https://github.com/alleninstitute/l5_ven
This repository contains code for reproducing the analysis of snRNA-seq data from human fronto-insula
https://github.com/alleninstitute/l5_ven
Last synced: about 1 year ago
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This repository contains code for reproducing the analysis of snRNA-seq data from human fronto-insula
- Host: GitHub
- URL: https://github.com/alleninstitute/l5_ven
- Owner: AllenInstitute
- License: other
- Created: 2019-03-08T22:54:18.000Z (over 7 years ago)
- Default Branch: master
- Last Pushed: 2022-07-27T17:25:59.000Z (almost 4 years ago)
- Last Synced: 2025-04-11T20:11:46.466Z (about 1 year ago)
- Language: R
- Size: 14 MB
- Stars: 6
- Watchers: 4
- Forks: 3
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# VENcelltypes
This repository contains code for reproducing the analysis of snRNA-seq data from human fronto-insula described in [Hodge, Miller, et al 2020](https://www.nature.com/articles/s41467-020-14952-3).
While this is set up as an R library for convenience, it is really just a wrapper for the analysis functions and does not follow all of the conventions of R libraries (function annotation, unit testing, etc.). Please be sure to cite the appropriate other R libraries if replicating the code.
Install using:
```
devtools::install_github("AllenInstitute/VENcelltypes")
```
There are several dependencies listed in the code books below, but one notable one is that [version **3.0** of Seurat](https://satijalab.org/seurat/pancreas_integration_label_transfer.html) needs to be installed.
```
devtools::install_github(repo = "satijalab/seurat", ref = "release/3.0")
```
## Code book
To replicate the figures in the paper, please use the code below:
1. **Code 1. Download and prepare the data** [(LINK TO SCRIPT)](http://htmlpreview.github.io/?https://github.com/AllenInstitute/VENcelltypes/blob/master/vignettes/Code1_prepareComparisonDataSets.nb.html) This script reads converts data downloaded from the [Allen Institute Cell Types Database](http://celltypes.brain-map.org/rnaseq) into a format compatible for use as comparison data to human fronto-insula.
2. **Code 2. Rename clusters and build tree** [(LINK TO SCRIPT)](http://htmlpreview.github.io/?https://github.com/AllenInstitute/VENcelltypes/blob/master/vignettes/Code2_clusterNames_buildTree_Fig1.nb.html) This script reads in the data and assigned clusters, organizes the clusters into a dendrogram, renames the clusters to include class information and informative genes, and then plots some summary plots.
3. **Code 3. Quality control assessment** [(LINK TO SCRIPT)](http://htmlpreview.github.io/?https://github.com/AllenInstitute/VENcelltypes/blob/master/vignettes/Code3_QC_assessment_FigS1.nb.html) This script reads in the data output to the feather files and uses it to calculate and plot some QC information for Supplementary figure 1.
4. **Code 4. Cross-species analysis** [(LINK TO SCRIPT)](http://htmlpreview.github.io/?https://github.com/AllenInstitute/VENcelltypes/blob/master/vignettes/Code4_crossSpeciesComparisons.nb.html) This script performs alignment of deep excitatory neurons in human fronto-insula, human middle temporal gyrus, mouse primary visual cortex, and mouse anterior lateral motor cortex. It also identifies genes with common and distinct patterning across these data sets.
5. **Code 5. Human FI vs. Human MTG comparison** [(LINK TO SCRIPT)](http://htmlpreview.github.io/?https://github.com/AllenInstitute/VENcelltypes/blob/master/vignettes/Code5_humanMTGvsFI.nb.html) This script identifies common and distinct CF-associated genes in human middle temporal gyrus as compared with human fronto-insula, and compares the proportions of cells across clusters for each brain region.
All code was tested in both a UNIX and Windows environment and show to produce the same result, with the exception of the UMAP visualization noted in Code 4.
Please e-mail jeremym@alleninstitute.org with any issues.
## License
The license for this package is available on Github at: https://github.com/AllenInstitute/VENcelltypes/blob/master/LICENSE
## Level of Support
This code will be updated only if figures change during review.
## Contribution Agreement
If you contribute code to this repository through pull requests or other mechanisms, you are subject to the Allen Institute Contribution Agreement, which is available in full at: https://github.com/AllenInstitute/VENcelltypes/blob/master/CONTRIBUTION