https://github.com/simonsfoundation/th17_trn_networks
Data and notebooks for "Leveraging ATAC-seq data for transcriptional regulatory inference in Th17 Cells" by Miraldi et al.
https://github.com/simonsfoundation/th17_trn_networks
Last synced: 9 months ago
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Data and notebooks for "Leveraging ATAC-seq data for transcriptional regulatory inference in Th17 Cells" by Miraldi et al.
- Host: GitHub
- URL: https://github.com/simonsfoundation/th17_trn_networks
- Owner: simonsfoundation
- License: apache-2.0
- Created: 2018-02-14T17:22:30.000Z (over 8 years ago)
- Default Branch: master
- Last Pushed: 2019-02-20T19:10:57.000Z (over 7 years ago)
- Last Synced: 2025-01-18T21:32:38.786Z (over 1 year ago)
- Language: Jupyter Notebook
- Homepage:
- Size: 103 MB
- Stars: 2
- Watchers: 5
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
[](https://mybinder.org/v2/gh/simonsfoundation/Th17_TRN_Networks/master)
# Th17_TRN_Networks
This repository contains interactive visualization of transcriptional regulatory networks and gene expression data from:
[Miraldi et al., Leveraging chromatin accessibility for transcriptional regulatory network inference in T Helper 17 Cells](https://genome.cshlp.org/content/early/2019/02/19/gr.238253.118).
The repository has been designed to run in the cloud based Binder service.
Click the binder link above to launch a binder container running the notebooks
The repository is designed to use
[`repo2docker`](https://repo2docker.readthedocs.io/en/latest/)
to build a `docker` container which includes
the code for running the analysis and all needed dependencies.
The `repo2docker` tool requires the `docker` infrastructure
and Python 3 to run. See the
[installation instructions](https://repo2docker.readthedocs.io/en/latest/install.html).
To build the docker image from the command line
```bash
jupyter-repo2docker --no-run \
--image-name th17 \
https://github.com/simonsfoundation/Th17_TRN_Networks
```
To run the image after it has been built use `docker run`:
```bash
docker run -it --rm -p 8888:8888 th17:latest
```
When the docker instance starts up the log output looks like this:
```
[I 19:34:40.443 NotebookApp] Writing notebook server cookie secret to /home/rstudio/.local/share/jupyter/runtime/notebook_cookie_secret
[I 19:34:40.935 NotebookApp] Serving notebooks from local directory: /home/rstudio
[I 19:34:40.935 NotebookApp] 0 active kernels
[I 19:34:40.935 NotebookApp] The Jupyter Notebook is running at:
[I 19:34:40.935 NotebookApp] http://0.0.0.0:8888/?token=7baca1829f0665df26adf9943c6f04279647171eb3ffd12c
[I 19:34:40.935 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
[W 19:34:40.935 NotebookApp] No web browser found: could not locate runnable browser.
[C 19:34:40.936 NotebookApp]
Copy/paste this URL into your browser when you connect for the first time,
to login with a token:
http://0.0.0.0:8888/?token=7baca1829f0665df26adf9943c6f04279647171eb3ffd12c
```
Paste the `http:...` URL into your browser including your token (which will be different
from the one shown above) to connect to the Jupyter server.