Exploratory data analysis for pooled CRISPR/Cas9 screens
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Latest commit 233360f Apr 5, 2016 @jwinter6 jwinter6 Update Readme.Rmd

Readme.Rmd

caRpools - a software package for the analysis CRISPR/Cas9 pooled screens

Register for Beta of caRpoolsInteractive

Anyone interested in the new, browser-based caRpoolsInteractive can drop me an email at jan.winter@dkfz-heidelberg.de and I will come back to you once we release the beta. No software installation will be necessary.

Issues

If you have issues or problems PLEASE us the ISSUES page.

Attention: Due to the downtime of the community-server of biomaRt, caRpools 0.82.5 does not function properly. Use 0.83 that uses by default the Ensembl servers for data annotation.

Additional Information

Dear users, the latest CRAN version is not compatible with the virtual machine due to rJava issues. I am right now working on a new version without any java dependencies and will release it for alpha/beta testing via the releases channel. In case you are interested in beta testing the new caRpools version, please send me an email (jan.winter@dkfz.de) so that I know who is using it and provide further support. In general, the beta release will be avaible for everyone.

Once the manual and vignette is updated for the new, far advanced version, it will be released on CRAN.

Description

CaRpools is an R package forexploratory data analysis of pooled CRISPR/Cas9 screens. It aims to provide a user-friendly pipeline for end-to-end analysis of screening data. As an output, it generates standardized PDF and HTML reports that include:

  • In-depth analysis of screening quality
  • Candidate hit calling using multiple, independent algorithms
  • In-depth analysis of sgRNA phenotypes
  • XLS output for storage and follow-up analysis
  • Annotation of candidate genes using biomaRt

Users fill out a configuration file and caRpools runs a complete analysis workflow, including NGS data extraction and mapping.

Download the VirtualBox appliance of caRpools

The VirtualBox appliance can be downloaded from HERE

It provides you a ready-to-use virtual appliance, so that you do not need to install any additional R packages or tools.

Download R package

You can download the R package either

  • within R via install.packages("caRpools")
  • or as a .tgz file directly from HERE

Manuals

Tip for Mac Users

If you can't get RStudio to call system commands, you need to start Rstudio from command line.
In order to allow RStudio to start system commands, please start RStudio via the terminal by typing:

open -a rstudio

Contact

Jan Winter (jan.winter@dkfz.de) Web http://www.dkfz-heidelberg.de/en/signaling

Reference

Winter, J., Breinig, M., Heigwer, F., Brueggemann, D., Leible, S., Pelz, O., Zhan, T., Boutros, M. (2015) caRpools: An R package for exploratory data analysis and documentation of pooled CRISPR/Cas9 screens. Bioinformatics

Changelog

1.0.241 ALPHA RELEASE

  • major overhaul to underlying R code
  • new MIACCS file structure with easier use
  • multiple replicates possible with automatic detection
  • comparing groups made straight-forward
  • more to follow...
  • ALPHA VERSION, if issues occur, please tell me! NO DOCUMENTATION SO FAR.

0.83 (latest CRAN)

  • changed data annotation to use Ensembl server for biomaRt - please see the changes in the miaccs file for "database"
  • updated Manual and Rd file

0.82.5

  • updated R documentation
  • improved speed

0.82.4

  • updated R documentation
  • modified carpools.read.count.vs for automatic replicate detection
  • modified package to allow usage of more than two replicates
  • fixed bugs
  • improved speed

0.82.3

  • updated R documentation

0.82.2

  • made biomaRt annotation faster (get.gene.info)
  • added additional sgRNA dropout information in Rmd templates
  • made compare.analysis faster
  • removed unnecessary code

0.82

  • fixed naming issues in perl files CRISPR-mapping.pl and CRISPR-extract.pl
  • fixed rare naming glitch in biomaRt annotation
  • streamlined code