From cfa28854663ba335621a99d52ca2467153130dc7 Mon Sep 17 00:00:00 2001 From: Jayoung Kim Ryu Date: Mon, 28 Aug 2023 22:40:37 -0400 Subject: [PATCH] Update README.md --- README.md | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 9e66afb..1c11fcf 100644 --- a/README.md +++ b/README.md @@ -25,7 +25,6 @@ Then download from PyPI: ``` pip install crispr-bean[model] ``` -**(takes 14.4 mins after pytorch installation with pytorch in Dell XPS 13 Ubuntu WSL.)* ### Mapping and data wrangling, without variant effect quantification ``` @@ -138,6 +137,7 @@ If you want to obtain amino acid level variant ``` bean-run variant[tiling] my_sorting_screen_masked.h5ad --scale-by-acc --acc-bw-path accessibility_signal.bw -o output_prefix/ --fit-negctrl ``` + ### Output Above command produces * `output_prefix/bean_element_result.[model_type].csv` with following columns: @@ -182,5 +182,8 @@ When negative control is provided, above columns with `_adj` suffix are provided import crispr_bean as be cdata = be.read_h5ad("bean_counts_sample.h5ad") ``` - See the [**ReporterScreen API tutorial**](docs/ReporterScreen_api.ipynb) for more detail. + +## Run time +* Installation takes 14.4 mins after pytorch installation with pytorch in Dell XPS 13 Ubuntu WSL. +* Full pipeline takes 90.1s in GitHub Action for toy dataset of 2 replicates and 30 guides.