Introduction | Methods - Statistical significance | P-value | E-value | BH-corrected P-value | Random Control (RC) | Prerequisites | Getting started | Acknowledgments | Reference | Session info
Package: TFactSR 0.99.1
TFactSR: Enrichment Approach to Predict Which Transcription Factors are Regulated
R implementation of 'TFactS' to predict which are the transcription factors (TFs), regulated in a biological condition based on lists of differentially expressed genes (DEGs) obtained from transcriptome experiments. This package is based on the 'TFactS' concept by Essaghir et al. (2010) <doi:10.1093/nar/gkq149> and expands it. It allows users to perform 'TFactS'-like enrichment approach. The package can import and use the original catalogue file from the 'TFactS' as well as users' defined catalogues of interest that are not supported by 'TFactS' (e.g., Arabidopsis).
Authors:
TFactSR_0.99.1.tar.gz
TFactSR_0.99.1.zip(r-4.7)TFactSR_0.99.1.zip(r-4.6)TFactSR_0.99.1.zip(r-4.5)
TFactSR_0.99.1.tgz(r-4.6-any)TFactSR_0.99.1.tgz(r-4.5-any)
TFactSR_0.99.1.tar.gz(r-4.7-any)TFactSR_0.99.1.tar.gz(r-4.6-any)
TFactSR_0.99.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
TFactSR/json (API)
| # Install 'TFactSR' in R: |
| install.packages('TFactSR', repos = c('https://afukushima.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/afukushima/tfactsr/issues
Pkgdown/docs site:https://afukushima.github.io
Datasets:
- ATRM - A list of ATRM TF-target genes (TG) in Arabidopsis thaliana.
- catalog - A list of TF-target genes (TG) in TFactS.
- DEGs - An example list of DEGs from DEMO data in TFactS.
- DEGs39 - An example list of 39 DEGs from DEMO data in TFactS.
- example.df - An example result of enrichment analysis
- example.list - An example list of result of enrichment analysis
- GenesUp_SH1H - An example list of 74 DEGs from AtGenExpress stress dataset.
networksoftwaredifferentialexpressiongenetargetgeneexpressionmicroarrayrnaseqtranscriptionnetworkenrichment
Last updated from:a9773380be. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 144 | ||
| source / vignettes | OK | 200 | ||
| linux-release-x86_64 | OK | 130 | ||
| macos-release-arm64 | OK | 88 | ||
| macos-oldrel-arm64 | OK | 78 | ||
| windows-devel | OK | 92 | ||
| windows-release | OK | 87 | ||
| windows-oldrel | OK | 91 | ||
| wasm-release | OK | 159 |
Exports:calculateEnrichmentTestcalculateEvaluecalculateFDRBHcalculateQvaluecalculateRCcalculateTFactSextractTFTGFASTcalculateRCformatETformatRC
Dependencies:clicpp11farverggplot2gluegtableisobandlabelinglifecyclemagrittrplyrqvalueR6RColorBrewerRcppreshape2rlangS7scalesstringistringrvctrsviridisLitewithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| A list of ATRM TF-target genes (TG) in Arabidopsis thaliana. | ATRM |
| performs enrichment analysis | calculateEnrichmentTest |
| calculates E-value | calculateEvalue |
| calculates FDR by Benjamini and Hochberg method | calculateFDRBH |
| calculates Q-value | calculateQvalue |
| calculates Random Control (RC) | calculateRC |
| calculates TFactS | calculateTFactS |
| A list of TF-target genes (TG) in TFactS. | catalog |
| An example list of DEGs from DEMO data in TFactS. | DEGs |
| An example list of 39 DEGs from DEMO data in TFactS. | DEGs39 |
| An example result of enrichment analysis | example.df |
| An example list of result of enrichment analysis | example.list |
| extracts transcription factor (TF) and target gene (TG) information | extractTFTG |
| calculates Random Control (RC) fastly? | FASTcalculateRC |
| formats the result of enrichment test (ET) | formatET |
| formats the result of Random Control (RC) | formatRC |
| An example list of 74 DEGs from AtGenExpress stress dataset. | GenesUp_SH1H |
| TFactSR: A package for identifying critical transcription factors. | TFactSR |
