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Expand file tree Collapse file tree Original file line number Diff line number Diff line change @@ -47,7 +47,7 @@ The following command will run a diffusion method on a given network with the gi
4747
4848
4949 2. **Generate a kernel with one of the seven methods implemented **
50- Generates the regularised Laplian kernel of a given graph. More information in the `documentation
50+ Generates the regularised Laplacian kernel of a given graph. More information in the `documentation
5151<https://diffupy.readthedocs.io/en/latest/kernels.html> `_.
5252
5353.. code-block :: sh
Original file line number Diff line number Diff line change @@ -17,7 +17,9 @@ the following columns to your dataset:
1717- LogFC [*]_
1818- p-value
1919
20- .. [* ] log :sub: `2` fold change
20+ .. [* ] |Log | fold change
21+
22+ .. |Log | replace :: Log\ :sub: `2`
2123
2224Input dataset examples
2325~~~~~~~~~~~~~~~~~~~~~~
@@ -42,7 +44,7 @@ entity type.
4244+------------+--------------+
4345
44462. You can also choose to provide a dataset with a column 'Node' containing node IDs as well as a column 'logFC' with
45- their log :sub: `2` FC .
47+ their | LogFC | .
4648
4749+--------------+------------+
4850| Node | LogFC |
@@ -56,8 +58,10 @@ their log :sub:`2` FC.
5658| Gene D | 3 |
5759+--------------+------------+
5860
59- 3. Finally, you can provide a dataset with a column 'Node' containing node IDs, a column 'logFC' with their log :sub: `2`
60- FC and a column 'p-value' with adjusted p-values.
61+ .. |LogFC | replace :: Log\ :sub: `2`\ FC
62+
63+ 3. Finally, you can provide a dataset with a column 'Node' containing node IDs, a column 'logFC' with their |LogFC | and
64+ a column 'p-value' with adjusted p-values.
6165
6266+--------------+------------+---------+
6367| Node | LogFC | p-value |
Original file line number Diff line number Diff line change @@ -15,7 +15,9 @@ the following columns to your dataset:
1515- LogFC [*]_
1616- p-value
1717
18- .. [* ] log :sub: `2` fold change
18+ .. [* ] |Log | fold change
19+
20+ .. |Log | replace :: Log\ :sub: `2`
1921
2022Input dataset examples
2123~~~~~~~~~~~~~~~~~~~~~~
@@ -40,7 +42,7 @@ entity type.
4042+------------+--------------+
4143
42442. You can also choose to provide a dataset with a column 'Node' containing node IDs as well as a column 'logFC' with
43- their log :sub: `2` FC .
45+ their | LogFC | .
4446
4547+--------------+------------+
4648| Node | LogFC |
@@ -54,8 +56,10 @@ their log :sub:`2` FC.
5456| Gene D | 3 |
5557+--------------+------------+
5658
57- 3. Finally, you can provide a dataset with a column 'Node' containing node IDs, a column 'logFC' with their log :sub: `2`
58- FC and a column 'p-value' with adjusted p-values.
59+ .. |LogFC | replace :: Log\ :sub: `2`\ FC
60+
61+ 3. Finally, you can provide a dataset with a column 'Node' containing node IDs, a column 'logFC' with their |LogFC | and
62+ a column 'p-value' with adjusted p-values.
5963
6064+--------------+------------+---------+
6165| Node | LogFC | p-value |
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