add intro

pinellolab · Mar 30, 2024 · 4bb61aa · 4bb61aa
1 parent c3cee14
commit 4bb61aa
Show file tree

Hide file tree

Showing 14 changed files with 21 additions and 15 deletions.
diff --git a/README.md b/README.md
@@ -1,13 +1,13 @@
-# <img src="imgs/bean_title2.svg" alt="crispr-bean" height="50"/>
+# <img src="docs/assets/bean_title2.svg" alt="crispr-bean" height="50"/>
 
 [![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. 
 
 
-<img src="docs/assets/summary.svg" alt="Reporter construct" width="700"/>
+<img src="docs/assets/summary.png" alt="Reporter construct" width="700"/>
 
 ## 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -1,4 +1,4 @@
 .. _input:
 Input file format
 ***********************
-.. mdinclude:: input.md
+.. mdinclude:: _input.md
diff --git 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
@@ -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
@@ -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
@@ -1,3 +1,3 @@
 ReporterScreen object
 ***********************
-.. mdinclude:: reporterscreen.md
+.. mdinclude:: _reporterscreen.md
diff --git a/docs/run.rst b/docs/run.rst
@@ -1,7 +1,7 @@
 .. _run:
 `bean run`
 ***********************
-.. mdinclude:: run.md
+.. mdinclude:: _run.md
 
 Full parameters
 ==================