MAGeCK Files

For a stable version of MAGeCK, please visit:

https://sourceforge.net/projects/mageck/

The doc/ folder includes the documentation of the software. For the latest MAGeCK documentation, please visit:

http://mageck.sourceforge.net

Version history

Version 0.4.4
*Improve the running speed of the RRA program.
*For gene testing, MAGeCK now accepts multiple -t and -c pairs, allowing generating one summary table containing results of multiple comparisons. (However, the integration with pathway analysis is not fully supported.)
*Modify the format of gene_summary.txt; the duplicated "item" column is now removed for positive selection results. Also, two more columns are added to better help users identify true hits: "lo": the RRA lo values; "goodsgrna": the number of sgRNAs in this gene whose ranking is higher than the alpha threshold. 
*MAGeCK now allows users specifying a set of control sgRNAs to generate null distributions.
*Fix two bugs in calculating the median factor during normalization (thanks to Bastiaan Evers).
*Add the "-v/--version" command.

Version 0.4.3
*Fix a bug where the program exits unexpectedly for certain samples with many 0 read counts.
*Fix a bug of pathway analysis where the RRA program stops early for certain gene belonging to too many pathways.

Version 0.4.2
*Create youtube tutorial videos for installation and sample comparisons.
*Improve the median normalization method to handle cases with many zero-count sgRNAs.
*The median normalized read count are provided in the count command.
*Modify the count command line options to accept combining reads from technical replicates.
*Provide simple statistics for processing fastq files.
*Provide library file for Synergistic Activation Mediators (SAM), a CRISPR activation protocol developed in Feng Zhang laboratory (http://www.addgene.org/crispr/libraries/sam/).

Version 0.4.1
*Increase the default alpha cutoff from 0.05 to 0.25.
*Provide some of the commonly used library files for the convenience of users.

Version 0.4
*Added the BSD license information.
*Improved the logging system.
*The control_id and treatment_id options now can be specified using sample strings.
*Merge positive selection and negative selection genes and pathways into one file.
*Add the --keep-tmp option to control intermediate files after running.
*Fixed one bug in FDR calculation.

2014.07.01 Version 0.3
*The installation method is changed so users can now more easily install the software.
*Added a new feature to detect enriched pathways (pathway command)
*Changed the input format of the program:
   The second column of the count table (generated by the count subcommand and used by the test subcommand) is now the gene name.
   For the count subcommand, the sgRNA information is provided with the library file.

2014.04.17 Version 0.2
Updated the demo and wiki page

2014.04.04 Version 0.1
The source code released.