Package: target 1.21.0
Mahmoud Ahmed
target: Predict Combined Function of Transcription Factors
Implement the BETA algorithm for infering direct target genes from DNA-binding and perturbation expression data Wang et al. (2013) <doi:10.1038/nprot.2013.150>. Extend the algorithm to predict the combined function of two DNA-binding elements from comprable binding and expression data.
Authors:
target_1.21.0.tar.gz
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target_1.21.0.tgz(r-4.4-any)target_1.21.0.tgz(r-4.3-any)
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target.pdf |target.html✨
target/json (API)
NEWS
| # Install 'target' in R: |
| install.packages('target', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/mahshaaban/target/issues
- real_peaks - AR peaks in LNCaP cell line
- real_transcripts - Differential expression of DHT treated LNCaP cell line
- sim_peaks - Simulated peaks
- sim_transcripts - Simulated transcripts The transcripts chromosome 1 of the mm10 mouse genome with randomly singed statistics assigned to each.
On BioConductor:target-1.21.0(bioc 3.21)target-1.20.0(bioc 3.20)
softwarestatisticalmethodtranscriptionalgorithmchip-seqdna-bindinggene-regulationtranscription-factors
Last updated 2 months agofrom:9383e81b1c. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 14 2024 |
| R-4.5-win | OK | Dec 14 2024 |
| R-4.5-linux | OK | Dec 14 2024 |
| R-4.4-win | OK | Dec 14 2024 |
| R-4.4-mac | OK | Dec 14 2024 |
| R-4.3-win | OK | Dec 14 2024 |
| R-4.3-mac | OK | Dec 14 2024 |
Exports:associated_peaksdirect_targetsfind_distancemerge_rangesplot_predictionsrank_productscore_peaksscore_regionstarget_apptest_predictions
Dependencies:askpassbase64encBiocGenericsbslibcachemclicommonmarkcrayoncurldigestfastmapfontawesomefsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesgluehtmltoolshttpuvhttrIRangesjquerylibjsonlitelaterlifecyclemagrittrmatrixStatsmemoisemimeopensslpromisesR6rappdirsRcpprlangS4VectorssassshinysourcetoolssysUCSC.utilswithrxtableXVectorzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Predict associated peaks | associated_peaks |
| Predict direct targets | direct_targets |
| Find the distance between peaks and regions | find_distance |
| Merge peaks and regions GRanges | merge_ranges |
| Plot the ECDF of ranks by groups | plot_predictions |
| Calculate the regions rank products | rank_product |
| AR peaks in LNCaP cell line | real_peaks |
| Differential expression of DHT treated LNCaP cell line | real_transcripts |
| Calculate peak scores | score_peaks |
| Calculate region scores | score_regions |
| Simulated peaks | sim_peaks |
| Simulated transcripts The transcripts chromosome 1 of the mm10 mouse genome with randomly singed statistics assigned to each. | sim_transcripts |
| 'target': Predict Combined Function of Transcription Factors. | target-package target |
| Run the shiny App | target_app |
| Test the ECDF ranks of groups are from same distribution | test_predictions |
