LPWC
Lag Penalized Weighted Correlation for Time Series Clustering
Science Score: 23.0%
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
Found 2 DOI reference(s) in README -
○Academic publication links
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✓Committers with academic emails
2 of 3 committers (66.7%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (16.1%) to scientific vocabulary
Keywords
Repository
Lag Penalized Weighted Correlation for Time Series Clustering
Basic Info
- Host: GitHub
- Owner: gitter-lab
- License: other
- Language: R
- Default Branch: master
- Homepage: https://doi.org/10.1186/s12859-019-3324-1
- Size: 1.6 MB
Statistics
- Stars: 21
- Watchers: 5
- Forks: 3
- Open Issues: 5
- Releases: 0
Topics
Metadata Files
README.md
LPWC: Lag Penalized Weighted Correlation for Time Series Clustering
Authors: Thevaa Chandereng and Anthony Gitter
Overview
Lag Penalized Weighted Correlation (LPWC) is a method for clustering short time series data. It is designed to identify groups of biological entities (for example, genes or phosphosites) that exhibit the same pattern of activity changes over time. LPWC allows lags to incorporate delayed responses in the biological data. For example, two genes may have similar expression changes over time, but one initiates those changes 5 minutes after the other. LPWC also supports irregular time intervals between time points collected in biological data. The LPWC website is available here.
Installation
Prior to analyzing your data, the R package needs to be installed.
The easiest way to install LPWC is through CRAN:
r
install.packages("LPWC")
There are other additional ways to download LPWC. The first option is most useful if want to download a specific version of LPWC (which can be found at https://github.com/gitter-lab/LPWC/releases). ``` r devtools::install_github("gitter-lab/LPWC@vx.xx.x")
OR
devtools::install_version("LPWC", version = "x.x.x", repos = "http://cran.us.r-project.org") ```
The second option is to download through GitHub.
r
devtools::install_github("gitter-lab/LPWC")
After successful installation, the package must be loaded into the working space:
r
library(LPWC)
Usage
See the vignette for usage instructions.
Examples
The LPWC example repository is available here. All the example code can be executed in binder.
Reference
If you use LPWC, please cite
Chandereng, T., Gitter, A. Lag penalized weighted correlation for time series clustering. BMC Bioinformatics 21, 21 (2020). https://doi.org/10.1186/s12859-019-3324-1
License
LPWC is available under the open source MIT license.
Owner
- Name: Gitter Lab
- Login: gitter-lab
- Kind: organization
- Website: https://www.biostat.wisc.edu/~gitter/
- Repositories: 29
- Profile: https://github.com/gitter-lab
Computational biology research group at UW-Madison and the Morgridge Institute
GitHub Events
Total
- Watch event: 1
Last Year
- Watch event: 1
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Thevaa Chandereng | c****g@w****u | 239 |
| Anthony Gitter | g****r@b****u | 40 |
| Anthony Gitter | a****r | 15 |
Committer Domains (Top 20 + Academic)
Packages
- Total packages: 1
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Total downloads:
- cran 207 last-month
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 5
- Total maintainers: 1
cran.r-project.org: LPWC
Lag Penalized Weighted Correlation for Time Series Clustering
- Homepage: https://github.com/gitter-lab/LPWC
- Documentation: http://cran.r-project.org/web/packages/LPWC/LPWC.pdf
- License: MIT + file LICENSE
- Status: removed
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Latest release: 1.0.0
published over 6 years ago
Rankings
Maintainers (1)
Dependencies
- R >= 3.0.2 depends
- nleqslv * imports
- devtools * suggests
- ggplot2 * suggests
- knitr * suggests
- pkgdown * suggests
- rmarkdown * suggests
- testthat * suggests