Location on server: /space/chen-syn01/1/data/cinliu/data/2020archive/reorder_cor
CH slack, Dec 30th 2020 - Jan 12th 2020)
Location on server: /space/chen-syn01/1/data/cinliu/data/gclust440_subsetdat
Breakdown gclust440 into 25 .txt files
outlook email title: break down a file - Feb 15th 2021
CH slack, Feb 16th 2021
Location on server: /space/chen-syn01/1/data/cinliu/data/netowrk_bio_toolkit/AD_Localization
Additions lab journal page: AD networktool kit
UKBio Data extraction and PRSice
Location on server: /space/chen-syn01/1/data/cinliu/data/UKB_extraction/
Outlook email title: Data extraction and PRSice - Oct 19th 2020
outlook email titiel: UKBio Factor extraction commands expatiation- Nov 15th 2020
(Also see: slack messages with Hao between Oct 19th 2020 & Slack with CH Nov 3rd 2020)
Slack CH April 7th 2021
location on server: /space/chen-syn01/1/data/cinliu/data/extract_clean_SNPID
For a more cleaned up version see: /space/chen-syn01/1/data/cinliu/data/extract_clean_SNPID/SNPmarker
Files stored: /space/chen-syn01/1/data/cinliu/data/clozapine/data_April2021/LD_proxy/
Instructions and explanation: /space/chen-syn01/1/data/cinliu/data/clozapine/data_April2021/LD_proxy/code_and_instructions
outlook email title: searching LD SNPs
June 20th 2021- email from CH
Stored on server: /space/chen-syn01/1/data/cinliu/data/merge_by_col1
Slack CH Sept 22nd 2021
path of this project on server: /space/chen-syn01/1/data/cinliu/data/clozapine/data_April2021/
Details: /space/chen-syn01/1/data/cinliu/data/clozapine/data_April2021/1.plink2raw.sh
April 21st 2021 - CH Slack
Location on server: /space/chen-syn01/1/data/cinliu/data/percent_match_check_Hao_vs_Tuo
Slack CH April 8th 2021 - April 17th 2021
data matching percentage check
Location on server: /space/chen-syn01/1/data/cinliu/data/dat4Tyler
email title: "data matching percentage check"
March 25th 2021 (date the final version of file was send out)
Location on server: /space/chen-syn01/1/data/cinliu/data/entrezID_to_gene_symb
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.
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 , and #separation_py2_and_py3 were 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 #####