Getting started¶

Install¶

The package is not on PyPI yet. Install it from GitHub; pip brings numpy, pandas and pysam along:

pip install "crispr-analysis-utils @ git+https://github.com/EngreitzLab/crispr-analysis-utils"

Aligning guides also needs the GEM3 aligner, which pip cannot install. To get it, or to work on the package, clone the repository and use pixi: one environment holds the package, pysam and GEM3, on Linux (x86-64) and macOS. bioconda builds GEM3 for x86-64 only, so on Apple silicon pixi installs that environment as an Intel macOS (osx-64) one, which runs under Rosetta 2 (softwareupdate --install-rosetta installs it):

git clone https://github.com/EngreitzLab/crispr-analysis-utils.git
cd crispr-analysis-utils
pixi install         # the package, pysam and GEM3
pixi install -e dev  # the same, plus the development tools

Use¶

import pandas as pd

import crispr_analysis_utils as cau

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

Module	What it does
`cau.accession`	Accession ids for SpCas9 guides, encoded from the guide's own sequence
`cau.counts_per_million`	Counts-per-million normalization of count matrices
`cau.guide_alignment`	Where a guide library maps: each guide's exact sites, class, coordinates and target site (also the `cau guide-alignment` command)
`cau.guide_annotation`	What those sites hit: genic or intergenic, exon or intron, every promoter they sit in, the gene and transcript, and the distances to the nearest TSS and the gene's 5' end (also the `cau guide-annotation` command)
`cau.element_mapping`	Which element of a screen each guide tests, and which guides are controls (also the `cau element-mapping` command)
`cau.igvf_export`	The guide design in the IGVF per-guide metadata format, ready to submit or to feed the CRISPR pipeline (also the `cau igvf-export` command)
`cau.mudata_builder`	A sequenced channel's gene and guide counts as one MuData, annotated and laid out like the IGVF pipeline's object (also the `cau mudata-builder` command)

The cau command line tool comes with the package:

cau --help