The misha package is a toolkit for analysis of genomic data. it implements an efficient data structure for storing genomic data, and provides a set of functions for data extraction, manipulation and analysis.
Installation
You can install the released version of misha from CRAN with:
install.packages("misha")And the development version from GitHub with:
remotes::install_github("tanaylab/misha")Usage
See the Genomes vignette for instructions on how to create a misha database for common genomes.
See the user manual for more usage details.
Running scripts from old versions of misha (< 4.2.0)
Starting in misha 4.2.0, the package no longer stores global variables such as ALLGENOME or GROOT. Instead, these variables are stored in a special environment called .misha. This means that scripts written for older versions of misha will no longer work. To run such scripts, either add a prefix of .misha$ to all those variables (.misha$ALLGENOME instead of ALLGENOME), or run the following command before running the script:
ALLGENOME <<- .misha$ALLGENOME
GROOT <<- .misha$GROOT
ALLGENOME <<- .misha$ALLGENOME
GINTERVID <<- .misha$GINTERVID
GITERATOR.INTERVALS <<- .misha$GITERATOR.INTERVALS
GROOT <<- .misha$GROOT
GWD <<- .misha$GWD
GTRACKS <<- .misha$GTRACKS