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Update README.md with installation speed
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jykr authored Aug 22, 2023
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Expand Up @@ -12,11 +12,11 @@ This is an analysis toolkit for the pooled CRISPR reporter or sensor data. The r

## Overview
`crispr-bean` supports the following functionalities.
* [`bean-count`, `bean-count-sample`](#count-reporter-screen-data): Base-editing-aware mapping of guide, optionally with reporter from `.fastq` files.
* [`bean-qc`](#bean-qc-qc-of-reporter-screen-data): Quality control report and filtering out / masking of aberrant sample and guides
* [`bean-filter`](#bean-filter-filtering-and-optionally-translating-alleles): Filter reporter alleles
* [`bean-run`](#bean-run-quantify-variant-effects): Quantify targeted variants' effect sizes from screen data.

* 1. [`bean-count`, `bean-count-sample`](#count-reporter-screen-data): Base-editing-aware mapping of guide, optionally with reporter from `.fastq` files.
* 2. [`bean-qc`](#bean-qc-qc-of-reporter-screen-data): Quality control report and filtering out / masking of aberrant sample and guides
* 3. [`bean-filter`](#bean-filter-filtering-and-optionally-translating-alleles): Filter reporter alleles
* 4. [`bean-run`](#bean-run-quantify-variant-effects): Quantify targeted variants' effect sizes from screen data.
We provide example

## Installation
### Full installation
Expand All @@ -25,6 +25,8 @@ Then download from PyPI:
```
pip install crispr-bean[model]
```
This takes 26.3 mins to install from scratch, 14.4 mins with pytorch in Dell XPS 13 Ubuntu WSL.

### Mapping and data wrangling, without variant effect quantification
```
pip install crispr-bean
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