• The path of where the files are located on the server can be found as the first line of each page.

• If the path leads you to a location where there is a directory and a .zip with the same name as the directory, then that means this file was originally ran and stored on my local computer.

  • I would advise downloading the .zip file from the server to your local computer and navigating those directory locally this way (some of the files might have images and file names that are not server/command line friend)

• Most of the dates you see here are referring to the first dates the task was assigned.

• Notes about the email line:

  • when you see in (outlook) that means I received the email through my ucsd health outlook account: cil001@health.ucsd.edu

  • when you see (gmail) that means I received the email through my gmail account: cinliu@berkeley.edu

  • CH = Chi Hua

Plots/ Data visaulization

Data Management/Analysis

8.reorder_cor_mat.R

Location on server: /space/chen-syn01/1/data/cinliu/data/2020archive/reorder_cor

CH slack, Dec 30th 2020 - Jan 12th 2020)

Breakdown gclust440

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

AD Localization

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)

Merge_SNPmarker

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

Searching LD SNPs

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

Merge 2 files by first column

Stored on server: /space/chen-syn01/1/data/cinliu/data/merge_by_col1

Slack CH Sept 22nd 2021

plink to raw

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

Correlation between 2 files

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)

gene symbol converstion

Location on server: /space/chen-syn01/1/data/cinliu/data/entrezID_to_gene_symb

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.

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 #####