Format of expression data | Format of steady-state expression data | How to run GENIE3 | Run GENIE3 with the default parameters | Restrict the candidate regulators to a subset of genes | Change the tree-based method and its settings | Parallel GENIE3 | Obtain more information | Get the list of the regulatory links | Get all the regulatory links | Get only the top-ranked links | Get only the links with a weight higher than some threshold | Important note on the interpretation of the weights
Package: GENIE3 1.35.0
Van Anh Huynh-Thu
GENIE3: GEne Network Inference with Ensemble of trees
This package implements the GENIE3 algorithm for inferring gene regulatory networks from expression data.
Authors:
GENIE3_1.35.0.tar.gz
GENIE3_1.35.0.zip(r-4.7-x86_64)GENIE3_1.35.0.zip(r-4.7-arm64)GENIE3_1.35.0.zip(r-4.6-x86_64)GENIE3_1.35.0.zip(r-4.6-arm64)GENIE3_1.35.0.zip(r-4.5-x86_64)
GENIE3_1.35.0.tgz(r-4.6-x86_64)GENIE3_1.35.0.tgz(r-4.6-arm64)GENIE3_1.35.0.tgz(r-4.5-x86_64)GENIE3_1.35.0.tgz(r-4.5-arm64)
GENIE3_1.35.0.tar.gz(r-4.7-arm64)GENIE3_1.35.0.tar.gz(r-4.7-x86_64)GENIE3_1.35.0.tar.gz(r-4.6-arm64)GENIE3_1.35.0.tar.gz(r-4.6-x86_64)
GENIE3_1.35.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
GENIE3/json (API)
| # Install 'GENIE3' in R: |
| install.packages('GENIE3', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:GENIE3-1.35.0(bioc 3.24)GENIE3-1.34.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
networkinferencesystemsbiologydecisiontreeregressionnetworkgraphandnetworkgeneexpression
Last updated from:0146353a24. Checks:1 ERROR, 13 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 162 | ||
| linux-devel-arm64 | NOTE | 131 | ||
| linux-devel-x86_64 | NOTE | 227 | ||
| source / vignettes | OK | 229 | ||
| linux-release-arm64 | NOTE | 130 | ||
| linux-release-x86_64 | NOTE | 276 | ||
| macos-release-arm64 | NOTE | 105 | ||
| macos-release-x86_64 | NOTE | 167 | ||
| macos-oldrel-arm64 | NOTE | 102 | ||
| macos-oldrel-x86_64 | NOTE | 297 | ||
| windows-devel-arm64 | NOTE | 281 | ||
| windows-devel-x86_64 | NOTE | 183 | ||
| windows-release-arm64 | NOTE | 211 | ||
| windows-release-x86_64 | NOTE | 98 | ||
| windows-oldrel-x86_64 | NOTE | 93 | ||
| wasm-release | OK | 122 |
Exports:GENIE3getLinkList
Dependencies:clidplyrgenericsgluelifecyclemagrittrpillarpkgconfigplyrR6Rcppreshape2rlangstringistringrtibbletidyselectutf8vctrswithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| GENIE3 | GENIE3 GENIE3,ExpressionSet-method GENIE3,matrix-method GENIE3,SummarizedExperiment-method |
| getLinkList | getLinkList |
