Adds to Documentation

docs/citation/index.rst

@@ -6,10 +6,12 @@ Authors and citations
 Cite orthomap
 -------------
 
-If you use orthomap please cite:
+If you use orthomap please cite::
 
-orthomap software development
------------------------------
+    Kristian Ullrich, Nikoleta E. Glynatsi, orthomap, (2019), GitHub repository,
+
+Development team
+-----------------
 
 orthomap is developed and maintained by `Kristian Ullrich <https://orcid.org/0000-0003-4308-9626>`_.
 Please post troubles or questions on `the Github repository <https://github.com/kullrich/orthomap/issues>`_.

docs/contact/index.rst

@@ -3,8 +3,8 @@
 Contact
 =======
 
-orthomap code issues
---------------------
+Opening issues
+---------------
 
 Please post troubles or questions on `the Github repository issue page <https://github.com/kullrich/orthomap/issues>`_.
 Also, please look at `the closed issue pages <https://github.com/kullrich/orthomap/issues?q=is%3Aissue+is%3Aclosed>`_. This might give an answer to your question.

docs/installation/index.rst

@@ -10,14 +10,15 @@ Please follow the guide below to install orthomap and its dependent software.
 Docker image
 ------------
 
-- Pre-built docker image is available through `Docker Hub <https://hub.docker.com/repository/docker/kkuweb/orthomap_ubuntu>`_ .
-
+Pre-built docker image is available through `Docker Hub <https://hub.docker.com/repository/docker/kkuweb/orthomap_ubuntu>`_ .
 ::
 
     docker pull kkuweb/orthomap_ubuntu:latest
 
 - This docker image was built based on Ubuntu 22.04.
+
 - Python dependent packages and orthomap are installed in an anaconda environment, `orthomap_env`. This environment will be activated automatically when you log in.
+
 - See additional information
 
 .. toctree::
@@ -49,7 +50,7 @@ Install orthomap
 Python Requirements
 ^^^^^^^^^^^^^^^^^^^
 
-- orthomap was developed using python 3.8. We do not support python 2.7x or python <=3.7.
+- orthomap was developed using Python `3.8`. We do not support Python `2.7x` or Python `<=3.7`.
 
 orthomap installation using conda and pip
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -59,7 +60,7 @@ orthomap installation using conda and pip
 
   The environment is created with `conda create` in which orthomap is installed.
 
-  If you do not have a working installation of Python 3.8 (or later), consider
+  If you do not have a working installation of Python `3.8` (or later), consider
   installing `Anaconda <https://docs.anaconda.com/anaconda/install/>`_ or `Miniconda <https://docs.conda.io/en/latest/miniconda.html>`_. Then run:
 
   ::

docs/license/index.rst

@@ -3,8 +3,6 @@
 License
 =======
 
-GNU GENERAL PUBLIC LICENSE::
-
 GNU GENERAL PUBLIC LICENSE
 Version 3, 29 June 2007
 

docs/notebooks/nematode_example.ipynb

@@ -246,7 +246,7 @@
     "\n",
     "`datasets.sun21_orthomap(datapath='data')` (download folder set to `'data'`).\n",
     "\n",
-    "The pre-calculated orthomap can be imported from the `orthomap2tei` submodule with the `orthomap2tei.read_orthomap()` function as follwos:"
+    "The pre-calculated orthomap can be imported from the `orthomap2tei` submodule with the `orthomap2tei.read_orthomap()` function as follows:"
    ]
   },
   {

docs/tutorials/geneset_overlap.rst

@@ -1,7 +1,15 @@
 .. _geneset_overlap:
 
-step 3
-======
+
+step 3 - map gene/transcript IDs
+================================
+
+To be able to link gene ages assignments from an orthomap and gene or transcript
+of scRNA dataset, one needs to check the overlap of the annotated gene names.
+
+With the `gtf2t2g` submodule of `orthomap` and the `gtf2t2g.parse_gtf()`
+function, one can extract gene and transcript names from a given gene feature
+file.
 
 How to match gene or transcript IDs between an orthomap and scRNA data
-----------------------------------------------------------------------
+----------------------------------------------------------------------

docs/tutorials/get_orthomap.rst

@@ -1,7 +1,7 @@
 .. _get_orthomap:
 
-step 2
-======
+step 2 - gene age class assignment
+==================================
 
 How to extract an orthomap (gene age class) from OrthoFinder results
---------------------------------------------------------------------
+--------------------------------------------------------------------