Introduction | Activity estimation | Load | Exploration | CollecTRI
Package: dorothea 1.25.0
Pau Badia-i-Mompel
dorothea: Collection Of Human And Mouse TF Regulons
DoRothEA is a gene regulatory network containing signed transcription factor (TF) - target gene interactions. DoRothEA regulons, the collection of a TF and its transcriptional targets, were curated and collected from different types of evidence for both human and mouse. A confidence level was assigned to each TF-target interaction based on the number of supporting evidence.
Authors:
dorothea_1.25.0.tar.gz
dorothea_1.25.0.tar.gz(r-4.7-any)dorothea_1.25.0.tar.gz(r-4.6-any)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
dorothea/json (API)
| # Install 'dorothea' in R: |
| install.packages('dorothea', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/saezlab/dorothea/issues
Pkgdown/docs site:https://saezlab.github.io
Datasets:
- dorothea_hs - Human DoRothEA
- dorothea_hs_pancancer - Human DoRothEA
- dorothea_mm - Mouse DoRothEA
- dorothea_mm_pancancer - Mouse DoRothEA
- entire_database - Entire database with associated meta data
On BioConductor:dorothea-1.25.0(data/experiment 3.24)dorothea-1.23.0(data/experiment 3.23)
experimentdatahomo_sapiens_datamus_musculus_databioconductor-packagefunctional-analysisgene-expressionregulonstf-activitiestranscription-factordatapkg
Last updated from:4feba311dc. Checks:1 WARNING, 2 ERROR, 1 OK. Indexed: yes.
This is a data package. Data packages may be large and do not get checked across all platforms.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | -3384 | ||
| linux-devel | ERROR | -3258 | ||
| source / vignettes | OK | 458 | ||
| linux-release | ERROR | -3271 |
Exports:%>%df2regulonrun_viper
Dependencies:backportsbcellViperBHBiobaseBiocGenericsBiocParallelbroomclicodetoolscpp11decoupleRdplyrformatRfutile.loggerfutile.optionsgenericsgluelambda.rlatticelifecyclemagrittrMatrixparallellypillarpkgconfigpurrrR6rlangsnowstringistringrtibbletidyrtidyselectutf8vctrswithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Construction of dorothea regulons for viper analysis | df2regulon |
| Human DoRothEA | dorothea_hs |
| Human DoRothEA (pancancer) | dorothea_hs_pancancer |
| Mouse DoRothEA | dorothea_mm |
| Mouse DoRothEA (pancancer) | dorothea_mm_pancancer |
| Entire database with associated meta data | entire_database |
| VIPER wrapper | run_viper |