update documentation

README.md

@@ -23,76 +23,10 @@ If you have a question, error, bug, or problem, please use [Github issue page](h
 - Rat: ["rn4", "rn5", "rn6"]
 - Drosophila: ["dm3", "dm6"]
 - C.elegans: ["ce6", "ce10"]
-- Arabidopsis: ["tair10"]
+- Arabidopsis: ["TAIR10"]
 - Chicken: ["galGal4", "galGal5", "galGal6"]
 
 
 ### Changelog
 
-
-
-- `0.6.5 <2021-3-25>`
-  - Minor bug fix in the installation process.
-
-- `0.6.4 <2021-2-18>`
-  - Minor change for oracle object. Metadata will be shown if you print oracle object.
-  - Add new function to oracle class.
-
-- `0.6.3 <2021-1-26>`
-  - Big fix to solve [this issue](https://github.com/morris-lab/CellOracle/issues/42).
-  - Bug fix. Anndata>=0.7.5 is required.
-
-- `0.6.2 <2020-12-16>`
-  - Big fix. h5py>=3.1.0 is required.  
-
-- `0.6.0 <2020-12-14>`
-  - Add new modules: dev_modules and analysis_helper.
-
-- `0.5.1 <2020-08-4>`
-  - Add new promoter-TSS reference data for several reference genomes; (1)"Xenopus": ["xenTro2", "xenTro3"], (2)"Rat": ["rn4", "rn5", "rn6"], (3)"Drosophila": ["dm3", "dm6"], (4)"C.elegans": ["ce6", "ce10"], (5)"Arabidopsis": ["tair10"].
-  - Add new motif data for several species: "Xenopus", "Rat", "Drosophila", "C.elegans" and "Arabidopsis".
-
-
-- `0.5.0 <2020-08-3>`
-  - Add new functions for custom motifs. You can select motifs from several options. Also, we updated our web tutorial to introduce how to load / make different motif data.
-  - Change default motifs for S.cerevisiae and zebrafish.
-  - Change requirements for dependent package: gimmemotifs and geomepy. Celloracle codes were updated to support new version of gimmemotifs (0.14.4) and genomepy (0.8.4).
-
-
-- `0.4.2 <2020-07-14>`
-  - Add promoter-TSS information for zebrafish reference genome (danRer7, danRer10 and danRer11).
-
-- `0.4.1 <2020-07-02>`
-  - Add promoter-TSS information for S.cerevisiae reference genome (sacCer2 and sacCer3).
-
-- `0.4.0 <2020-06-28>`
-  - Change requirements.
-  - From this version, pandas version 1.0.3 or later is required.
-  - From this version, scanpy version 1.5.3 or later is required.
-
-- `0.3.7 <2020-06-12>`
-  - Delete GO function from r-script
-  - Update some functions for network visualization
-
-- `0.3.6 <2020-06-08>`
-  - Fix a bug on the transition probability calculation in Markov simulation
-  - Add new function "count_cells_in_mc_results" to oracle class
-
-- `0.3.5 <2020-05-09>`
-  - Fix a bug on the function for gene cortography visualization
-  - Change some settings for installation
-  - Update data conversion module
-
-- `0.3.4 <2020-04-29>`
-  - Change pandas version restriction
-  - Fix a bug on the function for gene cortography visualization
-  - Add new functions for R-path configuration
-
-- `0.3.3 <2020-04-24>`
-  - Add promoter-TSS information for hg19 and hg38 reference genome
-
-- `0.3.1 <2020-03-23>`
-  - Fix an error when try to save file larger than 4GB file
-
-- `0.3.0 <2020-2-17>`
-  - Release beta version
+Please go to [this page](https://morris-lab.github.io/CellOracle.documentation/changelog/index.html).

docs/changelog/index.rst

@@ -4,22 +4,91 @@
 Changelog
 =========
 
+
+
+* `0.8.0 <2021-08-28>`
+ `-` Change requirements. From this version, numba>=0.50.1 is required.
+
+ `-` Update installation page in documentation.
+
+* `0.7.5 <2021-07-28>`
+ `-` Correct requirements.txt file name.
+
+* `0.7.4 <2021-07-27>`
+ `-` Update Arabidopsis promoter base GRN data.
+
+* `0.7.3 <2021-07-25>`
+ `-` Update Arabidopsis motif data.
+
+* `0.7.0 <2021-07-16>`
+ `-` Overhaul documentation.
+
+* `0.7.0 <2021-07-11>`
+ `-` Add pre-built promoter base GRNs.
+
+* `0.7.1 <2021-07-15>`
+ `-` Aad function for oracle transition probability calculation.
+
+* `0.7.0 <2021-07-11>`
+ `-` Add pre-built promoter base GRNs.
+
+* `0.6.17 <2021-07-08>`
+ `-` Add chcken and guinea pig motif
+
+ `-` Update Arabidopsis ref genome name
+
+* `0.6.12 <2021-06-11>`
+ `-` Add functions to oracle object to check current data status.
+
+* `0.6.11 <2021-06-09>`
+ `-` Add data loading function. Demo oracle data and links data can be loaded using data loadig functions.
+
+* `0.6.9 <2021-05-14>`
+ `-` Code refactoring in network visualization.
+
+* `0.6.8 <2021-05-10>`
+ `-` Update Seurat data conversion module.
+
+* `0.6.8 <2021-05-08>`
+ `-` Change requirements. From this version, numba=0.48.0  is required.
+
+* `0.6.7 <2021-05-5>`
+ `-` Add function to check status of installed dependent package version.
+
+* `0.6.5 <2021-03-25>`
+ `-` Minor bug fix in the installation process.
+
+* `0.6.4 <2021-02-18>`
+ `-` Minor change for oracle object. Metadata will be shown if you print oracle object.
+
+ `-` Add new function to oracle class.
+
+* `0.6.3 <2021-01-26>`
+ `-` Big fix to solve [this issue](https://github.com/morris-lab/CellOracle/issues/42).
+
+ `-` Bug fix. Anndata>=0.7.5 is required.
+
+* `0.6.2 <2021-12-16>`
+ `-` Big fix. h5py>=3.1.0 is required.
+
+* `0.6.0 <2021-12-14>`
+ `-` Add new modules: dev_modules and analysis_helper.
+
 * `0.5.1 <2020-08-4>`
- `-` Add new promoter-TSS reference data for several reference genomes; (1)"Xenopus": ["xenTro2", "xenTro3"],n(2)"Rat": ["rn4", "rn5", "rn6"], (3)"Drosophila": ["dm3", "dm6"], (4)"C.elegans": ["ce6", "ce10"], (5)"Arabidopsis": ["tair10"].
+ `-` Add new promoter-TSS reference data for several reference genomes; (1)"Xenopus": ["xenTro2", "xenTro3"], (2)"Rat": ["rn4", "rn5", "rn6"], (3)"Drosophila": ["dm3", "dm6"], (4)"C.elegans": ["ce6", "ce10"], (5)"Arabidopsis": ["tair10"].
 
  `-` Add new motif data for several species: "Xenopus", "Rat", "Drosophila", "C.elegans" and "Arabidopsis".
 
-
 * `0.5.0 <2020-08-3>`
- `-` Add now functions for custom motifs. You can select motifs from several options. Also, we updated our web tutorial to introduce how to load / make a different motif data.
+ `-` Add new functions for custom motifs. You can select motifs from several options. Also, we updated our web tutorial to introduce how to load / make different motif data.
 
- `-` Change default motifs for S.cerevisiae and Zebrafish.
+ `-` Change default motifs for S.cerevisiae and zebrafish.
 
  `-` Change requirements for dependent package: gimmemotifs and geomepy. Celloracle codes were updated to support new version of gimmemotifs (0.14.4) and genomepy (0.8.4).
 
 
 * `0.4.2 <2020-07-14>`
- `-` Add promoter-TSS information for Zebrafish reference genome (danRer7, danRer10 and danRer11).
+ `-` Add promoter-TSS information for zebrafish reference genome (danRer7, danRer10 and danRer11).
 
 * `0.4.1 <2020-07-02>`
  `-` Add promoter-TSS information for S.cerevisiae reference genome (sacCer2 and sacCer3).

docs/index.rst

@@ -26,6 +26,8 @@ For more information, please read our bioarxiv preprint: `CellOracle: Dissecting
 News
 ====
 
+- 8/28/2021: We updated installation page.
+
 - 7/16/2021: We overhauled our documentation and tutorial codes. Please re-download tutorial notebooks if you have old one. Also, we are updating CellOracle frequently. Please install the latest version of CellOracle if you have an old version. The latest version is 0.7.1.
 
 
@@ -71,7 +73,7 @@ Contents
 .. toctree::
 
    contact/index
-   
+
 
 Indices and tables
 ==================

docs/installation/index.rst

@@ -44,18 +44,43 @@ Python Requirements
 - Please install all dependent libraries before installing CellOracle according to the instructions below.
 - CellOracle is still a beta version and it is not available through PyPI or anaconda distribution yet. Please install CellOracle from our GitHub repository according to the instruction below.
 
+CellOracle installation using conda and pip
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-Quick CellOracle installation using pip
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-You can install CellOracle and its all dependencies by the following command.
+**1. Make a conda environment**
+  We recommend installing CellOracle in an independent conda environment to avoid dependent software conflicts.
+  Please make a new python environment for celloracle and install dependent libraries in it.
 
-::
+  ::
+
+      conda create -n celloracle_env python=3.6
+      conda activate celloracle_env
+
+  Installation of some libraries requires non-default anaconda channels. Please add the channels below. Instead, you can explicitly enter the channel when you install a library.
+
+  ::
+
+      conda config --add channels defaults
+      conda config --add channels bioconda
+      conda config --add channels conda-forge
+
+**2. Install dependencies using conda**
+
+  Run the following command to install some dependencies prior to celloracle installation.
+
+  ::
+
+      conda install pybedtools numba
+
+**3. Install CellOracle and other dependencies**
+
+  ::
 
-    pip install git+https://github.com/morris-lab/CellOracle.git
+      pip install git+https://github.com/morris-lab/CellOracle.git
 
 
 You may have an error in the installation process of CellOracle dependent libraries.
-If you have an error, please install dependent libraries stepwise.
+If you have an error, please look at the troubleshooting page.
 
 
 .. toctree::
@@ -70,6 +95,10 @@ R requirements
 CellOracle uses R libraries to calculate network graph score.
 Please install `R <https://www.r-project.org>`_ (>=3.5) and R libraries below.
 
+.. note::
+   These R libraries are needed for network analysis.
+   CellOracle gene perturbation simulation does not require the R libraries.
+   **You can skip R library installation if you do not perform network analysis.**
 
 .. code-block:: r
 

docs/installation/python_step_by_step_installation.rst

@@ -3,37 +3,14 @@
 Python dependent library installation troubleshooting
 =====================================================
 
-0. (Optional) Make a new conda environment
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-This step is optional, but we recommend installing CellOracle in an independent conda environment to avoid dependent software conflicts.
-Please make a new python environment for celloracle and install dependent libraries in it.
-
-::
-
-    conda create -n celloracle_env python=3.6
-    conda activate celloracle_env
-
-
-
-1. Add conda channels
-^^^^^^^^^^^^^^^^^^^^^
-Installation of some libraries requires non-default anaconda channels. Please add the channels below. Instead, you can explicitly enter the channel when you install a library.
-
-::
-
-    conda config --add channels defaults
-    conda config --add channels bioconda
-    conda config --add channels conda-forge
-
-
-2. Install `velocyto <http://velocyto.org/velocyto.py/install/index.html>`_
+Install `velocyto <http://velocyto.org/velocyto.py/install/index.html>`_
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-Please install velocyto with the following commands or `the author's instruction <http://velocyto.org/velocyto.py/install/index.html>`_ .
+If you failed CellOracle installation because of velocyto installation error, please try to install velocyto with the following commands or `the author's instruction <http://velocyto.org/velocyto.py/install/index.html>`_ .
 
 ::
 
-    conda install numpy scipy cython numba matplotlib scikit-learn h5py>=3.1.0 click pysam llvm louvain
+    conda install numpy scipy cython numba matplotlib scikit-learn h5py click pysam llvm louvain
 
 Then
 
@@ -50,27 +27,29 @@ You may find the solution with these links below.
 - `Solution 3 <https://github.com/morris-lab/CellOracle/issues/3>`_. This is the solution reported by a CellOracle user. Thank you very much!
 - `Other solutions on Velocyto GitHub issue page <https://github.com/velocyto-team/velocyto.py/issues?q=>`_
 
-3. Install `scanpy <https://scanpy.readthedocs.io/en/stable/installation.html>`_
+Install `scanpy <https://scanpy.readthedocs.io/en/stable/installation.html>`_
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-Please install scanpy with the following commands or `the author's instruction <https://scanpy.readthedocs.io/en/stable/installation.html>`_ .
+If you failed CellOracle installation because of scanpy installation error, please try to install scanpy with the following commands or `the author's instruction <https://scanpy.readthedocs.io/en/stable/installation.html>`_ .
 
 ::
 
     conda install scanpy
 
 
 
-4. Install other python libraries
+Install other python libraries
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-Please install other python libraries below with the following commands.
+Please install other python libraries below using conda prior to celloracle installation. It might solve some installation errors.
 
 ::
 
     conda install goatools pyarrow tqdm joblib jupyter gimmemotifs==0.14.4 genomepy==0.8.4
 
 
-5. install celloracle
-^^^^^^^^^^^^^^^^^^^^^
+Install celloracle
+^^^^^^^^^^^^^^^^^^
+After installing the dependent libraries above, please install CellOracle again.
+
 ::
 
     pip install git+https://github.com/morris-lab/CellOracle.git