diff --git a/.buildinfo b/.buildinfo index 381a1c3..40cfb8a 100644 --- a/.buildinfo +++ b/.buildinfo @@ -1,4 +1,4 @@ # Sphinx build info version 1 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done. -config: cc58d845cfaa992b2416162d1b1281e5 +config: 55b60ac254bb232864915e417b1f8d37 tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/.doctrees/environment.pickle b/.doctrees/environment.pickle index 2cd1e6c..8a6ccfe 100644 Binary files a/.doctrees/environment.pickle and b/.doctrees/environment.pickle differ diff --git a/.doctrees/installation/index.doctree b/.doctrees/installation/index.doctree index dea947a..ba3d68c 100644 Binary files a/.doctrees/installation/index.doctree and b/.doctrees/installation/index.doctree differ diff --git a/.doctrees/notebooks/02_motif_scan/02_atac_peaks_to_TFinfo_with_celloracle_20200801.doctree b/.doctrees/notebooks/02_motif_scan/02_atac_peaks_to_TFinfo_with_celloracle_20200801.doctree index 6d26090..4435f59 100644 Binary files a/.doctrees/notebooks/02_motif_scan/02_atac_peaks_to_TFinfo_with_celloracle_20200801.doctree and b/.doctrees/notebooks/02_motif_scan/02_atac_peaks_to_TFinfo_with_celloracle_20200801.doctree differ diff --git a/.doctrees/notebooks/05_simulation/Gata1_KO_simulation_with_Paul_etal_2015_data.doctree b/.doctrees/notebooks/05_simulation/Gata1_KO_simulation_with_Paul_etal_2015_data.doctree index 464ec27..50a9e80 100644 Binary files a/.doctrees/notebooks/05_simulation/Gata1_KO_simulation_with_Paul_etal_2015_data.doctree and b/.doctrees/notebooks/05_simulation/Gata1_KO_simulation_with_Paul_etal_2015_data.doctree differ diff --git a/.doctrees/notebooks/05_simulation/Pseudotime_calculation_with_Paul_etal_2015_data.doctree b/.doctrees/notebooks/05_simulation/Pseudotime_calculation_with_Paul_etal_2015_data.doctree index 2f197af..33d8951 100644 Binary files a/.doctrees/notebooks/05_simulation/Pseudotime_calculation_with_Paul_etal_2015_data.doctree and b/.doctrees/notebooks/05_simulation/Pseudotime_calculation_with_Paul_etal_2015_data.doctree differ diff --git a/_sources/installation/index.rst.txt b/_sources/installation/index.rst.txt index 9dde15c..7ca9aee 100644 --- a/_sources/installation/index.rst.txt +++ b/_sources/installation/index.rst.txt @@ -14,10 +14,10 @@ Docker image :: - docker pull kenjikamimoto126/celloracle_ubuntu:0.12.0 + docker pull kenjikamimoto126/celloracle_ubuntu:0.18.0 -- This docker image was built based on Ubuntu 20.04. +- This docker image was built based on Ubuntu 20.04 and python 3.10. - Python dependent packages and celloracle are installed in an anaconda environment, celloracle_env. This environment will be activated automatically when you log in. .. toctree:: diff --git a/_static/documentation_options.js b/_static/documentation_options.js index e247372..0781b64 100644 --- a/_static/documentation_options.js +++ b/_static/documentation_options.js @@ -1,6 +1,6 @@ var DOCUMENTATION_OPTIONS = { URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'), - VERSION: '0.17.1', + VERSION: '0.18.0', LANGUAGE: 'None', COLLAPSE_INDEX: false, BUILDER: 'html', diff --git a/changelog/index.html b/changelog/index.html index f84818a..a20978e 100644 --- a/changelog/index.html +++ b/changelog/index.html @@ -19,7 +19,7 @@ - Changelog — celloracle 0.17.1 documentation + Changelog — celloracle 0.18.0 documentation diff --git a/citation/index.html b/citation/index.html index 4d8ecf8..1fdf668 100644 --- a/citation/index.html +++ b/citation/index.html @@ -19,7 +19,7 @@ - Authors and citations — celloracle 0.17.1 documentation + Authors and citations — celloracle 0.18.0 documentation diff --git a/contact/index.html b/contact/index.html index 5be596b..491c03f 100644 --- a/contact/index.html +++ b/contact/index.html @@ -19,7 +19,7 @@ - Contact — celloracle 0.17.1 documentation + Contact — celloracle 0.18.0 documentation diff --git a/genindex.html b/genindex.html index 105960b..76fdf15 100644 --- a/genindex.html +++ b/genindex.html @@ -18,7 +18,7 @@ - Index — celloracle 0.17.1 documentation + Index — celloracle 0.18.0 documentation diff --git a/google_colab/index.html b/google_colab/index.html index 14f8c21..bdeab5c 100644 --- a/google_colab/index.html +++ b/google_colab/index.html @@ -19,7 +19,7 @@ - Google Colaboratoly — celloracle 0.17.1 documentation + Google Colaboratoly — celloracle 0.18.0 documentation diff --git a/index.html b/index.html index c526400..da998d1 100644 --- a/index.html +++ b/index.html @@ -19,7 +19,7 @@ - Welcome to CellOracle’s documentation! — celloracle 0.17.1 documentation + Welcome to CellOracle’s documentation! — celloracle 0.18.0 documentation diff --git a/installation/R_step_by_step_installation.html b/installation/R_step_by_step_installation.html index a686b59..e2adade 100644 --- a/installation/R_step_by_step_installation.html +++ b/installation/R_step_by_step_installation.html @@ -19,7 +19,7 @@ - R dependent library installation troubleshooting — celloracle 0.17.1 documentation + R dependent library installation troubleshooting — celloracle 0.18.0 documentation diff --git a/installation/check_installation.html b/installation/check_installation.html index 9f6f409..9e78993 100644 --- a/installation/check_installation.html +++ b/installation/check_installation.html @@ -19,7 +19,7 @@ - Check python library installation status — celloracle 0.17.1 documentation + Check python library installation status — celloracle 0.18.0 documentation diff --git a/installation/docker_additional_information.html b/installation/docker_additional_information.html index e85463c..1bc30da 100644 --- a/installation/docker_additional_information.html +++ b/installation/docker_additional_information.html @@ -19,7 +19,7 @@ - CellOracle docker image quick start and additional notes — celloracle 0.17.1 documentation + CellOracle docker image quick start and additional notes — celloracle 0.18.0 documentation diff --git a/installation/index.html b/installation/index.html index ea03f21..ade7eff 100644 --- a/installation/index.html +++ b/installation/index.html @@ -19,7 +19,7 @@ - Installation — celloracle 0.17.1 documentation + Installation — celloracle 0.18.0 documentation @@ -234,11 +234,11 @@ -
docker pull kenjikamimoto126/celloracle_ubuntu:0.12.0
+
docker pull kenjikamimoto126/celloracle_ubuntu:0.18.0
 

 

 
    
-
  • This docker image was built based on Ubuntu 20.04.
    • 
+
  • This docker image was built based on Ubuntu 20.04 and python 3.10.
    • 
 
  • Python dependent packages and celloracle are installed in an anaconda environment, celloracle_env. This environment will be activated automatically when you log in.
    • 
 

 

diff --git a/installation/python_step_by_step_installation.html b/installation/python_step_by_step_installation.html
index 25d1020..8760e16 100644
--- a/installation/python_step_by_step_installation.html
+++ b/installation/python_step_by_step_installation.html
@@ -19,7 +19,7 @@
     
   
   
-  Python dependent library installation troubleshooting — celloracle 0.17.1 documentation
+  Python dependent library installation troubleshooting — celloracle 0.18.0 documentation
   
 
   
diff --git a/license/index.html b/license/index.html
index bdf186d..17bec66 100644
--- a/license/index.html
+++ b/license/index.html
@@ -19,7 +19,7 @@
     
   
   
-  License — celloracle 0.17.1 documentation
+  License — celloracle 0.18.0 documentation
   
 
   
diff --git a/modules/celloracle.data.html b/modules/celloracle.data.html
index affe51d..8119d97 100644
--- a/modules/celloracle.data.html
+++ b/modules/celloracle.data.html
@@ -19,7 +19,7 @@
     
   
   
-  celloracle.data module — celloracle 0.17.1 documentation
+  celloracle.data module — celloracle 0.18.0 documentation
   
 
   
diff --git a/modules/celloracle.data_conversion.html b/modules/celloracle.data_conversion.html
index 21ebf8a..24cba0c 100644
--- a/modules/celloracle.data_conversion.html
+++ b/modules/celloracle.data_conversion.html
@@ -19,7 +19,7 @@
     
   
   
-  celloracle.data_conversion module — celloracle 0.17.1 documentation
+  celloracle.data_conversion module — celloracle 0.18.0 documentation
   
 
   
diff --git a/modules/celloracle.go_analysis.html b/modules/celloracle.go_analysis.html
index c8941a2..1356627 100644
--- a/modules/celloracle.go_analysis.html
+++ b/modules/celloracle.go_analysis.html
@@ -19,7 +19,7 @@
     
   
   
-  celloracle.go_analysis module — celloracle 0.17.1 documentation
+  celloracle.go_analysis module — celloracle 0.18.0 documentation
   
 
   
diff --git a/modules/celloracle.html b/modules/celloracle.html
index 7702c49..f174ce8 100644
--- a/modules/celloracle.html
+++ b/modules/celloracle.html
@@ -19,7 +19,7 @@
     
   
   
-  Custom class in celloracle — celloracle 0.17.1 documentation
+  Custom class in celloracle — celloracle 0.18.0 documentation
   
 
   
@@ -370,7 +370,7 @@ 
Custom class in celloracle
 
Parameters

 
    
-
  • links (Links) – See network_analysis.Links class for detail.
    • 
+
  • links (Links) – See network_analysis.Links class for detail.
    • 
 
  • gois (list of srt) – List of gene name to highlight.
    • 
 
  • clusters (list of str) – List of cluster name to analyze. If None, all clusters in Links object will be analyzed.
    • 
 
  • scatter (bool) – Whether to make a scatter plot.
    • 
@@ -395,7 +395,7 @@ 
    Custom class in celloracle
 
    Parameters
    
 
      
-
    • links (Links) – See network_analysis.Links class for detail.
      • 
+
    • links (Links) – See network_analysis.Links class for detail.
      • 
 
    • gois (list of srt) – List of gene name to highlight.
      • 
 
    • save (str) – Folder path to save plots. If the folder does not exist in the path, the function creates the folder.
 Plots will not be saved if [save=None]. Default is None.
      • 
@@ -412,7 +412,7 @@ 
      Custom class in celloracle
 
      Parameters
      
 
        
-
      • links (Links) – See network_analysis.Links class for detail.
        • 
+
      • links (Links) – See network_analysis.Links class for detail.
        • 
 
      • plot_model (bool) – Whether to plot linear approximation line.
        • 
 
      • save (str) – Folder path to save plots. If the folder does not exist in the path, the function creates the folder.
 Plots will not be saved if [save=None]. Default is None.
        • 
@@ -446,7 +446,7 @@ 
        Custom class in celloracle
 
        Parameters
        
 
          
-
        • links (Links) – See network_analysis.Links class for detail.
          • 
+
        • links (Links) – See network_analysis.Links class for detail.
          • 
 
        • value (srt) – The network score type.
          • 
 
        • cluster1 (str) – Cluster name. Network scores in cluster1 will be visualized in the x-axis.
          • 
 
        • cluster2 (str) – Cluster name. Network scores in cluster2 will be visualized in the y-axis.
          • 
@@ -467,7 +467,7 @@ 
          Custom class in celloracle
 
          Parameters
          
 
            
-
          • links (Links) – See Links class for details.
            • 
+
          • links (Links) – See Links class for details.
            • 
 
          • values (list of str) – The list of score to visualize. If it is None, all of the network score will be used.
            • 
 
          • method (str) – Plotting method. Select either “boxplot” or “barplot”.
            • 
 
          • save (str) – Folder path to save plots. If the folder does not exist in the path, the function creates the folder.
@@ -485,7 +485,7 @@ 
            Custom class in celloracle
 
            Parameters
            
 
              
-
            • links (Links) – See network_analysis.Links class for detail.
              • 
+
            • links (Links) – See network_analysis.Links class for detail.
              • 
 
            • goi (srt) – Gene name.
              • 
 
            • save (str) – Folder path to save plots. If the folder does not exist in the path, the function creates the folder.
 Plots will not be saved if [save=None]. Default is None.
              • 
@@ -501,7 +501,7 @@ 
              Custom class in celloracle
 
              Parameters
              
 
                
-
              • links (Links) – See network_analysis.Links class for detail.
                • 
+
              • links (Links) – See network_analysis.Links class for detail.
                • 
 
              • cluster (str) – Cluster name to analyze.
                • 
 
              • n_gene (int) – Number of genes to plot. Default is 50.
                • 
 
              • save (str) – Folder path to save plots. If the folder does not exist in the path, the function creates the folder.
@@ -1068,7 +1068,7 @@ 
                Custom class in celloracle
 
                Parameters
                
-
                links_object (Links) – Please see the explanation of Links class.
                
+
                links_object (Links) – Please see the explanation of Links class.
                
 
                
 
 
              
diff --git a/modules/celloracle.motif_analysis.html b/modules/celloracle.motif_analysis.html
index 03bf58e..9936389 100644
--- a/modules/celloracle.motif_analysis.html
+++ b/modules/celloracle.motif_analysis.html
@@ -19,7 +19,7 @@
     
   
   
-  celloracle.motif_analysis module — celloracle 0.17.1 documentation
+  celloracle.motif_analysis module — celloracle 0.18.0 documentation
   
 
   
diff --git a/modules/celloracle.network.html b/modules/celloracle.network.html
index 1fbdcf7..4a45dea 100644
--- a/modules/celloracle.network.html
+++ b/modules/celloracle.network.html
@@ -19,7 +19,7 @@
     
   
   
-  celloracle.network package — celloracle 0.17.1 documentation
+  celloracle.network package — celloracle 0.18.0 documentation
   
 
   
diff --git a/modules/celloracle.network_analysis.html b/modules/celloracle.network_analysis.html
index 82178bd..2f332e8 100644
--- a/modules/celloracle.network_analysis.html
+++ b/modules/celloracle.network_analysis.html
@@ -19,7 +19,7 @@
     
   
   
-  celloracle.network_analysis module — celloracle 0.17.1 documentation
+  celloracle.network_analysis module — celloracle 0.18.0 documentation
   
 
   
diff --git a/modules/celloracle.utility.html b/modules/celloracle.utility.html
index 7fadf90..51a559e 100644
--- a/modules/celloracle.utility.html
+++ b/modules/celloracle.utility.html
@@ -19,7 +19,7 @@
     
   
   
-  celloracle.utility module — celloracle 0.17.1 documentation
+  celloracle.utility module — celloracle 0.18.0 documentation
   
 
   
diff --git a/modules/index.html b/modules/index.html
index b029a49..3fba0c1 100644
--- a/modules/index.html
+++ b/modules/index.html
@@ -19,7 +19,7 @@
     
   
   
-  API — celloracle 0.17.1 documentation
+  API — celloracle 0.18.0 documentation
   
 
   
diff --git a/notebooks/01_ATAC-seq_data_processing/option1_scATAC-seq_data_analysis_with_cicero/01_atacdata_analysis_with_cicero_and_monocle3.html b/notebooks/01_ATAC-seq_data_processing/option1_scATAC-seq_data_analysis_with_cicero/01_atacdata_analysis_with_cicero_and_monocle3.html
index a90bb55..cdac493 100644
--- a/notebooks/01_ATAC-seq_data_processing/option1_scATAC-seq_data_analysis_with_cicero/01_atacdata_analysis_with_cicero_and_monocle3.html
+++ b/notebooks/01_ATAC-seq_data_processing/option1_scATAC-seq_data_analysis_with_cicero/01_atacdata_analysis_with_cicero_and_monocle3.html
@@ -19,7 +19,7 @@
     
   
   
-  Overview — celloracle 0.17.1 documentation
+  Overview — celloracle 0.18.0 documentation
   
 
   
diff --git a/notebooks/01_ATAC-seq_data_processing/option1_scATAC-seq_data_analysis_with_cicero/02_preprocess_peak_data.html b/notebooks/01_ATAC-seq_data_processing/option1_scATAC-seq_data_analysis_with_cicero/02_preprocess_peak_data.html
index 553c601..5d481f0 100644
--- a/notebooks/01_ATAC-seq_data_processing/option1_scATAC-seq_data_analysis_with_cicero/02_preprocess_peak_data.html
+++ b/notebooks/01_ATAC-seq_data_processing/option1_scATAC-seq_data_analysis_with_cicero/02_preprocess_peak_data.html
@@ -19,7 +19,7 @@
     
   
   
-  Overview — celloracle 0.17.1 documentation
+  Overview — celloracle 0.18.0 documentation
   
 
   
diff --git a/notebooks/01_ATAC-seq_data_processing/option1_scATAC-seq_data_analysis_with_cicero/misc/Make tss reference datafile from Ensembl database/1_make_tss_referenece_from_ensemble_gff3_file.html b/notebooks/01_ATAC-seq_data_processing/option1_scATAC-seq_data_analysis_with_cicero/misc/Make tss reference datafile from Ensembl database/1_make_tss_referenece_from_ensemble_gff3_file.html
index 874a964..f4aede8 100644
--- a/notebooks/01_ATAC-seq_data_processing/option1_scATAC-seq_data_analysis_with_cicero/misc/Make tss reference datafile from Ensembl database/1_make_tss_referenece_from_ensemble_gff3_file.html	
+++ b/notebooks/01_ATAC-seq_data_processing/option1_scATAC-seq_data_analysis_with_cicero/misc/Make tss reference datafile from Ensembl database/1_make_tss_referenece_from_ensemble_gff3_file.html	
@@ -19,7 +19,7 @@
     
   
   
-  Overview — celloracle 0.17.1 documentation
+  Overview — celloracle 0.18.0 documentation
   
 
   
diff --git a/notebooks/01_ATAC-seq_data_processing/option1_scATAC-seq_data_analysis_with_cicero/misc/Make tss reference datafile from Ensembl database/tss_annotation_using_custom_tss_data.html b/notebooks/01_ATAC-seq_data_processing/option1_scATAC-seq_data_analysis_with_cicero/misc/Make tss reference datafile from Ensembl database/tss_annotation_using_custom_tss_data.html
index 6e15b27..69c08d2 100644
--- a/notebooks/01_ATAC-seq_data_processing/option1_scATAC-seq_data_analysis_with_cicero/misc/Make tss reference datafile from Ensembl database/tss_annotation_using_custom_tss_data.html	
+++ b/notebooks/01_ATAC-seq_data_processing/option1_scATAC-seq_data_analysis_with_cicero/misc/Make tss reference datafile from Ensembl database/tss_annotation_using_custom_tss_data.html	
@@ -19,7 +19,7 @@
     
   
   
-  Overview — celloracle 0.17.1 documentation
+  Overview — celloracle 0.18.0 documentation
   
 
   
diff --git a/notebooks/01_ATAC-seq_data_processing/option1_scATAC-seq_data_analysis_with_cicero/misc/Make tss reference datafile from Xenbase database/1_make_tss_referenece_from_Xenbase_gff3_file.html b/notebooks/01_ATAC-seq_data_processing/option1_scATAC-seq_data_analysis_with_cicero/misc/Make tss reference datafile from Xenbase database/1_make_tss_referenece_from_Xenbase_gff3_file.html
index bbfefb1..7fa6079 100644
--- a/notebooks/01_ATAC-seq_data_processing/option1_scATAC-seq_data_analysis_with_cicero/misc/Make tss reference datafile from Xenbase database/1_make_tss_referenece_from_Xenbase_gff3_file.html	
+++ b/notebooks/01_ATAC-seq_data_processing/option1_scATAC-seq_data_analysis_with_cicero/misc/Make tss reference datafile from Xenbase database/1_make_tss_referenece_from_Xenbase_gff3_file.html	
@@ -19,7 +19,7 @@
     
   
   
-  Overview — celloracle 0.17.1 documentation
+  Overview — celloracle 0.18.0 documentation
   
 
   
diff --git a/notebooks/01_ATAC-seq_data_processing/option1_scATAC-seq_data_analysis_with_cicero/misc/Make tss reference datafile from homer database/make_tss_referenece_from_homer_data-Arabidopsis.html b/notebooks/01_ATAC-seq_data_processing/option1_scATAC-seq_data_analysis_with_cicero/misc/Make tss reference datafile from homer database/make_tss_referenece_from_homer_data-Arabidopsis.html
index 1b83ea1..f89ade8 100644
--- a/notebooks/01_ATAC-seq_data_processing/option1_scATAC-seq_data_analysis_with_cicero/misc/Make tss reference datafile from homer database/make_tss_referenece_from_homer_data-Arabidopsis.html	
+++ b/notebooks/01_ATAC-seq_data_processing/option1_scATAC-seq_data_analysis_with_cicero/misc/Make tss reference datafile from homer database/make_tss_referenece_from_homer_data-Arabidopsis.html	
@@ -19,7 +19,7 @@
     
   
   
-  1. Download and unzip annotation data — celloracle 0.17.1 documentation
+  1. Download and unzip annotation data — celloracle 0.18.0 documentation
   
 
   
diff --git a/notebooks/01_ATAC-seq_data_processing/option1_scATAC-seq_data_analysis_with_cicero/misc/Make tss reference datafile from homer database/make_tss_referenece_from_homer_data-other_species.html b/notebooks/01_ATAC-seq_data_processing/option1_scATAC-seq_data_analysis_with_cicero/misc/Make tss reference datafile from homer database/make_tss_referenece_from_homer_data-other_species.html
index f62d87e..163f0f9 100644
--- a/notebooks/01_ATAC-seq_data_processing/option1_scATAC-seq_data_analysis_with_cicero/misc/Make tss reference datafile from homer database/make_tss_referenece_from_homer_data-other_species.html	
+++ b/notebooks/01_ATAC-seq_data_processing/option1_scATAC-seq_data_analysis_with_cicero/misc/Make tss reference datafile from homer database/make_tss_referenece_from_homer_data-other_species.html	
@@ -19,7 +19,7 @@
     
   
   
-  1. Download and unzip annotation data — celloracle 0.17.1 documentation
+  1. Download and unzip annotation data — celloracle 0.18.0 documentation
   
 
   
diff --git a/notebooks/01_ATAC-seq_data_processing/option2_Bulk_ATAC-seq_data/01_preprocess_Bulk_ATAC_seq_peak_data.html b/notebooks/01_ATAC-seq_data_processing/option2_Bulk_ATAC-seq_data/01_preprocess_Bulk_ATAC_seq_peak_data.html
index fcf85f4..54f4dbd 100644
--- a/notebooks/01_ATAC-seq_data_processing/option2_Bulk_ATAC-seq_data/01_preprocess_Bulk_ATAC_seq_peak_data.html
+++ b/notebooks/01_ATAC-seq_data_processing/option2_Bulk_ATAC-seq_data/01_preprocess_Bulk_ATAC_seq_peak_data.html
@@ -19,7 +19,7 @@
     
   
   
-  Overview — celloracle 0.17.1 documentation
+  Overview — celloracle 0.18.0 documentation
   
 
   
diff --git a/notebooks/02_motif_scan/02_atac_peaks_to_TFinfo_with_celloracle_20200801.html b/notebooks/02_motif_scan/02_atac_peaks_to_TFinfo_with_celloracle_20200801.html
index f9e6f98..6e2724c 100644
--- a/notebooks/02_motif_scan/02_atac_peaks_to_TFinfo_with_celloracle_20200801.html
+++ b/notebooks/02_motif_scan/02_atac_peaks_to_TFinfo_with_celloracle_20200801.html
@@ -19,7 +19,7 @@
     
   
   
-  Overview — celloracle 0.17.1 documentation
+  Overview — celloracle 0.18.0 documentation
   
 
   
@@ -784,9 +784,9 @@ 
              2. Load datahttps://morris-lab.github.io/CellOracle.documentation/tutorials/base_grn.html#step1-scatac-seq-analysis-with-cicero
              
 
              The scATAC-seq file needs to be converted in a csv file three columns: - The first column is index. - The second column is peak_id. - The third column is gene_short_name.
              
 
              A correctly formatted file will look like this:
              
-
              66ee6e00d2d24f32ab2c4ec85653e98b
              
+
              d40f05aebe32473fae782aa511f0deda
              
 
              We will load the .csv file as a pandas.DataFrame using pd.read_csv().
              
-
              726b1d7a3bbf4ba8b9a56fb1aae87300
              
+
              23980a0a82e44b84a434a285ce496694
              
 
              You can download the demo file by running the following command.
              
 
              Note: If the file download fails, please manually download and unzip the data.
              
 
              https://raw.githubusercontent.com/morris-lab/CellOracle/master/docs/demo_data/processed_peak_file.csv
              
diff --git a/notebooks/02_motif_scan/motif_data_preparation/01_How_to_load_gimmemotifs_motif_data.html b/notebooks/02_motif_scan/motif_data_preparation/01_How_to_load_gimmemotifs_motif_data.html
index a98e822..7c47ebe 100644
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+++ b/notebooks/02_motif_scan/motif_data_preparation/01_How_to_load_gimmemotifs_motif_data.html
@@ -19,7 +19,7 @@
     
   
   
-  1 Import motifs from gimmemotifs dataset. — celloracle 0.17.1 documentation
+  1 Import motifs from gimmemotifs dataset. — celloracle 0.18.0 documentation
   
 
   
diff --git a/notebooks/02_motif_scan/motif_data_preparation/02_How_to_load_CisBPv2_motif_data.html b/notebooks/02_motif_scan/motif_data_preparation/02_How_to_load_CisBPv2_motif_data.html
index be3df8a..f2315fb 100644
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+++ b/notebooks/02_motif_scan/motif_data_preparation/02_How_to_load_CisBPv2_motif_data.html
@@ -19,7 +19,7 @@
     
   
   
-  1. Import motifs from Celloracle dataset. — celloracle 0.17.1 documentation
+  1. Import motifs from Celloracle dataset. — celloracle 0.18.0 documentation
   
 
   
diff --git a/notebooks/02_motif_scan/motif_data_preparation/03_How_to_make_custom_motif.html b/notebooks/02_motif_scan/motif_data_preparation/03_How_to_make_custom_motif.html
index f695088..01c63b4 100644
--- a/notebooks/02_motif_scan/motif_data_preparation/03_How_to_make_custom_motif.html
+++ b/notebooks/02_motif_scan/motif_data_preparation/03_How_to_make_custom_motif.html
@@ -19,7 +19,7 @@
     
   
   
-  1. Prepare input data — celloracle 0.17.1 documentation
+  1. Prepare input data — celloracle 0.18.0 documentation
   
 
   
diff --git a/notebooks/02_motif_scan/motif_data_preparation/04_How_to_prepare_CisBP_custom_motif.html b/notebooks/02_motif_scan/motif_data_preparation/04_How_to_prepare_CisBP_custom_motif.html
index 3d583da..66b7990 100644
--- a/notebooks/02_motif_scan/motif_data_preparation/04_How_to_prepare_CisBP_custom_motif.html
+++ b/notebooks/02_motif_scan/motif_data_preparation/04_How_to_prepare_CisBP_custom_motif.html
@@ -19,7 +19,7 @@
     
   
   
-  0. Overview: How to Make custom motifs for celloracle motif scan. — celloracle 0.17.1 documentation
+  0. Overview: How to Make custom motifs for celloracle motif scan. — celloracle 0.18.0 documentation
   
 
   
diff --git a/notebooks/02_motif_scan/motif_data_preparation/05_How_to_prepare_CisBP_custom_motif_Arabidopsis.html b/notebooks/02_motif_scan/motif_data_preparation/05_How_to_prepare_CisBP_custom_motif_Arabidopsis.html
index a0db3a6..79c0e69 100644
--- a/notebooks/02_motif_scan/motif_data_preparation/05_How_to_prepare_CisBP_custom_motif_Arabidopsis.html
+++ b/notebooks/02_motif_scan/motif_data_preparation/05_How_to_prepare_CisBP_custom_motif_Arabidopsis.html
@@ -19,7 +19,7 @@
     
   
   
-  0. Overview: How to Make custom motifs for celloracle motif scan. — celloracle 0.17.1 documentation
+  0. Overview: How to Make custom motifs for celloracle motif scan. — celloracle 0.18.0 documentation
   
 
   
diff --git a/notebooks/03_scRNA-seq_data_preprocessing/scanpy_preprocessing_with_Paul_etal_2015_data.html b/notebooks/03_scRNA-seq_data_preprocessing/scanpy_preprocessing_with_Paul_etal_2015_data.html
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+++ b/notebooks/03_scRNA-seq_data_preprocessing/scanpy_preprocessing_with_Paul_etal_2015_data.html
@@ -19,7 +19,7 @@
     
   
   
-  Overview — celloracle 0.17.1 documentation
+  Overview — celloracle 0.18.0 documentation
   
 
   
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index a5ed599..221bd52 100644
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+++ b/notebooks/04_Network_analysis/Network_analysis_with_Paul_etal_2015_data.html
@@ -19,7 +19,7 @@
     
   
   
-  Overview — celloracle 0.17.1 documentation
+  Overview — celloracle 0.18.0 documentation
   
 
   
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@@ -19,7 +19,7 @@
     
   
   
-  0. Import libraries — celloracle 0.17.1 documentation
+  0. Import libraries — celloracle 0.18.0 documentation
   
 
   
diff --git a/notebooks/05_simulation/Gata1_KO_simulation_with_Paul_etal_2015_data.html b/notebooks/05_simulation/Gata1_KO_simulation_with_Paul_etal_2015_data.html
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+++ b/notebooks/05_simulation/Gata1_KO_simulation_with_Paul_etal_2015_data.html
@@ -19,7 +19,7 @@
     
   
   
-  Overview — celloracle 0.17.1 documentation
+  Overview — celloracle 0.18.0 documentation
   
 
   
@@ -1037,7 +1037,7 @@ 
              5. [This step is optional] Compare simulation vector with development vector
 
            • The inner product will be a positive value when two vectors are pointing in the same direction.
              • 
 
            • Conversely, the inner product will be a negative value when two vectors are pointing in the opposing directions.
              • 
 
            
-
            51c9a14e23d94c219dae3531da1d3b3a
            
+
            1e002d595eac43c3874abf64a5d5d371
            
 
              
 
            • The length of the vectors also affects the magnitude of inner product value.
              • 
 
            
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--- a/notebooks/05_simulation/Pseudotime_calculation_with_Paul_etal_2015_data.html
+++ b/notebooks/05_simulation/Pseudotime_calculation_with_Paul_etal_2015_data.html
@@ -19,7 +19,7 @@
     
   
   
-  Overview — celloracle 0.17.1 documentation
+  Overview — celloracle 0.18.0 documentation
   
 
   
@@ -722,7 +722,7 @@ 
            2.2.1. (Optional step) Interactive visualization of cell namehttps://plotly.com
            
 

-
Using plotly, we can visualize cell IDs interactively. It helps us pick up a root cell. This is an example image. |540db22a64a7422ba178027eec8ecdb1|

+
Using plotly, we can visualize cell IDs interactively. It helps us pick up a root cell. This is an example image. |00a28c43e0ff4d52bbe8697f2c519730|

 
https://raw.githubusercontent.com/morris-lab/CellOracle/master/docs/demo_data/screenshot_01.png

 

 
[ ]:
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@@ -19,7 +19,7 @@
     
   
   
-  0. Import libraries — celloracle 0.17.1 documentation
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@@ -19,7 +19,7 @@
     
   
   
-  Overview — celloracle 0.17.1 documentation
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@@ -19,7 +19,7 @@
     
   
   
-  Read Me Before starting — celloracle 0.17.1 documentation
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@@ -19,7 +19,7 @@
     
   
   
-  0. Import libraries — celloracle 0.17.1 documentation
+  0. Import libraries — celloracle 0.18.0 documentation
   
 
   
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+++ b/notebooks/Net_class/scanpy_preprocessing_with_Paul_etal_2015_data.html
@@ -19,7 +19,7 @@
     
   
   
-  0. Import libraries — celloracle 0.17.1 documentation
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@@ -19,7 +19,7 @@
     
   
   
-  Set R path — celloracle 0.17.1 documentation
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cgan:26,tccgcan:26,tccgcccn:26,tccgccgn:26,tccgccn:26,tccgcctn:26,tccgcgcn:26,tccgcgn:26,tccgcn:26,tccggn:26,tccggtn:26,tccgn:26,tccgtccan:26,tccgtgn:26,tccgtgtgn:26,tccgtn:26,tccgttattn:26,tccgttcn:26,tccgttcttn:26,tccgttn:26,tccn:26,tcctaan:26,tcctacan:26,tcctaccn:26,tcctacn:26,tcctacttn:26,tcctagan:26,tcctagn:26,tcctan:26,tcctatggggn:26,tcctatgn:26,tcctatn:26,tcctattn:26,tcctcaccn:26,tcctcan:26,tcctcatcan:26,tcctcatn:26,tcctccan:26,tcctcccn:26,tcctccctttn:26,tcctccn:26,tcctcctctn:26,tcctcctn:26,tcctcgn:26,tcctcgtcgn:26,tcctcn:26,tcctctan:26,tcctctccatn:26,tcctctcn:26,tcctctgn:26,tcctctn:26,tcctcttcn:26,tcctcttn:26,tcctgattn:26,tcctgcan:26,tcctgccn:26,tcctgcn:26,tcctgctcn:26,tcctgctn:26,tcctggcn:26,tcctggn:26,tcctgn:26,tcctgtan:26,tcctgtgn:26,tcctgtn:26,tcctgttccn:26,tcctgttn:26,tcctn:26,tccttacn:26,tccttan:26,tccttatn:26,tccttcan:26,tccttcccn:26,tccttccctn:26,tccttccn:26,tccttcctn:26,tccttcn:26,tccttctn:26,tccttcttn:26,tccttgn:26,tccttgtcn:26,tccttgtn:26,tccttn:26,tcctttan:26,tcctttcn:26,tcctttctn:26,tcctttn:26,tccttttcn:26,tccttttn:26,tcf7:[41,42],tcfec:[41,42],tcg:[25,26],tcgcacan:26,tcgccan:26,tcgcccan:26,tcgccccn:26,tcgcccn:26,tcgccggn:26,tcgccgn:26,tcgccn:26,tcgcctn:26,tcgcgcan:26,tcgcn:26,tcgctan:26,tcgctccn:26,tcgctcn:26,tcgctgn:26,tcggaaggacn:26,tcggacn:26,tcggcgn:26,tcggcn:26,tcggctgn:26,tcgggn:[],tcggn:26,tcggtcn:26,tcggtgcn:26,tcggtn:26,tcgn:26,tcgtcan:26,tcgtcn:26,tcgtggcn:26,tcgtgn:26,tcgttcn:26,tcgtttgn:26,tcgtttn:26,tcmar:26,tcn:26,tcta:25,tctaaan:26,tctaacan:26,tctaacn:26,tctaagan:26,tctaagatn:26,tctaagn:26,tctaagtgatn:26,tctaan:26,tctaataatgn:26,tctaatan:26,tctaatcn:26,tctaatn:26,tctaattn:26,tctaatttn:26,tctacan:26,tctacatn:26,tctaccn:26,tctacn:26,tctactctatn:26,tctactn:26,tctacttn:26,tctagan:26,tctagatn:26,tctaggn:26,tctagn:26,tctagtn:26,tctagttn:26,tctan:26,tctataan:26,tctatacn:26,tctatactggn:26,tctatan:26,tctatatn:26,tctatccan:26,tctatcn:26,tctatctgn:26,tctatctn:26,tctatgatn:26,tctatgcn:26,tctatggggan:26,tctatggggcn:26,tctatggggn:26,tctatgggtcn:26,tctatgn:26,tctatn:26,tctattan:26,tctattcn:26,tctattn:26,tctatttan:26,tctatttn:26,tctattttn:26,tctcaan:26,tctcaatn:26,tctcacan:26,tctcacn:26,tctcactn:26,tctcagcn:26,tctcaggn:26,tctcagn:26,tctcagtgggn:26,tctcagtn:26,tctcan:26,tctcatcn:26,tctcatgtn:26,tctcatn:26,tctcattn:26,tctccacn:26,tctccan:26,tctccatn:26,tctcccacn:26,tctcccagtan:26,tctcccagtn:26,tctcccan:26,tctccccan:26,tctcccccn:26,tctccccn:26,tctcccn:26,tctccctn:26,tctcccttn:26,tctccgccn:26,tctccgcn:26,tctccgn:26,tctccn:26,tctcctcn:26,tctcctgn:26,tctcctn:26,tctccttn:26,tctcggn:26,tctcgn:26,tctcgtgn:26,tctcn:26,tctctan:26,tctctatgggn:26,tctctatgtgn:26,tctctcagn:26,tctctcccn:26,tctctccn:26,tctctcctn:26,tctctccttcn:26,tctctcn:26,tctctctccn:26,tctctctctgn:26,tctctctn:26,tctctcttn:26,tctctgcn:26,tctctgn:26,tctctgtn:26,tctctn:26,tctcttcn:26,tctcttctctn:26,tctcttgn:26,tctcttn:26,tctctttcn:26,tctctttgn:26,tctctttn:26,tctgaagn:26,tctgaan:26,tctgaatatcn:26,tctgacan:26,tctgagan:26,tctgagcn:26,tctgagn:26,tctgan:26,tctgatan:26,tctgatcn:26,tctgatn:26,tctgattn:26,tctgatttn:26,tctgcaan:26,tctgcacn:26,tctgcactn:26,tctgcagn:26,tctgcan:26,tctgccan:26,tctgcccn:26,tctgccn:26,tctgcctgn:26,tctgcn:26,tctgctan:26,tctgctcn:26,tctgctctn:26,tctgctgggcn:26,tctgctgn:26,tctgctn:26,tctgcttn:26,tctggan:26,tctggcan:26,tctggcn:26,tctggtgn:26,tctgn:26,tctgtaan:26,tctgtacn:26,tctgtagn:26,tctgtan:26,tctgtatn:26,tctgtccn:26,tctgtcn:26,tctgtctcn:26,tctgtctctcn:26,tctgtctn:26,tctgtgan:26,tctgtgatn:26,tctgtgcn:26,tctgtggn:26,tctgtgn:26,tctgtn:26,tctgttan:26,tctgttcn:26,tctgttgtn:26,tctgttn:26,tctgtttn:26,tctgttttn:26,tctn:26,tcttaagn:26,tcttaan:26,tcttaatn:26,tcttaccn:26,tcttacn:26,tcttactn:26,tcttagn:26,tcttan:26,tcttatan:26,tcttatatn:26,tcttatgn:26,tcttatn:26,tcttattgacn:26,tcttattn:26,tcttcacn:26,tcttcan:26,tcttcatn:26,tcttccan:26,tcttcccctn:26,tcttcccn:26,tcttccctn:26,tcttccn:26,tcttcctn:26,tcttccttn:26,tcttcgn:26,tcttcn:26,tcttctaatan:26,tcttctan:26,tcttctccn:26,tcttctcn:26,tcttctctcn:26,tcttctgn:26,tcttctn:26,tcttcttn:26,tcttctttn:26,tcttgan:26,tcttgcan:26,tcttgcn:26,tcttgctn:26,tcttgn:26,tcttgtaaacn:26,tcttgtan:26,tcttgtcn:26,tcttgtgn:26,tcttgtn:26,tcttgttn:26,tcttn:26,tctttaan:26,tctttaatn:26,tctttacn:26,tctttan:26,tctttatn:26,tctttcacn:26,tctttcan:26,tctttccgtn:26,tctttccn:26,tctttcctn:26,tctttccttcn:26,tctttcn:26,tctttctcn:26,tctttctgn:26,tctttctn:26,tctttcttn:26,tctttgan:26,tctttgcgcn:26,tctttgcgtn:26,tctttgcn:26,tctttggn:26,tctttgn:26,tctttgtgn:26,tctttgtn:26,tctttn:26,tcttttan:26,tcttttcn:26,tcttttctn:26,tcttttgn:26,tcttttn:26,tctttttan:26,tctttttn:26,tcttttttn:26,tcttttttttn:26,tcurat:[32,33],tcy:26,team:22,technic:[2,45],teladorsagia_circumcincta:[32,33],telo:[],telom:25,temporaliri:5,temporari:13,temporarili:0,ten:35,term:[10,11,17,36,44],termin:[5,7,10],terminado:[],test1:28,test:[0,4,8,36],test_command:44,test_instal:[],test_linkcomm:44,test_mod:[11,17,36],test_r_libraries_instal:[6,11,36],testpath:[],tetrahymena_thermophila:[32,33],tetranychus_urtica:[32,33],tetraodon_nigroviridi:[32,33],tetrapisispora_blatta:[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gan:26,tgtagcan:26,tgtagcn:26,tgtaggn:26,tgtagn:26,tgtagtan:26,tgtagtgn:26,tgtagtn:26,tgtan:26,tgtataan:26,tgtatacan:26,tgtatacn:26,tgtatagn:26,tgtatan:26,tgtatatan:26,tgtatatatan:26,tgtatatn:26,tgtatcan:26,tgtatccn:26,tgtatcn:26,tgtatgcan:26,tgtatgcn:26,tgtatgctn:26,tgtatggggcn:26,tgtatgn:26,tgtatgtgn:26,tgtatgtn:26,tgtatn:26,tgtattan:26,tgtattcn:26,tgtattn:26,tgtatttn:26,tgtcacccaan:26,tgtcaccccan:26,tgtcactn:26,tgtcagn:26,tgtcan:26,tgtcatcacgn:26,tgtcatcccn:26,tgtcatctn:26,tgtcatgn:26,tgtcatn:26,tgtcattn:26,tgtccan:26,tgtcccagn:26,tgtcccagtan:26,tgtcccan:26,tgtcccatggn:26,tgtcccatn:26,tgtccccaan:26,tgtccccacn:26,tgtccccagn:26,tgtccccan:26,tgtccccatan:26,tgtccccatn:26,tgtccccn:26,tgtcccn:26,tgtccn:26,tgtcctgn:26,tgtcctn:26,tgtccttn:26,tgtcn:26,tgtctacn:26,tgtctan:26,tgtctccn:26,tgtctcn:26,tgtctctatgn:26,tgtctggn:26,tgtctgn:26,tgtctgtcn:26,tgtctn:26,tgtcttan:26,tgtcttatn:26,tgtcttcn:26,tgtcttn:26,tgtctttcn:26,tgtctttn:26,tgtgaagn:26,tgtgaan:26,tgtgacan:26,tgtgaccn:26,tgtgacn:26,tgtgactgn:26,tgtgagan:26,tgtgagcn:26,tgtgaggn:26,tgtgagn:26,tgtgan:26,tgtgatan:26,tgtgatgn:26,tgtgatn:26,tgtgattcn:26,tgtgattn:26,tgtgcaan:26,tgtgcacn:26,tgtgcagn:26,tgtgcan:26,tgtgcatgn:26,tgtgcatn:26,tgtgccacccn:26,tgtgccan:26,tgtgcccn:26,tgtgccn:26,tgtgcctn:26,tgtgcgcn:26,tgtgcgn:26,tgtgcn:26,tgtgctatan:26,tgtgctcn:26,tgtgctgcn:26,tgtgctgn:26,tgtgctn:26,tgtgcttn:26,tgtggacn:26,tgtggagn:26,tgtggan:26,tgtggcan:26,tgtggccn:26,tgtggcn:26,tgtgggan:26,tgtggn:26,tgtggtan:26,tgtggtgcn:26,tgtggtn:26,tgtggttn:26,tgtgn:26,tgtgtacatgn:26,tgtgtan:26,tgtgtatan:26,tgtgtcatcan:26,tgtgtccan:26,tgtgtccctan:26,tgtgtcn:26,tgtgtctn:26,tgtgtgcn:26,tgtgtgctgtn:26,tgtgtggtgn:26,tgtgtggtgtn:26,tgtgtgn:26,tgtgtgtan:26,tgtgtgtcn:26,tgtgtgtgtn:26,tgtgtgtn:26,tgtgtgttgcn:26,tgtgtgttgn:26,tgtgtn:26,tgtgttan:26,tgtgttcn:26,tgtgttgn:26,tgtgttn:26,tgtgtttn:26,tgtn:26,tgttaacn:26,tgttaagn:26,tgttaan:26,tgttaatn:26,tgttaccn:26,tgttacn:26,tgttactn:26,tgttagan:26,tgttaggn:26,tgttagn:26,tgttagtn:26,tgttan:26,tgttatan:26,tgttatccatagtn:26,tgttatcn:26,tgttatn:26,tgttattactn:26,tgttattn:26,tgttatttn:26,tgttcacn:26,tgttcan:26,tgttcatgn:26,tgttcatn:26,tgttccan:26,tgttcccn:26,tgttccn:26,tgttcn:26,tgttctan:26,tgttctcn:26,tgttctctn:26,tgttctn:26,tgttcttn:26,tgttgaan:26,tgttgacn:26,tgttgan:26,tgttgatn:26,tgttgcactgn:26,tgttgcan:26,tgttgccn:26,tgttgcn:26,tgttgctgcn:26,tgttgctn:26,tgttggan:26,tgttggn:26,tgttggtn:26,tgttgn:26,tgttgtan:26,tgttgtgn:26,tgttgtn:26,tgttgttn:26,tgttn:26,tgtttaan:26,tgtttacn:26,tgtttagn:26,tgtttan:26,tgtttatn:26,tgtttcan:26,tgtttccgtn:26,tgtttccn:26,tgtttcn:26,tgtttctn:26,tgtttgan:26,tgtttgcn:26,tgtttgn:26,tgtttgtcn:26,tgtttgtn:26,tgtttn:26,tgttttagctn:26,tgttttan:26,tgttttcan:26,tgttttcn:26,tgttttgn:26,tgttttgtatn:26,tgttttn:26,tgtttttgn:26,tgtttttn:26,tgttttttn:26,tgttttttttn:26,tgultr5:26,tgultr5d:26,tgy:26,thalassiosira_pseudonana:[32,33],than:[0,11,17,26,34,35,36,37,39,43,45],thank:[4,9],thbs4:27,the1:[],the1a:[],the1b:[],the1c:[],the1d:[],thecamonas_trahen:[32,33],thei:[47,48],theileria_annulata:[32,33],theileria_parva:[32,33],thelazia_callipaeda:[32,33],them:[20,22,23,24,29,34,35,37,40,41,42],theobroma_cacao:[32,33],theori:[10,35,48],therefor:[],thereof:10,theses:31,thi:[0,2,4,5,7,8,9,10,11,14,15,16,17,18,20,21,26,27,28,29,30,31,32,33,34,35,36,39,41,43,45,46,47,48,49,53,54],thielavia_terrestri:[32,33],thing:45,third:[10,28,31],those:10,thousand:[],thr:26,thread_numb:[11,17],threadpoolctl:[],three:[11,21,28,34],threshold:[11,15,16,17,20,28,35,36,37],threshold_numb:[11,17,35,36],threshold_p:[11,16],thrid:31,through:[5,7,8,10,21,28],thu:[9,35,36],ticklabel_format:36,tigger10:[],tigger11a:[],tigger12:[],tigger12a:[],tigger12c:[],tigger13a:[],tigger14a:[],tigger15a:[],tigger16a:[],tigger16b:[],tigger1:[],tigger1a_art:[],tigger1a_mar:[],tigger2:[],tigger2a:[],tigger2a_car:[],tigger2b:[],tigger2b_pri:[],tigger3:[],tigger3a:[],tigger3b:[],tigger3c:[],tigger3d:[],tigger4:[],tigger4a:[],tigger4b:[],tigger5:[],tigger6a:[],tigger6b:[],tigger7:[],tigger8:[],tigger9a:[],tigger9b:[],tigger:26,tilletiaria_anomala:[32,33],time:[11,16,25,26,28,34,35,36,37,38,39,41,42,45,48],time_rang:11,timepoint:11,tip100:26,tip:[],tissu:[11,16,35,36],titl:[10,45],tmem74:22,tmp:[25,26],tmtc3:[21,28],tn1000:26,tnat1a:25,tnat2a:25,tnks2:[],to_csv:[21,22,23,24,25,26,27,32,33,35,36],to_datafram:[15,22,24,28],to_df:43,to_dictionari:15,to_hdf5:[11,15,16,17,28,35,36,37,38],to_list:[22,24],to_parquet:28,togninia_minima:[32,33],token:7,toml:[],too:[37,41,45],tool:48,toolkit:[38,48,53],top2a:[35,36],top:[11,17,34,35,36,40],topic:44,toplevel:22,tornado:[],torrubiella_hemipterigena:[32,33],tort:10,torulaspora_delbrueckii:[32,33],total:[26,34,41,43,45,47],toward:39,toxocara_cani:[32,33],toxoplasma_gondii:[32,33],tqdm:[21,22,23,24,25,26,27,28,38,41,42],tqdm_notebook:27,traceback:[],trachipleistophora_homini:[32,33],track:10,trade:10,trademark:10,train:37,traitlet:[],trajectori:[11,34,35,36,37,38,42,45],trametes_cinnabarina:[32,33],transcript:[12,15,22,23,24,27,34,46,47,48],transcript_filt:22,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and citations","Contact","Google Colaboratoly","Welcome to CellOracle\u2019s documentation!","R dependent library installation troubleshooting","Check python library installation status","CellOracle docker image quick start and additional notes","Installation","Python dependent library installation troubleshooting","License","Custom class in celloracle","celloracle.data module","celloracle.data_conversion module","celloracle.go_analysis module","celloracle.motif_analysis module","celloracle.network package","celloracle.network_analysis module","celloracle.utility module","API","Overview","Overview","Overview","Overview","Overview","1. 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and citations","Contact","Google Colaboratoly","Welcome to CellOracle\u2019s documentation!","R dependent library installation troubleshooting","Check python library installation status","CellOracle docker image quick start and additional notes","Installation","Python dependent library installation troubleshooting","License","Custom class in celloracle","celloracle.data module","celloracle.data_conversion module","celloracle.go_analysis module","celloracle.motif_analysis module","celloracle.network package","celloracle.network_analysis module","celloracle.utility module","API","Overview","Overview","Overview","Overview","Overview","1. 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In silico gene perturbation with 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diff --git a/tutorials/atac.html b/tutorials/atac.html
index 583cc9f..306ab7d 100644
--- a/tutorials/atac.html
+++ b/tutorials/atac.html
@@ -19,7 +19,7 @@
     
   
   
-  ATAC-seq data preprocessing — celloracle 0.17.1 documentation
+  ATAC-seq data preprocessing — celloracle 0.18.0 documentation
   
 
   
diff --git a/tutorials/base_grn.html b/tutorials/base_grn.html
index 511347f..cc00eae 100644
--- a/tutorials/base_grn.html
+++ b/tutorials/base_grn.html
@@ -19,7 +19,7 @@
     
   
   
-  3. Base GRN input data preparation — celloracle 0.17.1 documentation
+  3. Base GRN input data preparation — celloracle 0.18.0 documentation
   
 
   
diff --git a/tutorials/index.html b/tutorials/index.html
index ddb4703..a568be5 100644
--- a/tutorials/index.html
+++ b/tutorials/index.html
@@ -19,7 +19,7 @@
     
   
   
-  Tutorial — celloracle 0.17.1 documentation
+  Tutorial — celloracle 0.18.0 documentation
   
 
   
diff --git a/tutorials/motifscan.html b/tutorials/motifscan.html
index 996a65a..21256ad 100644
--- a/tutorials/motifscan.html
+++ b/tutorials/motifscan.html
@@ -19,7 +19,7 @@
     
   
   
-  1. Transcription factor binding motif scan — celloracle 0.17.1 documentation
+  1. Transcription factor binding motif scan — celloracle 0.18.0 documentation
   
 
   
diff --git a/tutorials/networkanalysis.html b/tutorials/networkanalysis.html
index 5dd65ee..2ddc2ac 100644
--- a/tutorials/networkanalysis.html
+++ b/tutorials/networkanalysis.html
@@ -19,7 +19,7 @@
     
   
   
-  1. GRN model construction and network analysis — celloracle 0.17.1 documentation
+  1. GRN model construction and network analysis — celloracle 0.18.0 documentation
   
 
   
diff --git a/tutorials/prepare_input_data.html b/tutorials/prepare_input_data.html
index af82b2b..ac1cdec 100644
--- a/tutorials/prepare_input_data.html
+++ b/tutorials/prepare_input_data.html
@@ -19,7 +19,7 @@
     
   
   
-  scRNA-seq data preprocessing — celloracle 0.17.1 documentation
+  scRNA-seq data preprocessing — celloracle 0.18.0 documentation
   
 
   
diff --git a/tutorials/pseudotime.html b/tutorials/pseudotime.html
index 2c9afdb..15e6cbc 100644
--- a/tutorials/pseudotime.html
+++ b/tutorials/pseudotime.html
@@ -19,7 +19,7 @@
     
   
   
-  2. Pseudotime calculation — celloracle 0.17.1 documentation
+  2. Pseudotime calculation — celloracle 0.18.0 documentation
   
 
   
diff --git a/tutorials/scrnaprocess.html b/tutorials/scrnaprocess.html
index affb9d5..965f1f4 100644
--- a/tutorials/scrnaprocess.html
+++ b/tutorials/scrnaprocess.html
@@ -19,7 +19,7 @@
     
   
   
-  1. scRNA-seq data preparation — celloracle 0.17.1 documentation
+  1. scRNA-seq data preparation — celloracle 0.18.0 documentation
   
 
   
diff --git a/tutorials/simulation.html b/tutorials/simulation.html
index 860dadf..6122360 100644
--- a/tutorials/simulation.html
+++ b/tutorials/simulation.html
@@ -19,7 +19,7 @@
     
   
   
-  1. In silico gene perturbation with GRNs — celloracle 0.17.1 documentation
+  1. In silico gene perturbation with GRNs — celloracle 0.18.0 documentation