From bd68bca6a84f0f35eea842887a6df33c34ffabd6 Mon Sep 17 00:00:00 2001 From: er-eis Date: Tue, 2 Feb 2021 22:12:12 -0500 Subject: [PATCH 1/2] README references correct modular file --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 97c7a39..c688ad4 100644 --- a/README.md +++ b/README.md @@ -23,7 +23,7 @@ These six steps are as follows: 5. Consensus alignment (reassigns locations of path nodes in the topology to more accurately reflect paths observed in the data) 6. Scoring (compares the constructed topologies based on dissimilarity to produce a p-Creode score) -Current p-Creode methodology entails running steps one through five 100 times and then running step 6 one time. Each of the six steps can be found within the [_functions.py_](https://github.com/KenLauLab/pCreode/blob/master/pcreode/functions.py) file. +Current p-Creode methodology entails running steps one through five 100 times and then running step 6 one time. Each of the six steps can be found within the [algorithm.py](https://github.com/KenLauLab/pCreode/blob/master/pcreode/algorithm.py) file. ### Installation for Linux (recommended) @@ -40,7 +40,7 @@ pip install . pip install scanpy ``` -3. Verify everything works as expected by running the 'pCreode_tutorial.ipynb' file. The file should run without errors. +3. Verify everything works as expected by running the [pCreode_tutorial.ipynb](https://github.com/KenLauLab/pCreode/blob/master/notebooks/pCreode_tutorial.ipynb) file. The file should run without errors. ### Installation for Mac From 819ff0246c360360f8fd8538b1f88824db2478ab Mon Sep 17 00:00:00 2001 From: er-eis Date: Tue, 2 Feb 2021 22:12:32 -0500 Subject: [PATCH 2/2] Base algorithm file --- pcreode/algorithm.py | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) create mode 100644 pcreode/algorithm.py diff --git a/pcreode/algorithm.py b/pcreode/algorithm.py new file mode 100644 index 0000000..cecdc30 --- /dev/null +++ b/pcreode/algorithm.py @@ -0,0 +1,17 @@ +def down_sampling(data): + return + +def graph_construction(data): + return + +def end_state_identification(data): + return + +def hierarchical_placement(data): + return + +def consensus_alignment(data): + return + +def scoring(data): + return \ No newline at end of file