Science Score: 39.0%
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
Found 8 DOI reference(s) in README -
○Academic publication links
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○Committers with academic emails
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (18.2%) to scientific vocabulary
Keywords
gene-expression-signatures
gene-set-enrichment
r-package
rstats
Last synced: 10 months ago
·
JSON representation
Repository
A Tidy Framework to Hack Gene Expression Signatures
Basic Info
- Host: GitHub
- Owner: Acare
- License: other
- Language: R
- Default Branch: master
- Homepage: https://acare.github.io/hacksig/
- Size: 7.36 MB
Statistics
- Stars: 19
- Watchers: 1
- Forks: 4
- Open Issues: 1
- Releases: 2
Topics
gene-expression-signatures
gene-set-enrichment
r-package
rstats
Created over 4 years ago
· Last pushed about 1 year ago
Metadata Files
Readme
Changelog
License
README.Rmd
---
output: github_document
---
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
options(tibble.print_min = 5L, tibble.print_max = 5L)
```
# hacksig 
[](https://lifecycle.r-lib.org/articles/stages.html#experimental) [](https://CRAN.R-project.org/package=hacksig) [](https://app.codecov.io/gh/Acare/hacksig?branch=master) [](https://github.com/Acare/hacksig/actions)
[](https://github.com/Acare/hacksig/actions/workflows/R-CMD-check.yaml)
The goal of `hacksig` is to provide a simple and tidy interface to compute single sample scores for gene signatures and methods applied in cancer transcriptomics.
Scores can be obtained either for custom lists of genes or for a manually curated collection of gene signatures, including:
- [CINSARC](https://doi.org/10.1038/nm.2174);
- [ESTIMATE](https://doi.org/10.1038/ncomms3612);
- [Immunophenoscore](https://doi.org/10.1016/j.celrep.2016.12.019);
- [Cytolitic activity](https://doi.org/10.1016/j.cell.2014.12.033);
- and more (use `get_sig_info()` to get a complete list of the implemented signatures)
At present, signature scores can be obtained either with the original publication method or using one of three single sample scoring alternatives, namely: *combined z-score*, *single sample GSEA* and *singscore*.
## Installation
You can install the last stable version of hacksig from [CRAN](https://CRAN.R-project.org) with:
```{r, eval=FALSE}
install.packages("hacksig")
```
Or the development version from [GitHub](https://github.com/) with:
```{r, eval=FALSE}
# install.packages("devtools")
devtools::install_github("Acare/hacksig")
```
## Usage
You can learn more about usage of the package in `vignette("hacksig")`.
```{r, message=FALSE}
library(hacksig)
library(dplyr)
library(future)
```
### Available signatures
```{r}
get_sig_info()
```
### Check your signatures
```{r}
check_sig(test_expr, signatures = "estimate")
```
### Compute single sample scores
```{r}
hack_sig(test_expr, signatures = c("ifng", "cinsarc"), method = "zscore")
```
### Stratify your samples
```{r}
test_expr %>%
hack_sig("estimate", method = "singscore", direction = "up") %>%
stratify_sig(cutoff = "median")
```
### Speed-up computation time
```{r}
plan(multisession)
hack_sig(test_expr, method = "ssgsea")
```
## Contributing
If you have any suggestions about adding new features or signatures to `hacksig`, please create an issue on [GitHub](https://github.com/Acare/hacksig/issues). Gene-level information about gene signatures are stored in `data-raw/hacksig_signatures.csv` and can be used as a template for requests.
Owner
- Name: Andrea Carenzo
- Login: Acare
- Kind: user
- Repositories: 2
- Profile: https://github.com/Acare
GitHub Events
Total
- Push event: 6
- Fork event: 1
Last Year
- Push event: 6
- Fork event: 1
Issues and Pull Requests
Last synced: over 2 years 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
- niuniueiko (1)
Pull Request Authors
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- cran 182 last-month
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 2
- Total maintainers: 1
cran.r-project.org: hacksig
A Tidy Framework to Hack Gene Expression Signatures
- Homepage: https://github.com/Acare/hacksig
- Documentation: http://cran.r-project.org/web/packages/hacksig/hacksig.pdf
- License: MIT + file LICENSE
- Status: removed
-
Latest release: 0.1.2
published over 4 years ago
Rankings
Forks count: 14.9%
Stargazers count: 15.6%
Dependent packages count: 29.8%
Average: 33.7%
Dependent repos count: 35.5%
Downloads: 72.6%
Maintainers (1)
Last synced:
10 months ago
Dependencies
DESCRIPTION
cran
- R >= 4.0 depends
- dplyr >= 1.0.7 imports
- future.apply >= 1.8.1 imports
- rlang >= 0.4.11 imports
- stats >= 4.0.5 imports
- tibble >= 3.1.5 imports
- tidyr >= 1.1.4 imports
- covr * suggests
- future >= 1.22.1 suggests
- ggplot2 >= 3.3.5 suggests
- knitr >= 1.36 suggests
- msigdbr >= 7.4.1 suggests
- purrr >= 0.3.4 suggests
- rmarkdown >= 2.11 suggests
.github/workflows/R-CMD-check.yaml
actions
- actions/checkout v2 composite
- r-lib/actions/check-r-package v1 composite
- r-lib/actions/setup-pandoc v1 composite
- r-lib/actions/setup-r v1 composite
- r-lib/actions/setup-r-dependencies v1 composite
.github/workflows/pkgdown.yaml
actions
- JamesIves/github-pages-deploy-action v4.4.1 composite
- actions/checkout v3 composite
- r-lib/actions/setup-pandoc v2 composite
- r-lib/actions/setup-r v2 composite
- r-lib/actions/setup-r-dependencies v2 composite