https://github.com/stjudecloud/expression-classification
https://github.com/stjudecloud/expression-classification
Last synced: 12 months ago
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- Host: GitHub
- URL: https://github.com/stjudecloud/expression-classification
- Owner: stjudecloud
- License: mit
- Created: 2019-12-06T18:36:24.000Z (over 6 years ago)
- Default Branch: master
- Last Pushed: 2025-04-11T15:03:21.000Z (about 1 year ago)
- Last Synced: 2025-07-11T14:27:22.320Z (12 months ago)
- Language: Python
- Size: 483 KB
- Stars: 2
- Watchers: 3
- Forks: 0
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.md
- License: LICENSE.md
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README
# Interactive t-SNE
Code used to generate interactive t-SNE plots using RNA-Seq counts data.
## Getting Started
These instructions will get you a copy of the project up and running on your local machine for development and testing purposes. See deployment for notes on how to deploy the project on a live system.
### Prerequisites
To get started, you'll want to have Python 3 and R 3.6.1.
```bash
conda create -n itsne-dev \
-c conda-forge \
-c bioconda \
r-base=3.6.1 \
python=3.7 \
logzero \
numpy \
pandas \
scikit-learn \
bioconductor-biocinstaller \
bioconductor-sva \
bioconductor-deseq2 \
r-tsne r-getopt r-plotly r-optparse r-rtsne r-pracma r-data.table -y
conda activate itsne-dev
```
Alternatively, you can install the anaconda dependencies directly from the `environment.yml` file.
```bash
conda env create -f environment.yml
```
### Installing
First, the author recommends you run the following command line script to ensure all R
packages are loaded before your first run:
```bash
Rscript scripts/itsne-normalize-matrix.R
```
From here, you can install the python package:
```bash
python3 setup.py install
```
Download the relevant gene model:
```bash
curl ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_31/gencode.v31.annotation.gtf.gz -o gencode.v31.annotation.gtf.gz
```
And try out the script:
```bash
itsne-main counts/* \
-b reference/gene.excludelist.tsv \
-c reference/covariates.tsv \
-g gencode.v31.annotation.gtf.gz \
-o tsne.html
```
## Running the tests
No tests currently exist. If and when tests are added, the authors will fill in this section.
## Contributing
Please read [CONTRIBUTING.md](CONTRIBUTING.md) for details on our code of conduct, and the process for submitting pull requests to us.
## Versioning
We use [SemVer](http://semver.org/) for versioning. For the versions available, see the [tags on this repository](https://github.com/stjudecloud/expression-classification/tags).
## License
This project is licensed under the MIT License - see the [LICENSE.md](LICENSE.md) file for details