CB2-Experiments

CB2-Experiments is the repository of scripts and data of experiments were performed to compare the performance of CB² to other methods (HitSelect, MAGeCK, PBNPA, PinAPL-Py, RIGER, RSA, ScreenBEAM, sgRSEA).

CB2-Experiments contains four different directories. Each directory contains README.md to assist running scripts.

Folder name	Contents
01_gene-level-analysis	Contains scripts and data used for "CB2 is more sensitive in target gene identification than existing methods" section.
02_sgRNA-level-analysis	Contains scripts and data used for "CB2" is more specific in target gene detection than existing methods" section.
03_quantification	Contains scripts used for "CB2 provides more accurate alignment without parameter tuning" section.
util	A collection of utility scripts.

Requirements

The following bash command line enumerate the list of required/used R packages to use the script in CB2-Experiments.

$ grep -e "^library" * -R | sed 's/:/ /g' | awk '{ print $2 }' | sort -u | sed 's/library(//g' | sed 's/)//g'
CB2
PBNPA
RColorBrewer
ScreenBEAM
argparse
cowplot
edgeR
eulerr
gghighlight
ggsci
glue
here
pheatmap
precrec
sgRSEA
tidyverse

If you don't have some of the packages than please use the following installation snippet in R:

# Install packages in `cran`
install.packages(c("PBNPA", "RColorBrewer", "argparse", "cowplot", "eulerr", "gghighlight", "ggsci", "glue", "here", "pheatmap", "precrec", "sgRSEA", "tidyverse", "CB2"))

# Install packages `devtools`
install.packages("devtools")
devtools::install_github("jyyu/ScreenBEAM")

Since many of scripts written in Snakemake, so it is necessary to install the Snakemake package.

pip install snakemake --user

If you plan to run wrapper scripts of RIGER and RSA, you have to download and install the programs and have to specify the location and version in the wrapper scripts.

• RIGER is available to download at https://github.com/broadinstitute/rigerj.
• RSA is available to download at https://admin-ext.gnf.org/publications/RSA/.

Please use the following command if you haven't installed MAGeCK and want to run any scripts related to the method:

pip install mageck --user

In 01_gene-level-analysis/wrapper/run_RIGER.R, please change line 20 and 21 as follows:

RIGER_PATH <- "/Users/hyunhwan/Projects/InProgress/rigerj" # path of `RIGER`
RIGER_VERSION <- "2.0.2" # path of the version of `RIGER`

In 01_gene-level-analysis/wrapper/run_RSA, please change line 21 and 22 as follows:

PY3_PATH <- "/Users/hyunhwan/miniconda3/bin/python3" # path of `python3`, can lookup using `which python3`
RSA_PATH <- "/Users/hyunhwan/Projects/InProgress/RSA" # path of `RSA`
  
  
## Questions

If you have any questions or issues with the repository, please add your issue to this repository or send an email to `hyunhwaj@bcm.edu`.