Package: tfboot 1.0.1
tfboot: Bootstrapping and statistical analysis for TFBS-disrupting SNPs
Bootstrap motifbreakR results for statistical analysis on TFBS-disrupting SNPs in upstream regions of a set of genes of interest.
Authors:
tfboot_1.0.1.tar.gz
tfboot_1.0.1.zip(r-4.5)tfboot_1.0.1.zip(r-4.4)tfboot_1.0.1.zip(r-4.3)
tfboot_1.0.1.tgz(r-4.4-any)tfboot_1.0.1.tgz(r-4.3-any)
tfboot_1.0.1.tar.gz(r-4.5-noble)tfboot_1.0.1.tar.gz(r-4.4-noble)
tfboot_1.0.1.tgz(r-4.4-emscripten)tfboot_1.0.1.tgz(r-4.3-emscripten)
tfboot.pdf |tfboot.html✨
tfboot/json (API)
NEWS
| # Install 'tfboot' in R: |
| install.packages('tfboot', repos = c('https://stephenturner.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/colossal-compsci/tfboot/issues
- vignettedata - Vignette data
Last updated 8 months agofrom:32e2518007. Checks:OK: 6 NOTE: 1. Indexed: no.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Sep 12 2024 |
| R-4.5-win | OK | Sep 12 2024 |
| R-4.5-linux | OK | Sep 12 2024 |
| R-4.4-win | OK | Sep 12 2024 |
| R-4.4-mac | OK | Sep 12 2024 |
| R-4.3-win | OK | Aug 13 2024 |
| R-4.3-mac | NOTE | Aug 13 2024 |
Exports:get_upstreamget_upstream_snpsmb_bootstatsmb_bootstrapmb_summarizemb_to_tibbleplot_bootstatsread_vcfsplit_gr_by_id
Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobBSgenomecachemclicodetoolscolorspacecpp11crayoncurldata.tableDBIDelayedArraydplyrfansifarverfastmapformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegtablehttrIRangesisobandjsonliteKEGGRESTlabelinglambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimeMotifDbmunsellnlmeopensslpillarpkgconfigplogrplyrangespngpurrrR6RColorBrewerRCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsscalessnowSparseArraysplitstackshapestringistringrSummarizedExperimentsystibbletidyrtidyselectUCSC.utilsutf8VariantAnnotationvctrsviridisLitewithrXMLXVectoryamlzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Get upstream intervals | get_upstream |
| Get SNPs in upstream regions | get_upstream_snps |
| Bootstrap statistics | mb_bootstats |
| Bootstrap motifbreakR results | mb_bootstrap |
| Summarize motifbreakR results | mb_summarize |
| motifbreakR results to tibble | mb_to_tibble |
| Plot bootstrap distributions | plot_bootstats |
| Read in SNPs from a VCF | read_vcf |
| Split GRanges by gene | split_gr_by_id |
| Vignette data | vignettedata |
