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ZhenyiWangTHU · Jul 20, 2024 · b45d515 · b45d515
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diff --git a/.Rproj.user/11F4C4A8/sources/prop/44D79FA3 b/.Rproj.user/11F4C4A8/sources/prop/44D79FA3
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diff --git a/.Rproj.user/11F4C4A8/sources/session-632a36d8/6F98DDE3 b/.Rproj.user/11F4C4A8/sources/session-632a36d8/6F98DDE3
@@ -3,7 +3,7 @@
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diff --git a/.Rproj.user/11F4C4A8/sources/session-632a36d8/6F98DDE3-contents b/.Rproj.user/11F4C4A8/sources/session-632a36d8/6F98DDE3-contents
@@ -140,20 +140,7 @@ pip config set global.extra-index-url http://mirrors.aliyun.com/pypi/simple/
 -   Install required packages
 
 ```         
-pip install matplotlib==3.7.2
-pip install pot==0.9.1
-pip install anndata==0.9.2
-pip install scanpy==1.9.4
-pip install scipy==1.11.2
-pip install seaborn==0.12.2
-pip install commot==0.0.3
-pip install scvi-tools==1.0.3
-pip install cell2location==0.1.3 
-pip install phate==1.0.11
-pip install scvelo==0.2.5
-pip install arboreto==0.1.6
-pip install numpy==1.23.5
-pip install pandas==1.3.5
+pip install anndata==0.10.8 arboreto==0.1.6 cell2location==0.1.3 commot==0.0.3 karateclub==1.2.2 matplotlib==3.9.1 networkx==3.3 numpy==1.26.4 pandas==2.0.3 phate==1.0.11 pot==0.9.4 scanpy==1.10.2 scipy==1.13.1 scvelo==0.3.2 scvi-tools==1.1.5 seaborn==0.13.2
 ```
 
 ## The installed packages with versions
@@ -683,7 +670,7 @@ jaxlib                   0.4.30
 Jinja2                   3.1.4
 jmespath                 1.0.1
 joblib                   1.4.2
-karateclub               1.3.3
+karateclub               1.2.2
 kiwisolver               1.4.5
 legacy-api-wrap          1.4
 leidenalg                0.10.2
@@ -699,7 +686,7 @@ lz4                      4.3.3
 mapclassify              2.6.0
 markdown-it-py           3.0.0
 MarkupSafe               2.1.5
-matplotlib               3.7.2
+matplotlib               3.9.1
 mdurl                    0.1.2
 mgwr                     2.2.1
 ml_collections           0.1.1
@@ -712,9 +699,9 @@ multidict                6.0.5
 multipledispatch         1.0.0
 natsort                  8.4.0
 nest-asyncio             1.6.0
-networkx                 2.6.3
+networkx                 3.3
 numba                    0.60.0
-numpy                    1.23.5
+numpy                    1.26.4
 numpy-groupies           0.11.1
 numpyro                  0.15.1
 nvidia-cublas-cu12       12.1.3.1
@@ -735,7 +722,7 @@ optax                    0.2.1
 orbax-checkpoint         0.5.21
 ordered-set              4.1.0
 packaging                24.1
-pandas                   1.3.5
+pandas                   2.0.3
 partd                    1.4.2
 patsy                    0.5.6
 phate                    1.0.11
@@ -744,7 +731,7 @@ pip                      24.1.2
 platformdirs             4.2.2
 plotly                   5.22.0
 pointpats                2.4.0
-POT                      0.9.1
+POT                      0.9.4
 protobuf                 5.27.2
 psutil                   6.0.0
 PuLP                     2.9.0
@@ -781,13 +768,13 @@ Rtree                    1.3.0
 runs                     1.2.2
 s_gd2                    1.8.1
 s3transfer               0.10.2
-scanpy                   1.9.4
+scanpy                   1.10.2
 scikit-learn             1.5.1
-scipy                    1.11.2
+scipy                    1.13.1
 scprep                   1.2.3
-scvelo                   0.2.5
-scvi-tools               1.0.3
-seaborn                  0.12.2
+scvelo                   0.3.2
+scvi-tools               1.1.5
+seaborn                  0.13.2
 segregation              2.5
 session_info             1.0.0
 setuptools               71.0.1

diff --git a/HemaScope_installation_tutorial.Rmd b/HemaScope_installation_tutorial.Rmd
@@ -140,20 +140,7 @@ pip config set global.extra-index-url http://mirrors.aliyun.com/pypi/simple/
 -   Install required packages
 
 ```         
-pip install matplotlib==3.7.2
-pip install pot==0.9.1
-pip install anndata==0.9.2
-pip install scanpy==1.9.4
-pip install scipy==1.11.2
-pip install seaborn==0.12.2
-pip install commot==0.0.3
-pip install scvi-tools==1.0.3
-pip install cell2location==0.1.3 
-pip install phate==1.0.11
-pip install scvelo==0.2.5
-pip install arboreto==0.1.6
-pip install numpy==1.23.5
-pip install pandas==1.3.5
+pip install anndata==0.10.8 arboreto==0.1.6 cell2location==0.1.3 commot==0.0.3 karateclub==1.2.2 matplotlib==3.9.1 networkx==3.3 numpy==1.26.4 pandas==2.0.3 phate==1.0.11 pot==0.9.4 scanpy==1.10.2 scipy==1.13.1 scvelo==0.3.2 scvi-tools==1.1.5 seaborn==0.13.2
 ```
 
 ## The installed packages with versions
@@ -683,7 +670,7 @@ jaxlib                   0.4.30
 Jinja2                   3.1.4
 jmespath                 1.0.1
 joblib                   1.4.2
-karateclub               1.3.3
+karateclub               1.2.2
 kiwisolver               1.4.5
 legacy-api-wrap          1.4
 leidenalg                0.10.2
@@ -699,7 +686,7 @@ lz4                      4.3.3
 mapclassify              2.6.0
 markdown-it-py           3.0.0
 MarkupSafe               2.1.5
-matplotlib               3.7.2
+matplotlib               3.9.1
 mdurl                    0.1.2
 mgwr                     2.2.1
 ml_collections           0.1.1
@@ -712,9 +699,9 @@ multidict                6.0.5
 multipledispatch         1.0.0
 natsort                  8.4.0
 nest-asyncio             1.6.0
-networkx                 2.6.3
+networkx                 3.3
 numba                    0.60.0
-numpy                    1.23.5
+numpy                    1.26.4
 numpy-groupies           0.11.1
 numpyro                  0.15.1
 nvidia-cublas-cu12       12.1.3.1
@@ -735,7 +722,7 @@ optax                    0.2.1
 orbax-checkpoint         0.5.21
 ordered-set              4.1.0
 packaging                24.1
-pandas                   1.3.5
+pandas                   2.0.3
 partd                    1.4.2
 patsy                    0.5.6
 phate                    1.0.11
@@ -744,7 +731,7 @@ pip                      24.1.2
 platformdirs             4.2.2
 plotly                   5.22.0
 pointpats                2.4.0
-POT                      0.9.1
+POT                      0.9.4
 protobuf                 5.27.2
 psutil                   6.0.0
 PuLP                     2.9.0
@@ -781,13 +768,13 @@ Rtree                    1.3.0
 runs                     1.2.2
 s_gd2                    1.8.1
 s3transfer               0.10.2
-scanpy                   1.9.4
+scanpy                   1.10.2
 scikit-learn             1.5.1
-scipy                    1.11.2
+scipy                    1.13.1
 scprep                   1.2.3
-scvelo                   0.2.5
-scvi-tools               1.0.3
-seaborn                  0.12.2
+scvelo                   0.3.2
+scvi-tools               1.1.5
+seaborn                  0.13.2
 segregation              2.5
 session_info             1.0.0
 setuptools               71.0.1

diff --git a/_book/installation.html b/_book/installation.html
@@ -381,20 +381,7 @@ <h2><span class="header-section-number">2.5</span> Install required Python-packa
 <ul>
 <li>Install required packages</li>
 </ul>
-<pre><code>pip install matplotlib==3.7.2
-pip install pot==0.9.1
-pip install anndata==0.9.2
-pip install scanpy==1.9.4
-pip install scipy==1.11.2
-pip install seaborn==0.12.2
-pip install commot==0.0.3
-pip install scvi-tools==1.0.3
-pip install cell2location==0.1.3 
-pip install phate==1.0.11
-pip install scvelo==0.2.5
-pip install arboreto==0.1.6
-pip install numpy==1.23.5
-pip install pandas==1.3.5</code></pre>
+<pre><code>pip install anndata==0.10.8 arboreto==0.1.6 cell2location==0.1.3 commot==0.0.3 karateclub==1.2.2 matplotlib==3.9.1 networkx==3.3 numpy==1.26.4 pandas==2.0.3 phate==1.0.11 pot==0.9.4 scanpy==1.10.2 scipy==1.13.1 scvelo==0.3.2 scvi-tools==1.1.5 seaborn==0.13.2</code></pre>
 </div>
 <div id="the-installed-packages-with-versions" class="section level2 hasAnchor" number="2.6">
 <h2><span class="header-section-number">2.6</span> The installed packages with versions<a href="installation.html#the-installed-packages-with-versions" class="anchor-section" aria-label="Anchor link to header"></a></h2>
@@ -925,7 +912,7 @@ <h2><span class="header-section-number">2.6</span> The installed packages with v
 Jinja2                   3.1.4
 jmespath                 1.0.1
 joblib                   1.4.2
-karateclub               1.3.3
+karateclub               1.2.2
 kiwisolver               1.4.5
 legacy-api-wrap          1.4
 leidenalg                0.10.2
@@ -941,7 +928,7 @@ <h2><span class="header-section-number">2.6</span> The installed packages with v
 mapclassify              2.6.0
 markdown-it-py           3.0.0
 MarkupSafe               2.1.5
-matplotlib               3.7.2
+matplotlib               3.9.1
 mdurl                    0.1.2
 mgwr                     2.2.1
 ml_collections           0.1.1
@@ -954,9 +941,9 @@ <h2><span class="header-section-number">2.6</span> The installed packages with v
 multipledispatch         1.0.0
 natsort                  8.4.0
 nest-asyncio             1.6.0
-networkx                 2.6.3
+networkx                 3.3
 numba                    0.60.0
-numpy                    1.23.5
+numpy                    1.26.4
 numpy-groupies           0.11.1
 numpyro                  0.15.1
 nvidia-cublas-cu12       12.1.3.1
@@ -977,7 +964,7 @@ <h2><span class="header-section-number">2.6</span> The installed packages with v
 orbax-checkpoint         0.5.21
 ordered-set              4.1.0
 packaging                24.1
-pandas                   1.3.5
+pandas                   2.0.3
 partd                    1.4.2
 patsy                    0.5.6
 phate                    1.0.11
@@ -986,7 +973,7 @@ <h2><span class="header-section-number">2.6</span> The installed packages with v
 platformdirs             4.2.2
 plotly                   5.22.0
 pointpats                2.4.0
-POT                      0.9.1
+POT                      0.9.4
 protobuf                 5.27.2
 psutil                   6.0.0
 PuLP                     2.9.0
@@ -1023,13 +1010,13 @@ <h2><span class="header-section-number">2.6</span> The installed packages with v
 runs                     1.2.2
 s_gd2                    1.8.1
 s3transfer               0.10.2
-scanpy                   1.9.4
+scanpy                   1.10.2
 scikit-learn             1.5.1
-scipy                    1.11.2
+scipy                    1.13.1
 scprep                   1.2.3
-scvelo                   0.2.5
-scvi-tools               1.0.3
-seaborn                  0.12.2
+scvelo                   0.3.2
+scvi-tools               1.1.5
+seaborn                  0.13.2
 segregation              2.5
 session_info             1.0.0
 setuptools               71.0.1

diff --git a/_book/search_index.json b/_book/search_index.json
diff --git a/docs/installation.html b/docs/installation.html
@@ -381,20 +381,7 @@ <h2><span class="header-section-number">2.5</span> Install required Python-packa
 <ul>
 <li>Install required packages</li>
 </ul>
-<pre><code>pip install matplotlib==3.7.2
-pip install pot==0.9.1
-pip install anndata==0.9.2
-pip install scanpy==1.9.4
-pip install scipy==1.11.2
-pip install seaborn==0.12.2
-pip install commot==0.0.3
-pip install scvi-tools==1.0.3
-pip install cell2location==0.1.3 
-pip install phate==1.0.11
-pip install scvelo==0.2.5
-pip install arboreto==0.1.6
-pip install numpy==1.23.5
-pip install pandas==1.3.5</code></pre>
+<pre><code>pip install anndata==0.10.8 arboreto==0.1.6 cell2location==0.1.3 commot==0.0.3 karateclub==1.2.2 matplotlib==3.9.1 networkx==3.3 numpy==1.26.4 pandas==2.0.3 phate==1.0.11 pot==0.9.4 scanpy==1.10.2 scipy==1.13.1 scvelo==0.3.2 scvi-tools==1.1.5 seaborn==0.13.2</code></pre>
 </div>
 <div id="the-installed-packages-with-versions" class="section level2 hasAnchor" number="2.6">
 <h2><span class="header-section-number">2.6</span> The installed packages with versions<a href="installation.html#the-installed-packages-with-versions" class="anchor-section" aria-label="Anchor link to header"></a></h2>
@@ -925,7 +912,7 @@ <h2><span class="header-section-number">2.6</span> The installed packages with v
 Jinja2                   3.1.4
 jmespath                 1.0.1
 joblib                   1.4.2
-karateclub               1.3.3
+karateclub               1.2.2
 kiwisolver               1.4.5
 legacy-api-wrap          1.4
 leidenalg                0.10.2
@@ -941,7 +928,7 @@ <h2><span class="header-section-number">2.6</span> The installed packages with v
 mapclassify              2.6.0
 markdown-it-py           3.0.0
 MarkupSafe               2.1.5
-matplotlib               3.7.2
+matplotlib               3.9.1
 mdurl                    0.1.2
 mgwr                     2.2.1
 ml_collections           0.1.1
@@ -954,9 +941,9 @@ <h2><span class="header-section-number">2.6</span> The installed packages with v
 multipledispatch         1.0.0
 natsort                  8.4.0
 nest-asyncio             1.6.0
-networkx                 2.6.3
+networkx                 3.3
 numba                    0.60.0
-numpy                    1.23.5
+numpy                    1.26.4
 numpy-groupies           0.11.1
 numpyro                  0.15.1
 nvidia-cublas-cu12       12.1.3.1
@@ -977,7 +964,7 @@ <h2><span class="header-section-number">2.6</span> The installed packages with v
 orbax-checkpoint         0.5.21
 ordered-set              4.1.0
 packaging                24.1
-pandas                   1.3.5
+pandas                   2.0.3
 partd                    1.4.2
 patsy                    0.5.6
 phate                    1.0.11
@@ -986,7 +973,7 @@ <h2><span class="header-section-number">2.6</span> The installed packages with v
 platformdirs             4.2.2
 plotly                   5.22.0
 pointpats                2.4.0
-POT                      0.9.1
+POT                      0.9.4
 protobuf                 5.27.2
 psutil                   6.0.0
 PuLP                     2.9.0
@@ -1023,13 +1010,13 @@ <h2><span class="header-section-number">2.6</span> The installed packages with v
 runs                     1.2.2
 s_gd2                    1.8.1
 s3transfer               0.10.2
-scanpy                   1.9.4
+scanpy                   1.10.2
 scikit-learn             1.5.1
-scipy                    1.11.2
+scipy                    1.13.1
 scprep                   1.2.3
-scvelo                   0.2.5
-scvi-tools               1.0.3
-seaborn                  0.12.2
+scvelo                   0.3.2
+scvi-tools               1.1.5
+seaborn                  0.13.2
 segregation              2.5
 session_info             1.0.0
 setuptools               71.0.1

diff --git a/docs/search_index.json b/docs/search_index.json