https://github.com/alleninstitute/scrattch.hicat
Hierarchical, iterative clustering for analysis of transcriptomics data in R
Science Score: 54.0%
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
Found codemeta.json file -
○.zenodo.json file
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✓DOI references
Found 1 DOI reference(s) in README -
✓Academic publication links
Links to: zenodo.org -
✓Committers with academic emails
9 of 12 committers (75.0%) from academic institutions -
✓Institutional organization owner
Organization alleninstitute has institutional domain (alleninstitute.org) -
○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (13.6%) to scientific vocabulary
Keywords
Keywords from Contributors
Repository
Hierarchical, iterative clustering for analysis of transcriptomics data in R
Basic Info
Statistics
- Stars: 114
- Watchers: 14
- Forks: 31
- Open Issues: 21
- Releases: 2
Topics
Metadata Files
README.md
scrattch.hicat: Hierarchical, Iterative Clustering for Analysis of Transcriptomics
Master: 
Dev: 
Installation
scrattch.hicat has several dependencies, including two from BioConductor and one from Github:
```
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("limma")
devtools::install_github("JinmiaoChenLab/Rphenograph") ```
Once these dependencies are installed, scrattch.hicat can be installed with:
devtools::install_github("AllenInstitute/scrattch.hicat")
Vignettes
An overview of the main functions in scrattch.hicat
Tutorials
An interactive walkthrough of the major steps in clustering for scrattch.hicat.
Roadmap
The next few updates to scrattch.hicat will be aimed at getting code testing in place for major clustering functions:
0.0.22: Current version; Tests in place for de.genes.R functions.
0.0.23: Tests in place for cluster.R functions.
0.1.0: Vignette re-integrated; Adding pkgdown page; Update to Master branch.
Previous updates:
0.0.21: Added TravisCI and covr integration.
The scrattch suite
scrattch.hicat is one component of the scrattch suite of packages for Single Cell RNA-seq Analysis for Transcriptomic Type CHaracterization from the Allen Institute.
License
The license for this package is available on Github at: https://github.com/AllenInstitute/scrattch.hicat/blob/master/LICENSE
Level of Support
We are planning on occasional updating this tool with no fixed schedule. Community involvement is encouraged through both issues and pull requests.
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/scrattch.hicat/blob/master/CONTRIBUTION
Image attribution:
By Internet Archive Book Images [No restrictions], via Wikimedia Commons
Owner
- Name: Allen Institute
- Login: AllenInstitute
- Kind: organization
- Location: Seattle, WA
- Website: https://alleninstitute.org
- Repositories: 184
- Profile: https://github.com/AllenInstitute
Please visit http://alleninstitute.github.io/ for more information.
GitHub Events
Total
- Issues event: 1
- Watch event: 6
- Issue comment event: 1
- Push event: 1
Last Year
- Issues event: 1
- Watch event: 6
- Issue comment event: 1
- Push event: 1
Committers
Last synced: about 1 year ago
Top Committers
| Name | Commits | |
|---|---|---|
| Zizhen Yao | z****y@a****g | 142 |
| Lucas Graybuck | l****g@a****g | 86 |
| cvanvelt | 4****t | 50 |
| jeremymiller | j****m@a****g | 27 |
| Saroja Somu | s****s@h****u | 9 |
| Trygve Bakken | t****b@a****g | 7 |
| adrisede | a****s@a****g | 7 |
| lawrenceh | l****h@a****g | 4 |
| Fahimeh Baftizadeh Baghal | f****b@l****l | 3 |
| Olivia Fong | o****f@a****g | 2 |
| yilinzhao1615 | 5****5 | 1 |
| Emir Turkes | e****s@b****u | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 10 months ago
All Time
- Total issues: 53
- Total pull requests: 94
- Average time to close issues: 8 months
- Average time to close pull requests: about 2 months
- Total issue authors: 20
- Total pull request authors: 14
- Average comments per issue: 0.77
- Average comments per pull request: 0.1
- Merged pull requests: 81
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 8
- Pull requests: 2
- Average time to close issues: 15 days
- Average time to close pull requests: 1 minute
- Issue authors: 4
- Pull request authors: 1
- Average comments per issue: 0.0
- Average comments per pull request: 0.0
- Merged pull requests: 2
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- hypercompetent (7)
- tebakken (5)
- tmchartrand (2)
- carmensandoval (2)
- SarojaSomu (1)
- Rushil-Chakra (1)
- DiracZhu1998 (1)
- deevdevil88 (1)
- JordanWean (1)
- yeetingc (1)
- bharris12 (1)
- dana-mcc (1)
- pnama (1)
- salwanbutrus (1)
- aarzalluz (1)
Pull Request Authors
- hypercompetent (17)
- y-gao (7)
- cvanvelt (6)
- adrisede (5)
- Fahimeh1983 (4)
- yzizhen (4)
- lawrenceh123 (2)
- rhngla (2)
- jeremymiller (2)
- SarojaSomu (2)
- leechangkyu (2)
- yilinzhao1615 (1)
- gs512 (1)
- eturkes (1)
Top Labels
Issue Labels
Pull Request Labels
Dependencies
- R >= 3.3.0 depends
- Rtsne * imports
- WGCNA * imports
- data.table * imports
- dendextend * imports
- devtools * imports
- doParallel * imports
- dplyr * imports
- foreach * imports
- ggplot2 * imports
- grid * imports
- limma * imports
- matrixStats * imports
- pvclust * imports
- qlcMatrix * imports
- Rphenograph * suggests
- covr * suggests
- knitr * suggests
- rmarkdown * suggests
- testthat * suggests