https://github.com/brocklab/cmduo-analysis
Science Score: 26.0%
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○Scientific vocabulary similarity
Low similarity (8.1%) to scientific vocabulary
Repository
Basic Info
- Host: GitHub
- Owner: brocklab
- Language: R
- Default Branch: main
- Size: 7 MB
Statistics
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
This repo contains all code to reproduce analysis and figures in "Mapping cell-cell fusion at single-cell resolution" (https://doi.org/10.1101/2024.12.11.627873)
Accessing raw data
Raw and processed single cell RNA-sequencing can be downloaded from GEO with accession number GSE286213. Targeted barcode sequencing to generate a list of barcodes in the samples using pycashier can be downloaded from Gene Expression Omnibus (GEO) with accession number GSE286212.
In notebooks 7-13, the h1806_colors_cellclass_hclust_nb-barassigned_ccclustered_precc_singlets.rds is equivalent to
GSE286213_CMDuo_seurat_qc_barcodeAnnotated_HCC1806_samples.rds from GEO, and mb231_colors_cellclass_hclust_nb-barassigned_ccclustered_precc_singlets.rds is equivalent to GSE286213_CMDuo_seurat_qc_barcodeAnnotated_MDAMB231_samples.rds. Start here if you want to perform downstream analysis. These objects can also be used as the starting point in notebooks 3-6, the objects in notebooks 1-2 need to be built from raw.
Raw data processing
To start from raw sequencing data, follow the notes in 00_Raw_data_processing_and_alignment_notes.md
Setting up the Rstudio analysis environment
To setup your analysis environment, download the Docker Image which is equipped to launch Rstudio with all the necessary packages and versions:
docker pull phdidi/cmduo_rocker:latest
Port Rstudio to your local browser from your server by running:
docker run --rm -ti -e PASSWORD=makeapassword -e USERID="$(id -u)" -e GROUPID="$(id -g)" -p 8770:8787 -v "$(pwd)":/home/rstudio/workspace cmduo_rocker
On your local machine run (change 'user' to your username on your server and 'host' to your server name)
ssh -NL 8770:localhost:8770 -p 22 user@host
Then open a browser and navigate to: http://localhost:8770/
When prompted, enter 'rstudio' as your username and 'makeapassword' (or whatever you set this to) as your password to launch Rstudio.
Owner
- Name: brocklab
- Login: brocklab
- Kind: organization
- Location: Austin, TX
- Website: http://www.brocklab.com/
- Repositories: 4
- Profile: https://github.com/brocklab
GitHub Events
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- Push event: 1
- Public event: 1
Last Year
- Push event: 1
- Public event: 1