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CRISPR Analysis Utils

Documentation: https://engreitzlab.github.io/crispr-analysis-utils/

Utilities and reusable scripts for CRISPR screen analysis, preprocessing, plotting, and downstream workflows.

This repository is set up as a small two-language package:

  • Python package: crispr_analysis_utils
  • R package: crisprAnalysisUtils

The goal is that collaborators can clone the repository, install the functions locally, and read rendered examples/API documentation on GitHub Pages.

Install

From a local clone:

git clone https://github.com/EngreitzLab/crispr-analysis-utils.git
cd crispr-analysis-utils
python -m pip install -e .
install.packages("remotes")
remotes::install_github("EngreitzLab/crispr-analysis-utils")

For Python plotting helpers, install the optional plotting dependencies:

python -m pip install -e ".[plots]"

Use

Python:

import pandas as pd
from crispr_analysis_utils import counts_per_million

counts = pd.DataFrame(
    {"sample_a": [100, 300], "sample_b": [50, 50]},
    index=["guide_1", "guide_2"],
)

cpm = counts_per_million(counts)

R:

library(crisprAnalysisUtils)

counts <- matrix(
  c(100, 300, 50, 50),
  nrow = 2,
  dimnames = list(c("guide_1", "guide_2"), c("sample_a", "sample_b"))
)

cpm <- counts_per_million(counts)

Documentation

Python functions are documented from docstrings with MkDocs and mkdocstrings. R functions are documented from roxygen comments with pkgdown.

Build the combined documentation site locally with:

python -m pip install -e ".[docs]"
mkdocs build --strict --site-dir site
Rscript -e 'roxygen2::roxygenise(); pkgdown::build_site(new_process = FALSE, override = list(destination = "site/r"))'

GitHub Pages is configured through .github/workflows/docs.yml. In the GitHub repository settings, set Pages to deploy from GitHub Actions.

Repository layout 

src/crispr_analysis_utils/  Python package
R/                         R package functions
docs/                      MkDocs source pages
tests/                     Python and R tests
.github/workflows/         GitHub Actions workflows

Development

Install pre-commit hooks:

python -m pip install pre-commit
pre-commit install
pre-commit run --all-files

Run Python tests:

python -m pip install -e ".[dev]"
python -m pytest

Run R tests:

testthat::test_local(load_package = "source")