. pathfindR is designed to improve enrichment analysis by firstly identifying active…
GeneTonic: an R/Bioconductor package for streamlining the interpretation of RNA-seq data | BMC Bioinformatics
1. Van den Berge K, Hembach KM, Soneson C, Tiberi S, Clement L, Love MI, Patro R, Robinson MD. RNA sequencing data: Hitchhikers guide to expression analysis. Annu Rev Biomed Data Sci. 2019;2(1):139–73. doi.org/10.1146/annurev-biodatasci-072018-021255. Article Google Scholar 2. Conesa A, Madrigal P, Tarazona S, Gomez-Cabrero D, Cervera A, McPherson A,…
Introducing NA by coercion error message when running pathfindR
Since the weekend I’ve been getting an “NAs introduced by coercion” error message when i run the pathfindR package. An example of some of my data is Gene.symbol <- c(“ACAA2”, “ACADVL”, “ACAT1”, “ACOT9”, “ACOX1”, “ADH5”, “AKR1A1”) logFC <- c(“3.3”, “3.9”, “1.5”, “1.7”, “2.4”, “1.9”, “1.7”) adj.P.Val <- c(“0.02”, “0.03”, “0.02”,…
issues installing pathfindR package
issues installing pathfindR package 1 Hi I am trying to use the pathfindR package to do enrichment analysis on my data. According to the vignette the package is downloaded from CRAN by install.packages(“pathfindR”) this gives the following output Installing package into �� (as �lib� is unspecified) Warning in install.packages :…