https://github.com/epigen/artemether_scrna
Single cell RNA-seq analysis of pancreatic islets with drug treatment
https://github.com/epigen/artemether_scrna
Last synced: about 1 year ago
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Single cell RNA-seq analysis of pancreatic islets with drug treatment
- Host: GitHub
- URL: https://github.com/epigen/artemether_scrna
- Owner: epigen
- Created: 2019-12-19T09:18:35.000Z (over 6 years ago)
- Default Branch: master
- Last Pushed: 2020-03-25T10:34:55.000Z (about 6 years ago)
- Last Synced: 2023-10-20T19:42:16.091Z (over 2 years ago)
- Language: R
- Size: 294 KB
- Stars: 1
- Watchers: 6
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# Artemether_scRNA
Single cell RNA-seq analysis of pancreatic islets with drug treatment. This is the code used to analyze this dataset.
# Structure
Scripts to analyze all data are in src/, see the readme file in this directory for more details.
Additional data (i.e. list of marker genes, etc) are in the folder metadata/.
# System requirements
The code provided requires the setting of two environmental variables $CODEBASE (where the code is) and $PROCESSED (where the data is and analysis results will be stored). For example:
```
export CODEBASE="$HOME/code/"
export PROCESSED="$HOME/projects/"
```
Genome alignments are based on CellRanger (version 2.1.0).
Statistical analysis is based on R (version 3.4.0), using the following packages:
- SoupX (version 0.1.1)
- Seurat (version 2.0.1)
- cowplot (version 0.8.0)
- Rtsne (version 0.13)
- ROCR (version 1.0-7)
- gplots (version 3.0.1.1)
- rhdf5 (version 2.20.0)
- pryr (version 0.1.4)
- project.init (version 0.0.1)
- pheatmap (version 1.0.12)
- glmnet (version 2.0-18)
- enrichR (version 1.0)
- dplyr (version 0.7.2)
- doMC (version 1.3.4)
- iterators (version 1.0.12)
- foreach (version 1.4.3)
- data.table (version 1.12.2)
- cellrangerRkit (version 2.0.0)
- Rmisc (version 1.5)
- plyr (version 1.8.4)
- lattice (version 0.20-38)
- ggplot2 (version 3.1.1)
- RColorBrewer (version 1.1-2)
- Matrix (version 1.2-17)