Introduction | Installation | From CRAN (stable version) | From GitHub (development version) | Example workflow | 1. Submit a gene list | 2. Inspect top results | 3. Extract the result for one particular collection | 4. Generate the visualization | Session info | Citation | Resources
Package: rChEA3 1.0.1
rChEA3: R Client for the 'ChEA3' Transcription Factor Enrichment API
Interface to the 'ChEA3' transcription factor enrichment API. 'ChEA3' integrates evidence from ChIP-seq, co-expression, and literature resources to prioritize transcription factors regulating a given set of genes. This package provides convenient R functions to query the API, retrieve ranked results across collections (including integrated scores), and standardize output for downstream analysis in R/Bioconductor workflows. See <https://maayanlab.cloud/chea3/> or Keenan (2019) <doi:10.1093/nar/gkz446> for further details.
Authors:
rChEA3_1.0.1.tar.gz
rChEA3_1.0.1.zip(r-4.7)rChEA3_1.0.1.zip(r-4.6)rChEA3_1.0.1.zip(r-4.5)
rChEA3_1.0.1.tgz(r-4.6-any)rChEA3_1.0.1.tgz(r-4.5-any)
rChEA3_1.0.1.tar.gz(r-4.7-any)rChEA3_1.0.1.tar.gz(r-4.6-any)
rChEA3_1.0.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
rChEA3/json (API)
| # Install 'rChEA3' in R: |
| install.packages('rChEA3', repos = c('https://ckntav.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/ckntav/rchea3/issues
Pkgdown/docs site:https://ckntav.github.io
Datasets:
- a549_dex_downreg - A549 Downregulated Genes
Last updated from:60c788137e. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 147 | ||
| source / vignettes | OK | 187 | ||
| linux-release-x86_64 | OK | 133 | ||
| macos-release-arm64 | OK | 167 | ||
| macos-oldrel-arm64 | OK | 217 | ||
| windows-devel | OK | 85 | ||
| windows-release | OK | 111 | ||
| windows-oldrel | OK | 116 | ||
| wasm-release | OK | 102 |
Exports:displayTopNexportResultsqueryChEA3saveViztodayvisualizeRank
Dependencies:askpassclicpp11crayoncurldplyrfarvergenericsggplot2gluegtablehttrisobandjsonlitelabelinglifecyclelubridatemagrittrmimeopensslpillarpkgconfigR6RColorBrewerrlangS7scalessystibbletidyselecttimechangeutf8vctrsviridisLitewithrwritexl
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| A549 Downregulated Genes (Dex) | a549_dex_downreg |
| Print the top-n rows for each ChEA3 collection | displayTopN |
| Export rChEA3 Results to Excel | exportResults |
| Query ChEA3 API for TF enrichment | queryChEA3 |
| Save a Visualization to File (PDF, PNG, or SVG) | saveViz |
| Today's Date at Package Load Time | today |
| Visualize top transcription factors (TFs) from ChEA3 results | visualizeRank |
