README.md

In sy-lou/ChIASim: ChIASim

ChIASim

ChIA-Sim (Lou and Lin, 2021) is an in silico experimental protocol built on a realistic simulation scheme to mimic the biological experimental protocols of ChIA-PET, Hi-ChIP, or PLAC-seq, so that data simulated represent realistic specific-protein-mediated long-range interaction data.

Installation

ChIASim can be installed from GitHub using following commands:

install.packages("devtools")
devtools::install_git("https://github.com/sy-lou/ChIASim")

ChIASim depends on other packages, i.e., parallel, BSgenome.Hsapiens.UCSC.hg19, and GenomicFeatures. They need to be installed, one may use the commands below, in advance to run ChIASim.

  if (!requireNamespace("parallel", quietly = TRUE)) install.packages("parallel")
  if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")
  if (!requireNamespace("BSgenome.Hsapiens.UCSC.hg19", quietly = TRUE)) BiocManager::install("BSgenome.Hsapiens.UCSC.hg19")
  if (!requireNamespace("GenomicFeatures", quietly = TRUE)) BiocManager::install("GenomicFeatures")

Example

``` library(ChIASim) data("POL2") data("TSS") output.base<- chiaSim(n.cells = 500, N.E=100, N.P=100, N.nE=100, N.nP=100, mc.cores.user = 1) head(output.base) ````

You may refer to the vignette for more details.

sy-lou/ChIASim documentation built on April 15, 2023, 11 p.m.