Science Score: 36.0%
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
Found .zenodo.json file -
○DOI references
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○Academic publication links
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✓Committers with academic emails
14 of 38 committers (36.8%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (8.4%) to scientific vocabulary
Keywords from Contributors
bioconductor-package
genomics
gene
feature-detection
peak-detection
single-cell-rna-seq
mass-spectrometry
single-cell
metabolomics
core-package
Last synced: 10 months ago
·
JSON representation
Repository
Cytometry dATa anALYsis Tools
Statistics
- Stars: 69
- Watchers: 11
- Forks: 31
- Open Issues: 16
- Releases: 0
Created over 9 years ago
· Last pushed 12 months ago
Metadata Files
Readme
Changelog
README.md
Welcome to CATALYST 
CATALYST leverages existing R/Bioconductor infrastructure by building around Biocondcutor's SingleCellExperiment class, and by providing an interface for conversion to other data structures established in the cytometry community (e.g., flowCore's flowFrame/Set classes), thus facilitating communication with existing tools for visualization (e.g., ggcyto) and gating (e.g., openCyto). The package currently provides:
- an extensive suit of visualizations for differential discovery
- a pipeline for preprocessing of cytometry data, including
- normalization using bead standards
- single-cell deconvolution
- bead-based compensation
References
- Chevrier S☆, Crowell HL☆, Zanotelli VRT☆, Engler S, Robinson MD & Bodenmiller B (2018):
Compensation of Signal Spillover in Suspension and Imaging Mass Cytometry. Cell Systems 6(5):612-620.e5. - Nowicka M, Krieg C, Crowell HL, Weber LM, Hartmann FJ, Guglietta S, Becher B, Levesque MP & Robinson MD (2017):
CyTOF workflow: differential discovery in high-throughput high-dimensional cytometry datasets. F1000Resaearch 6:748.
Got a problem (or an idea)?
CATALYST is still under active development. We greatly welcome (and highly encourage!) all feedback, bug reports and suggestions for improvement HERE. Please make sure to raise issues with a reproducible example and the output of your sessionInfo().
Owner
- Name: Helena L. Crowell
- Login: HelenaLC
- Kind: user
- Location: University of Zurich, Switzerland
- Website: https://helenalc.github.io
- Repositories: 7
- Profile: https://github.com/HelenaLC
GitHub Events
Total
- Issues event: 23
- Watch event: 3
- Issue comment event: 43
- Push event: 17
- Create event: 2
Last Year
- Issues event: 23
- Watch event: 3
- Issue comment event: 43
- Push event: 17
- Create event: 2
Committers
Last synced: about 1 year ago
Top Committers
| Name | Commits | |
|---|---|---|
| HelenaLC | h****a@c****u | 1,824 |
| HelenaLC | c****h@s****h | 553 |
| h.crowell | h****l@b****8 | 203 |
| votti | v****i@g****m | 68 |
| markrobinsonuzh | m****n@i****h | 29 |
| HelenaLC | H****C@d****h | 28 |
| HelenaLC | H****C@H****l | 28 |
| HelenaLC | H****C@d****h | 20 |
| HelenaLC | H****C@d****h | 16 |
| HelenaLC | h****l@u****h | 16 |
| Nitesh Turaga | n****a@g****m | 14 |
| HelenaLC | H****C@d****h | 12 |
| HelenaLC | H****C@d****h | 12 |
| J Wokaty | j****y@s****u | 10 |
| Helena Lucia Crowell | h****c@d****h | 8 |
| HelenaLC | H****C@d****h | 8 |
| HelenaLC | H****C@d****h | 8 |
| HelenaLC | H****C@d****h | 8 |
| HelenaLC | H****C@d****h | 4 |
| HelenaLC | H****C@d****h | 4 |
| HelenaLC | H****C@d****h | 4 |
| HelenaLC | H****C@d****h | 4 |
| HelenaLC | H****C@d****h | 4 |
| HelenaLC | H****C@d****h | 4 |
| HelenaLC | H****C@d****h | 4 |
| Hervé Pagès | h****s@f****g | 4 |
| HelenaLC | h****a@c****u | 3 |
| Kayla-Morrell | k****l@r****g | 2 |
| Lukas Weber | l****r@g****m | 2 |
| vobencha | v****a@g****m | 2 |
| and 8 more... | ||
Committer Domains (Top 20 + Academic)
fhcrc.org: 4
roswellpark.org: 2
sph.cuny.edu: 2
crowells.eu: 1
student.ethz.ch: 1
imls.uzh.ch: 1
dhcp-wlan-uzh-10-12-176-056.uzh.ch: 1
dhcp-wlan-uzh-10-12-123-011.uzh.ch: 1
dhcp-wlan-eduroam-192-41-132-114.uzh.ch: 1
uzh.ch: 1
dhcp-wlan-eduroam-192-41-132-034.uzh.ch: 1
dhcp-wlan-uzh-10-12-118-166.uzh.ch: 1
dhcp-nwap-il-y11-89-206-120-244.uzh.ch: 1
dhcp-wlan-eduroam-192-41-133-083.uzh.ch: 1
dhcp-wlan-eduroam-192-41-134-220.uzh.ch: 1
dhcp-wlan-eduroam-192-41-135-035.uzh.ch: 1
dhcp-wlan-eduroam-192-41-132-158.uzh.ch: 1
dhcp-wlan-eduroam-192-41-134-021.uzh.ch: 1
dhcp-wlan-eduroam-192-41-134-144.uzh.ch: 1
dhcp-wlan-eduroam-192-41-134-178.uzh.ch: 1
dhcp-wlan-eduroam-192-41-135-111.uzh.ch: 1
dhcp-wlan-eduroam-192-41-135-249.uzh.ch: 1
Issues and Pull Requests
Last synced: 10 months ago
All Time
- Total issues: 202
- Total pull requests: 13
- Average time to close issues: 3 months
- Average time to close pull requests: about 2 months
- Total issue authors: 117
- Total pull request authors: 7
- Average comments per issue: 2.78
- Average comments per pull request: 0.46
- Merged pull requests: 4
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 20
- Pull requests: 0
- Average time to close issues: 6 days
- Average time to close pull requests: N/A
- Issue authors: 16
- Pull request authors: 0
- Average comments per issue: 3.0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- denvercal1234GitHub (15)
- schevrie (14)
- votti (8)
- bioguy2018 (5)
- joe-jhou2 (5)
- TongzhenXu (4)
- SamGG (4)
- Tregwiz (4)
- yamihn (3)
- MargolinGaby (3)
- shanh1 (3)
- LukaTandaric (3)
- mtrussart (3)
- grhogg (3)
- Ind2022 (2)
Pull Request Authors
- markrobinsonuzh (5)
- votti (3)
- sameetmehta (1)
- esimonds (1)
- sellth (1)
- sorjuela (1)
- lmweber (1)
Top Labels
Issue Labels
bug (6)
enhancement (4)
question (1)
Pull Request Labels
bug (1)
enhancement (1)
Packages
- Total packages: 1
-
Total downloads:
- bioconductor 64,514 total
- Total dependent packages: 5
- Total dependent repositories: 0
- Total versions: 8
- Total maintainers: 1
bioconductor.org: CATALYST
Cytometry dATa anALYSis Tools
- Homepage: https://github.com/HelenaLC/CATALYST
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/CATALYST/inst/doc/CATALYST.pdf
- License: GPL (>=2)
-
Latest release: 1.32.0
published about 1 year ago
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Forks count: 0.4%
Stargazers count: 2.8%
Average: 4.9%
Downloads: 21.3%
Maintainers (1)
Last synced:
11 months ago
Dependencies
DESCRIPTION
cran
- R >= 4.0 depends
- SingleCellExperiment * depends
- ComplexHeatmap * imports
- ConsensusClusterPlus * imports
- FlowSOM * imports
- Matrix * imports
- RColorBrewer * imports
- Rtsne * imports
- S4Vectors * imports
- SummarizedExperiment * imports
- circlize * imports
- cowplot * imports
- data.table * imports
- dplyr * imports
- drc * imports
- flowCore * imports
- ggplot2 * imports
- ggrepel * imports
- ggridges * imports
- grDevices * imports
- graphics * imports
- grid * imports
- gridExtra * imports
- magrittr * imports
- matrixStats * imports
- methods * imports
- nnls * imports
- purrr * imports
- reshape2 * imports
- scales * imports
- scater * imports
- stats * imports
- BiocStyle * suggests
- diffcyt * suggests
- flowWorkspace * suggests
- ggcyto * suggests
- knitr * suggests
- openCyto * suggests
- rmarkdown * suggests
- testthat * suggests
- uwot * suggests
.github/workflows/check-bioc.yml
actions
- JamesIves/github-pages-deploy-action releases/v4 composite
- actions/cache v3 composite
- actions/checkout v3 composite
- actions/upload-artifact master composite
- docker/build-push-action v1 composite
- r-lib/actions/setup-pandoc v2 composite
- r-lib/actions/setup-r v2 composite