https://github.com/nuno-agostinho/ctrap
Identification of candidate causal perturbations from differential gene expression data
https://github.com/nuno-agostinho/ctrap
bioconductor bioinformatics cmap gene-expression l1000 r r-package
Last synced: about 2 months ago
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Identification of candidate causal perturbations from differential gene expression data
- Host: GitHub
- URL: https://github.com/nuno-agostinho/ctrap
- Owner: nuno-agostinho
- License: other
- Created: 2018-09-25T10:23:35.000Z (about 7 years ago)
- Default Branch: devel
- Last Pushed: 2025-07-28T07:26:59.000Z (3 months ago)
- Last Synced: 2025-07-28T09:24:34.044Z (3 months ago)
- Topics: bioconductor, bioinformatics, cmap, gene-expression, l1000, r, r-package
- Language: R
- Homepage: https://nuno-agostinho.github.io/cTRAP
- Size: 479 MB
- Stars: 6
- Watchers: 1
- Forks: 1
- Open Issues: 4
-
Metadata Files:
- Readme: README.md
- Changelog: NEWS.md
- License: LICENSE
Awesome Lists containing this project
README
# cTRAP
[![GitHub Actions Build status][ghActionsIcon]][ghActions]
[![Coverage status][codecovBadge]][codecov]
`cTRAP` is an R package designed to compare differential gene
expression results with those from known cellular perturbations (such as gene
knock-down, overexpression or small molecules) derived from the
[Connectivity Map][clue.io] [(Subramanian et al., Cell 2017)][subramanian2017].
Such analyses allow not only to infer the molecular causes of the observed
difference in gene expression but also to identify small molecules that could
drive or revert specific transcriptomic alterations.
## Installing
### Bioconductor
[cTRAP is available in Bioconductor][bioconductor] and can be installed with:
``` r
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("cTRAP")
```
### GitHub
cTRAP can also be installed from GitHub instead:
``` r
install.packages("remotes")
remotes::install_github("nuno-agostinho/cTRAP")
```
### Docker
The Docker images are based on [Bioconductor Docker][biocDocker] and contain cTRAP and its dependencies.
1. Pull the latest Docker image:
```
docker pull ghcr.io/nuno-agostinho/ctrap:latest
```
2. Start RStudio Web from the Docker image:
```
docker run -e PASSWORD=bioc -p 8787:8787 ghcr.io/nuno-agostinho/ctrap:latest
```
3. Go to RStudio Web via your web browser at https://localhost:8787
4. Login in RStudio Web with user `rstudio` and password `bioc`
5. Load the package in RStudio Web using `library(cTRAP)`
[clue.io]: https://clue.io/
[subramanian2017]: https://doi.org/10.1016/j.cell.2017.10.049
[codecov]: https://codecov.io/github/nuno-agostinho/cTRAP?branch=master
[codecovBadge]: https://img.shields.io/codecov/c/github/nuno-agostinho/cTRAP/master.svg
[ghActions]: https://github.com/nuno-agostinho/cTRAP/actions
[ghActionsIcon]: https://github.com/nuno-agostinho/cTRAP/workflows/R-CMD-check-bioc/badge.svg
[bioconductor]: http://bioconductor.org/packages/cTRAP
[biocDocker]: https://github.com/Bioconductor/bioconductor_docker