https://github.com/hbhargava7/bp205b-project

https://github.com/hbhargava7/bp205b-project

Last synced: 7 days ago
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• Host: GitHub
• URL: https://github.com/hbhargava7/bp205b-project
• Owner: hbhargava7
• Created: 2020-01-10T23:39:26.000Z (almost 5 years ago)
• Default Branch: master
• Last Pushed: 2020-02-24T23:00:38.000Z (almost 5 years ago)
• Last Synced: 2024-10-28T10:19:26.637Z (about 2 months ago)
• Language: Jupyter Notebook
• Size: 10.4 MB
• Stars: 0
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
# bp205b-project

Assigns cell barcode to corresponding multiseq barcode

Applies Monocle Trajectory Analysis to cell barcoded expression data

## Jupyter notebooks

* data-analysis.ipynb - contains the functions necessary for mapping, as well as run_all function (takes in read1 and read2 gz files, cell barcode whitelist, multiseq barcode whitelist). Generates mapping csv and plots

* specific files - has files filled in, generates specific csv and plot when run

  * data-analysis-aa.ipynb

  * data-analysis-mk.ipynb

  * data-analysis-gbc.ipynb

## R Script

* TJ_Analysis_Clean.R - contains functions required for Monocle workflow. Applies clustering, trajectory analysis, DEx Gene branch analysis.

## Subfolders

* dataset folders - read1 and read2 gz files, whitelisted barcodes

  * aa_dataset

  * mk_dataset

  * gbc_dataset

* results - generated plots and mapping csvs