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cTRAP

Identification of candidate causal perturbations from differential gene expression data

https://github.com/nuno-agostinho/ctrap

Science Score: 49.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 2 DOI reference(s) in README
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    1 of 4 committers (25.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (9.8%) to scientific vocabulary

Keywords

bioconductor bioinformatics cmap gene-expression l1000 r r-package

Keywords from Contributors

alternative-splicing data-analyses differential-gene-expression differential-splicing-analysis gtex recount2 rna-seq-data splicing-quantification sra survival
Last synced: 6 months ago · JSON representation

Repository

Identification of candidate causal perturbations from differential gene expression data

Basic Info
Statistics
  • Stars: 7
  • Watchers: 1
  • Forks: 1
  • Open Issues: 4
  • Releases: 12
Topics
bioconductor bioinformatics cmap gene-expression l1000 r r-package
Created over 7 years ago · Last pushed 6 months ago
Metadata Files
Readme Changelog License

README.md

cTRAP

GitHub Actions Build status Coverage status <!-- badges: end -->

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 (Subramanian et al., Cell 2017). 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 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 and contain cTRAP and its dependencies.

  1. Pull the latest Docker image:

docker pull ghcr.io/nuno-agostinho/ctrap:latest

  1. Start RStudio Web from the Docker image:

docker run -e PASSWORD=bioc -p 8787:8787 ghcr.io/nuno-agostinho/ctrap:latest

  1. Go to RStudio Web via your web browser at https://localhost:8787
  2. Login in RStudio Web with user rstudio and password bioc
  3. Load the package in RStudio Web using library(cTRAP)

Owner

  • Name: Nuno Agostinho
  • Login: nuno-agostinho
  • Kind: user
  • Location: Cambridge, United Kingdom
  • Company: European Bioinformatics Institute | EMBL-EBI

Molecular Biologist & Computer Scientist 🧬👨🏻‍💻 Scientific Programmer at EMBL-EBI

GitHub Events

Total
  • Watch event: 2
  • Delete event: 1
  • Push event: 32
  • Pull request review event: 1
  • Pull request event: 2
  • Create event: 1
Last Year
  • Watch event: 2
  • Delete event: 1
  • Push event: 32
  • Pull request review event: 1
  • Pull request event: 2
  • Create event: 1

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 341
  • Total Committers: 4
  • Avg Commits per committer: 85.25
  • Development Distribution Score (DDS): 0.026
Past Year
  • Commits: 11
  • Committers: 3
  • Avg Commits per committer: 3.667
  • Development Distribution Score (DDS): 0.182
Top Committers
Name Email Commits
Nuno Agostinho n****o@g****m 332
Nuno Agostinho n****o@e****k 5
Unknown u****n@e****m 2
github-actions g****s@g****m 2
Committer Domains (Top 20 + Academic)
github.com: 1 ebi.ac.uk: 1

Issues and Pull Requests

Last synced: 6 months ago

Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 11,769 total
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 6
  • Total maintainers: 1
bioconductor.org: cTRAP

Identification of candidate causal perturbations from differential gene expression data

  • Versions: 6
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 11,769 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Average: 24.1%
Downloads: 72.3%
Maintainers (1)
nunodanielagostinho@gmail.com
Last synced: 6 months ago

Dependencies

DESCRIPTION cran
  • R >= 4.0 depends
  • AnnotationDbi * imports
  • AnnotationHub * imports
  • DT * imports
  • R.utils * imports
  • binr * imports
  • cowplot * imports
  • data.table * imports
  • dplyr * imports
  • fastmatch * imports
  • fgsea * imports
  • ggplot2 * imports
  • ggrepel * imports
  • graphics * imports
  • highcharter * imports
  • htmltools * imports
  • httr * imports
  • limma * imports
  • methods * imports
  • parallel * imports
  • pbapply * imports
  • purrr * imports
  • qs * imports
  • readxl * imports
  • reshape2 * imports
  • rhdf5 * imports
  • rlang * imports
  • scales * imports
  • shiny >= 1.7.0 imports
  • shinycssloaders * imports
  • stats * imports
  • tibble * imports
  • tools * imports
  • utils * imports
  • biomaRt * suggests
  • covr * suggests
  • knitr * suggests
  • remotes * suggests
  • rmarkdown * suggests
  • spelling * suggests
  • testthat * suggests
.github/workflows/R-CMD-check.yaml actions
  • actions/checkout v3 composite
  • actions/upload-artifact master composite
  • r-lib/actions/check-r-package v2 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
.github/workflows/docker.yaml actions
  • actions/checkout v2 composite
  • docker/build-push-action v2 composite
  • docker/login-action v1 composite
  • docker/metadata-action v3 composite
  • docker/setup-buildx-action v1 composite
.github/workflows/pkgdown.yml actions
  • 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
.github/workflows/update-license-year.yml actions
  • FantasticFiasco/action-update-license-year v2 composite
  • actions/checkout v3 composite
Dockerfile docker
  • bioconductor/bioconductor_docker latest build