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.
You can install the released version of misha from CRAN with:
install.packages("misha")Or from conda:
conda install -c aviezerl r-mishaAnd the development version from GitHub with:
remotes::install_github("tanaylab/misha")The package ships a small example database, so there is nothing to download before the first query:
library(misha)
gdb.init_examples() # a tiny example genome, unpacked into tempdir()
gtrack.ls() # what is in it
#> [1] "array_track" "dense_track" "rects_track"
#> [4] "sparse_track" "subdir.dense_track2"
gextract("dense_track", gintervals(1, 0, 500), iterator = 100) # signal in 100 bp bins
#> chrom start end dense_track intervalID
#> 1 chr1 0 100 0.1688889 1
#> 2 chr1 100 200 0.1700000 1
#> 3 chr1 200 300 0.1800000 1
#> 4 chr1 300 400 0.1600000 1
#> 5 chr1 400 500 0.1100000 1
head(gscreen("dense_track > 0.2", gintervals(1, 0, 50000), iterator = 100)) # bins above a threshold
#> chrom start end
#> 1 chr1 17200 17300
#> 2 chr1 20000 20100
#> 3 chr1 23300 23400
#> 4 chr1 26200 26300
#> 5 chr1 32600 32800
#> 6 chr1 32900 33000Every misha analysis is that shape: a scope (where to look), an iterator (in what chunks), and a track expression evaluated over it.
Start with the Misha Basics short guide.
See the Genomes vignette for instructions on how to create a misha database for common genomes.
See the user manual for more usage details.
Drop-in prompt (no clone needed). Paste the block below into your agent at the start of a misha task. It points the agent at the raw files on GitHub, so it works without a local checkout:
Before writing any misha code, fetch and read:
- https://raw.githubusercontent.com/tanaylab/misha/master/agent-guides/misha-core.md (mandatory: concepts + everyday recipes)
- https://raw.githubusercontent.com/tanaylab/misha/master/agent-guides/misha-anti-patterns.md (silent footguns; cross-referenced from core)
- https://raw.githubusercontent.com/tanaylab/misha/master/agent-guides/misha-advanced.md (consult on demand: 2D / Hi-C, PWM, import/export, new genomes)
Follow the conventions in those files. When you hit a recipe with an "Avoid:" block, treat it as a hard rule.For agents (Claude Code, Copilot, Cursor, etc.) writing misha analysis code in a downstream project, point them at the maintained agent guides in this repo:
agent-guides/misha-core.md
- concepts, bootstrap, and the everyday recipes (intervals, annotation,
distance, extract, vtracks, gscreen, gdist, gtrack.create). Start
here.agent-guides/misha-advanced.md
- 2D / Hi-C pile-ups, insulation, sequence and PWM tracks, bulk
import/export, new genomes and cross-species.agent-guides/misha-anti-patterns.md
- silent footguns referenced inline from the above.agent-guides/skills/
- deep playbooks for specific tasks. Currently: importing-tracks
(format chooser across all gtrack.*import* variants +
pre/post-import validation). Load when the task specifically calls for
one of these.The core guide is ~4k words and targets a system-prompt-sized
context. For Claude Code-style setups, dropping
misha-core.md (or all three) into the project’s
CLAUDE.md / AGENTS.md is the intended use.
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