Science Score: 26.0%
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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○Academic email domains
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (11.5%) to scientific vocabulary
Keywords
Repository
simPIC: simulating single cell ATAC-seq data
Basic Info
- Host: GitHub
- Owner: sagrikachugh
- Language: R
- Default Branch: devel
- Homepage: https://github.com/sagrikachugh/simPIC
- Size: 5.87 MB
Statistics
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
- Releases: 0
Topics
Metadata Files
README.md
simPIC
Overview
simPIC is an R package for simple simulation of single-cell Assay for Transposase Accessible Chromatin sequencing (scATAC-seq) data. simPIC provides an easy to use interface for:
- estimating simulation parameters
- Objects for storing those parameters
- simulating counts using those parameters
News
Version 1.5.3 (Development Version)
- Major updates to
simPICsimulatefunction to allow simulating multiple cell-types and batch effects.
For full change logs, please refer to the NEWS file.
Installation
The package can be installed from Bioconductor using the following code
r
if(!requireNamespace("BiocManager", quietly=TRUE))
install.packages("BiocManager")
BiocManager::install("simPIC")
For development version
r
BiocManager::install(
"sagrikachugh/simPIC",
dependencies = TRUE,
build_vignettes = TRUE
)
Getting started
To get started, check out the vignette for a quick start and detailed look into simPIC.
r
library(simPIC)
browseVignettes("simPIC")
Owner
- Name: Sagrika Chugh
- Login: sagrikachugh
- Kind: user
- Location: Melbourne, Australia
- Company: University of Melbourne
- Twitter: sagrikachugh
- Repositories: 1
- Profile: https://github.com/sagrikachugh
PhD candidate at the University of Melbourne and St. Vincent's Institute of Medical Research
GitHub Events
Total
- Delete event: 1
- Push event: 16
- Create event: 2
Last Year
- Delete event: 1
- Push event: 16
- Create event: 2
Issues and Pull Requests
Last synced: about 1 year ago
All Time
- Total issues: 0
- Total pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Total issue authors: 0
- Total 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
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
Pull Request Authors
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- bioconductor 3,653 total
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 3
- Total maintainers: 1
bioconductor.org: simPIC
simPIC: flexible simulation of paired-insertion counts for single-cell ATAC-sequencing data
- Homepage: https://github.com/sagrikachugh/simPIC
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/simPIC/inst/doc/simPIC.pdf
- License: GPL-3
-
Latest release: 1.4.0
published over 1 year ago
Rankings
Maintainers (1)
Dependencies
- R >= 4.4.0 depends
- SingleCellExperiment * depends
- BiocGenerics * imports
- Matrix * imports
- S4Vectors * imports
- SummarizedExperiment * imports
- actuar * imports
- checkmate >= 2.0.0 imports
- fitdistrplus * imports
- matrixStats * imports
- methods * imports
- rlang * imports
- scales * imports
- scuttle * imports
- stats * imports
- BiocStyle * suggests
- ggplot2 >= 3.4.0 suggests
- knitr * suggests
- rmarkdown * suggests
- testthat >= 3.0.0 suggests
- actions/checkout v4 composite
- r-lib/actions/setup-r v2 composite