Analysis

Network Analysis Notebooks

location on server: /space/chen-syn01/1/data/cinliu/network_analysis_notebooks

Details:

This directory contains all the network analysis notebooks I have very been in contact in this lab

Content explained:

##AD_Localization_py2

contains files for running localization - this is the only file I still run in py2

#NOTE: localization is the only process that has not been converted to python 3 (at least the localization I have ran for this lab were all using py2).

If you would like to see a copy of localization being ran on python 3 I believe the makers of the network_bio_tool_kit has an example that might be helpful for you here: https://github.com/ucsd-ccbb/network_bio_toolkit/blob/master/notebooks/clustering_notebooks/Heat3_with_annotation.ipynb

##archive_mostly_py2

#AD_network_localization_seperation_py2

Contains localization and separation results as well as a power point summarizing the results. I did this in 2019

Some of the pdf have important comments (directly commented on the pdf file), you might only be able to see the comments on google drive: https://drive.google.com/drive/folders/1ZGlkD5DzSCj0JcolhTuNlePRyYc9nKTr?usp=sharing

#cluster_annotations_py3

#this is basically the same as the file in py3_ready_notebooks/cluster-DE-analysis_py3 but with the addition of outputting the annotation list by clusters. I don’t think it’s very pessary as py3_ready_notebooks/cluster-DE-analysis_py3 pretty much cover everything. But the is here if you need it

#Gwas_clusterDE_results_py2

#this is the cluster_DE )differential expression) python 2 version. I ran this in Jun 2020. An updated version can be found in py3_ready_notebooks/cluster-DE-analysis_py3

##py3_ready_notebooks

#cluster-DE-analysis_py3,

#cmap_notebook_python3

#separation_py2_and_py3

Are all from Anna. (Thank you Anna!)

Anna converted them from python2 to python3 (cmap_notebook_python3 was already in py3 but just needed some small adjustments) Aug 2021

She converted them using package py2to3 if you are interested: https://docs.python.org/3/library/2to3.html

#netcoloc_example_notebook were worked on by Anna, Anjali, and I .

This folder contains some video explanations in /netcoloc_example_notebook/video_tutorials

At the time right now cdapsutil is still experimental so I have a feeling this notebook will be outdated quite quickly with other updates and adjustments. Be on the looks out for that!

###Documentation date: Sept 2021 #####