From 4bb61aacb34a51e53bfb4097a3780c9ce6fc7fc1 Mon Sep 17 00:00:00 2001 From: jykr Date: Sat, 30 Mar 2024 12:01:12 -0400 Subject: [PATCH] add intro --- README.md | 6 +++--- docs/cds.rst | 2 +- docs/count.rst | 2 +- docs/count_samples.rst | 2 +- docs/create_screen.rst | 2 +- docs/filter.rst | 2 +- docs/gwas.rst | 2 +- docs/index.rst | 6 ++++++ docs/input.rst | 2 +- docs/profile.rst | 2 +- docs/prolif_gwas.rst | 2 +- docs/qc.rst | 2 +- docs/reporterscreen.rst | 2 +- docs/run.rst | 2 +- 14 files changed, 21 insertions(+), 15 deletions(-) diff --git a/README.md b/README.md index a451910..5ad9a83 100755 --- a/README.md +++ b/README.md @@ -1,13 +1,13 @@ -# crispr-bean +# crispr-bean [![PyPI pyversions](https://img.shields.io/pypi/pyversions/crispr-bean)](https://pypi.org/project/crispr-bean/) [![PyPI version](https://img.shields.io/pypi/v/crispr-bean)](https://pypi.org/project/crispr-bean/) [![Code style](https://img.shields.io/badge/code%20style-black-black)](https://github.com/psf/black) -`bean` (**B**ase **E**diting reporter screens with guide **A**ctivity **N**ormalization) is an analysis toolkit for the pooled CRISPR reporter or sensor data. The reporter technique transfects cells with plasmid with not only sgRNA but with the **target sequence surrogate** which we call **reporter** or **sensor**. +`bean` unconfounds variant effect of CRISPR reporter screens by considering genotypic outcome from *reporter* sequence. -Reporter construct +Reporter construct ## Overview `bean` supports end-to-end analysis of pooled sorting screens, with or without reporter. diff --git a/docs/cds.rst b/docs/cds.rst index c566387..dc4ea75 100755 --- a/docs/cds.rst +++ b/docs/cds.rst @@ -1,5 +1,5 @@ Coding sequence tiling library *********************** -.. mdinclude:: ldl_cds.md +.. mdinclude:: _ldl_cds.md See :ref:`subcommands` for the full details. diff --git a/docs/count.rst b/docs/count.rst index fdbe236..9a186dc 100755 --- a/docs/count.rst +++ b/docs/count.rst @@ -1,6 +1,6 @@ `bean count` *********************** -.. mdinclude:: count.md +.. mdinclude:: _count.md Full parameters ================== diff --git a/docs/count_samples.rst b/docs/count_samples.rst index fbbf8f1..db89732 100755 --- a/docs/count_samples.rst +++ b/docs/count_samples.rst @@ -1,7 +1,7 @@ .. _count_samples: `bean count-samples` *********************** -.. mdinclude:: commands/count.md +.. mdinclude:: _count.md Full parameters ================== diff --git a/docs/create_screen.rst b/docs/create_screen.rst index ee36bfc..485ee04 100755 --- a/docs/create_screen.rst +++ b/docs/create_screen.rst @@ -1,6 +1,6 @@ `bean create-screen` *********************** -.. mdinclude:: create-screen.md +.. mdinclude:: _create-screen.md Full parameters ================== diff --git a/docs/filter.rst b/docs/filter.rst index e0450cf..3b10bc4 100755 --- a/docs/filter.rst +++ b/docs/filter.rst @@ -1,7 +1,7 @@ .. _filter: `bean filter` *********************** -.. mdinclude:: filter.md +.. mdinclude:: _filter.md Full parameters ================== diff --git a/docs/gwas.rst b/docs/gwas.rst index 09d76fa..31e8c68 100755 --- a/docs/gwas.rst +++ b/docs/gwas.rst @@ -1,5 +1,5 @@ GWAS variant library *********************** -.. mdinclude:: ldl_var.md +.. mdinclude:: _ldl_var.md See :ref:`subcommands` for the full details. diff --git a/docs/index.rst b/docs/index.rst index 8ef251d..14287f9 100755 --- a/docs/index.rst +++ b/docs/index.rst @@ -5,6 +5,12 @@ Welcome to `bean`'s documentation! ================================ +`bean` unconfounds variant effect of CRISPR reporter screens by considering genotypic outcome from *reporter* sequence. + +.. image:: assets/summary.png + :width: 700 + :alt: BEAN schematic + =================== Workflows =================== diff --git a/docs/input.rst b/docs/input.rst index d018e97..79285ff 100755 --- a/docs/input.rst +++ b/docs/input.rst @@ -1,4 +1,4 @@ .. _input: Input file format *********************** -.. mdinclude:: input.md \ No newline at end of file +.. mdinclude:: _input.md \ No newline at end of file diff --git a/docs/profile.rst b/docs/profile.rst index 7316d9e..c25a422 100755 --- a/docs/profile.rst +++ b/docs/profile.rst @@ -1,6 +1,6 @@ `bean profile` *********************** -.. mdinclude:: profile.md +.. mdinclude:: _profile.md Full parameters ================== diff --git a/docs/prolif_gwas.rst b/docs/prolif_gwas.rst index 34adb83..26bdbe6 100644 --- a/docs/prolif_gwas.rst +++ b/docs/prolif_gwas.rst @@ -1,5 +1,5 @@ Proliferation screen with GWAS library ********************************************** -.. mdinclude:: profile_gwas.md +.. mdinclude:: _profile_gwas.md See :ref:`subcommands` for the full details. diff --git a/docs/qc.rst b/docs/qc.rst index 8cb0c7a..bd233cf 100755 --- a/docs/qc.rst +++ b/docs/qc.rst @@ -1,7 +1,7 @@ .. _qc: `bean qc` *********************** -.. mdinclude:: qc.md +.. mdinclude:: _qc.md Full parameters ================== diff --git a/docs/reporterscreen.rst b/docs/reporterscreen.rst index dcd0a00..687a31b 100644 --- a/docs/reporterscreen.rst +++ b/docs/reporterscreen.rst @@ -1,3 +1,3 @@ ReporterScreen object *********************** -.. mdinclude:: reporterscreen.md +.. mdinclude:: _reporterscreen.md diff --git a/docs/run.rst b/docs/run.rst index 8378dbe..db09224 100755 --- a/docs/run.rst +++ b/docs/run.rst @@ -1,7 +1,7 @@ .. _run: `bean run` *********************** -.. mdinclude:: run.md +.. mdinclude:: _run.md Full parameters ==================