https://github.com/bricoletc/single-cell-rna-seq-4predocs
Science Score: 36.0%
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Found 2 DOI reference(s) in README -
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Repository
Basic Info
- Host: GitHub
- Owner: bricoletc
- License: mit
- Language: R
- Default Branch: master
- Size: 1.3 MB
Statistics
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
Snakemake workflow: single-cell-rna-seq
A single cell RNA-seq workflow following Lun, McCarthy and Marioni 2016 and Soneson and Robinson 2018, with added more recent functionality.
Authors
- Johannes Köster, https://koesterlab.github.io
Usage
In any case, if you use this workflow in a paper, don't forget to give credits to the authors by citing the URL of this (original) repository and, if available, its DOI (see above).
Step 1: Obtain a copy of this workflow
- Create a new github repository using this workflow as a template.
- Clone the newly created repository to your local system, into the place where you want to perform the data analysis.
Step 2: Configure workflow
Configure the workflow according to your needs via editing the file config.yaml.
Step 3: Execute workflow
Test your configuration by performing a dry-run via
snakemake --use-conda -n
Execute the workflow locally via
snakemake --use-conda --cores $N
using $N cores or run it in a cluster environment via
snakemake --use-conda --cluster qsub --jobs 100
or
snakemake --use-conda --drmaa --jobs 100
If you not only want to fix the software stack but also the underlying OS, use
snakemake --use-conda --use-singularity
in combination with any of the modes above. See the Snakemake documentation for further details.
Step 4: Investigate results
After successful execution, you can create a self-contained interactive HTML report with all results via:
snakemake --report report.html
This report can, e.g., be forwarded to your collaborators. An example (using some trivial test data) can be seen here.
Step 5: Commit changes
Whenever you change something, don't forget to commit the changes back to your github copy of the repository:
git commit -a
git push
Step 6: Contribute back
In case you have also changed or added steps, please consider contributing them back to the original repository:
- Fork the original repo to a personal or lab account.
- Clone the fork to your local system, to a different place than where you ran your analysis.
- Copy the modified files from your analysis to the clone of your fork, e.g.,
cp -r envs rules scripts path/to/fork. Make sure to not accidentally copy config file contents or sample sheets. - Commit and push your changes to your fork.
- Create a pull request against the original repository.
Testing
Test cases are in the subfolder .test. They are automtically executed via continuous integration with Travis CI.
Owner
- Name: Brice Letcher
- Login: bricoletc
- Kind: user
- Company: EMBL-EBI
- Twitter: bricoletc
- Repositories: 2
- Profile: https://github.com/bricoletc
Bioinformatician and early-career researcher - EMBL-EBI and CNRS ~~~~~~ Parsing my way through DNA sequence data
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| Name | Commits | |
|---|---|---|
| Brice Letcher | b****r@e****k | 1 |
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