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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:Stephen Turner [aut, cre], Colossal Biosciences [cph]

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

Datasets:

vignettedata - Vignette data

On CRAN:

bioconductor bioinformatics

3.30 score 4 stars 3 scripts 9 exports 100 dependencies

Last updated 10 months agofrom:32e2518007. Checks:OK: 7. Indexed: no.

Target	Result	Date
Doc / Vignettes	OK	Nov 11 2024
R-4.5-win	OK	Nov 11 2024
R-4.5-linux	OK	Nov 11 2024
R-4.4-win	OK	Nov 11 2024
R-4.4-mac	OK	Nov 11 2024
R-4.3-win	OK	Nov 11 2024
R-4.3-mac	OK	Oct 12 2024

Exports:get_upstream get_upstream_snps mb_bootstats mb_bootstrap mb_summarize mb_to_tibble plot_bootstats read_vcf split_gr_by_id

Dependencies:abind AnnotationDbi askpass BH Biobase BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob BSgenome cachem cli codetools colorspace cpp11 crayon curl data.table DBI DelayedArray dplyr fansi farver fastmap formatR futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges ggplot2 glue gtable httr IRanges isoband jsonlite KEGGREST labeling lambda.r lattice lifecycle magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime MotifDb munsell nlme openssl pillar pkgconfig plogr plyranges png purrr R6 RColorBrewer RCurl restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors scales snow SparseArray splitstackshape stringi stringr SummarizedExperiment sys tibble tidyr tidyselect UCSC.utils utf8 VariantAnnotation vctrs viridisLite withr XML XVector yaml zlibbioc

Statistical analysis of TFBS disruption with tfboot

Rendered fromintro.Rmdusingknitr::rmarkdownon Nov 11 2024.

Last update: 2024-02-07
Started: 2023-05-30

Citation

Development and contributors

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