singlecellseq
Batch effects and the effective design of single-cell gene expression studies
Science Score: 20.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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○codemeta.json file
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○.zenodo.json file
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○DOI references
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✓Academic publication links
Links to: ncbi.nlm.nih.gov, nature.com -
✓Committers with academic emails
3 of 10 committers (30.0%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (8.1%) to scientific vocabulary
Last synced: 11 months ago
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JSON representation
Repository
Batch effects and the effective design of single-cell gene expression studies
Basic Info
- Host: GitHub
- Owner: jdblischak
- License: other
- Language: R
- Default Branch: master
- Homepage: http://jdblischak.github.io/singleCellSeq/analysis
- Size: 1.3 GB
Statistics
- Stars: 101
- Watchers: 11
- Forks: 68
- Open Issues: 2
- Releases: 0
Created over 11 years ago
· Last pushed about 7 years ago
Metadata Files
Readme
Contributing
License
Citation
README.md
SingleCellSeq
Important links
See the site to view the results.
Read the paper.
Download the raw FASTQ files at GEO record GSE77288.
See the contributing guidelines to add a new analysis.
Project organization
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analysis/contains the R Markdown files documenting the results -
paper/contains the R Markdown files used to write the paper -
code/contains command-line scripts -
data/contains various summarized data files -
tests/contains some sanity checks
The majority of the generated content, e.g. figures and HTML files, are in the analysis/ subdirectory of the gh-pages branch.
Useful data files
- reads.txt - tab-delimited file contains read counts for the 19,027 Ensembl protein-coding genes with at least one observed read in at least one of the 864 single cell samples
- molecules.txt - same as
reads.txt, but for the molecule counts - reads-filter.txt - tab-delimited file contains read counts for the 13,106 Ensembl protein-coding genes that passed our expression level filter for the 564 single cells that passed our quality control filters
- molecules-filter.txt - same as
reads-filter.txt, but for the molecule counts - molecules-final.txt - tab-delimited file contains the final gene expression values after all of our processing steps
Owner
- Name: John Blischak
- Login: jdblischak
- Kind: user
- Location: Ohio, USA
- Website: https://jdblischak.com/
- Twitter: jdblischak
- Repositories: 39
- Profile: https://github.com/jdblischak
Freelance Scientific Software Developer
GitHub Events
Total
- Watch event: 6
- Fork event: 1
Last Year
- Watch event: 6
- Fork event: 1
Committers
Last synced: over 1 year ago
Top Committers
| Name | Commits | |
|---|---|---|
| John Blischak | j****k@g****m | 552 |
| Po Yuan Tung | p****g@u****u | 312 |
| jhsiao999 | j****1@g****m | 280 |
| PYTiMac | p****g@n****u | 3 |
| David Knowles | d****s@D****t | 2 |
| David Knowles | d****s@D****t | 2 |
| David Knowles | k****4@g****m | 2 |
| David Knowles | d****s@I****l | 1 |
| PYTiMac | p****g@n****u | 1 |
| jhsiao999 | j****1@d****m | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: about 1 year ago
All Time
- Total issues: 5
- Total pull requests: 54
- Average time to close issues: 3 months
- Average time to close pull requests: about 18 hours
- Total issue authors: 4
- Total pull request authors: 3
- Average comments per issue: 3.4
- Average comments per pull request: 0.48
- Merged pull requests: 53
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- WT215 (2)
- ateissan (1)
- jhsiao999 (1)
- mbuttner (1)
Pull Request Authors
- jhsiao999 (39)
- jdblischak (13)
- davidaknowles (2)