-RGeneDamIDSeq-

All in R DamID sequencing pipeline (use genes as bin)

Includes adapter removal, Mapping and enrichment finding for DamID-Seq reads. This version includes gene level bins.

For more information see also: Tools for DNA adenine methyltransferase identification analysis of nuclear organization during C. elegans development

install

1. Install R (only 64 bit version!)
   R Project

2. Download GeneDamIDseq_0.1.4.tar.gz

3. install additional packages needed for the pipeline in R

install.packages(c('corrplot', 'aqfig'))
source("https://bioconductor.org/biocLite.R")
biocLite()
biocLite(c("QuasR", "ShortRead", "GenomicRanges", "S4Vectors", "IRanges",
"BiocInstaller", "Biobase", "Biostrings", "BSgenome", "GenomicFeatures",
"GenomicAlignments", "BiocParallel", "GenomeInfoDb", "rtracklayer",
"GenomicFiles", "Rbowtie", "biomaRt"))

4. install GeneDamIDSeq in R
   (exchange PATH with the path to the installation file on your disk)

install.packages("PATH/GeneDamIDseq_0.1.4.tar.gz", repos = NULL, type = "source")