A tutorial for those cannot install dmrseq via devtools like me:sob::sob::sob:
- install miniconda
- set bioconda channel:
(conda config --add channels r)
conda config --add channels defaults
conda config --add channels conda-forge
conda config --add channels bioconda - install r 3.4.1 (3.4.2 have some conflict in bsseq package)
conda install -c r r=3.4.1 - install dmrseq dependencies via conda (skip packages you already have)
conda install bioconductor-bsseq
conda install bioconductor-genomicranges
conda install r-ggplot2
conda install r-rcolorbrewer
conda install bioconductor-biocparallel
conda install r-outliers
conda install bioconductor-GenomicFeatures
conda install bioconductor-AnnotationHub
conda install r-readr
conda install bioconductor-bumphunter
conda install bioconductor-TxDb.Hsapiens.UCSC.hg18.knownGene - install annotatr via bioconductor (skip packages you already have)
source("https://bioconductor.org/biocLite.R")
biocLite("annotatr")#remove previous R_LIBS in your bashrc file to install this package in miniconda - download dmrseq source code and install it manually
git clone https://github.com/kdkorthauer/dmrseq.git
R CMD INSTALL $PWD/dmrseq -l $HOME/miniconda2/lib/R/library/
You are all set!!! Cheer:sparkles::bear::sparkles: