Package: tidyCoverage 1.1.0

Jacques Serizay

tidyCoverage: Extract and aggregate genomic coverage over features of interest

`tidyCoverage` framework enables tidy manipulation of collections of genomic tracks and features using `tidySummarizedExperiment` methods. It facilitates the extraction, aggregation and visualization of genomic coverage over individual or thousands of genomic loci, relying on `CoverageExperiment` and `AggregatedCoverage` classes. This accelerates the integration of genomic track data in genomic analysis workflows.

Authors:Jacques Serizay [aut, cre]

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tidyCoverage.pdf |tidyCoverage.html✨
tidyCoverage/json (API)

# Install 'tidyCoverage' in R:

install.packages('tidyCoverage', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/js2264/tidycoverage/issues

Datasets:

ac - Example 'CoverageExperiment' and 'AggregatedCoverage' objects
ce - Example 'CoverageExperiment' and 'AggregatedCoverage' objects

On BioConductor:tidyCoverage-1.1.0(bioc 3.20)tidyCoverage-1.0.0(bioc 3.19)

bioconductor-package

6 exports 1.00 score 68 dependencies

Last updated 2 months agofrom:4ff03fe76c

Exports:aggregate as_tibble coarsen CoverageExperiment expand show

Dependencies:abind askpass BH Biobase BiocGenerics BiocIO BiocParallel Biostrings bitops cli codetools cpp11 crayon curl DelayedArray dplyr fansi formatR futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicRanges glue httr IRanges jsonlite lambda.r lattice lifecycle magrittr Matrix MatrixGenerics matrixStats mime openssl pillar pkgconfig purrr R6 RCurl restfulr Rhtslib rjson rlang Rsamtools rtracklayer S4Arrays S4Vectors snow SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect UCSC.utils utf8 vctrs withr XML XVector yaml zlibbioc

Introduction to tidyCoverage

Rendered fromtidyCoverage.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2024-01-09
Started: 2023-11-27

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
aggregate	aggregate,CoverageExperiment-method AggregatedCoverage
as_tibble	as_tibble-methods as_tibble.AggregatedCoverage
CoverageExperiment	coarsen coarsen,CoverageExperiment-method CoverageExperiment CoverageExperiment,BigWigFile,GRanges-method CoverageExperiment,BigWigFile,GRangesList-method CoverageExperiment,BigWigFile,list-method CoverageExperiment,BigWigFileList,GRanges-method CoverageExperiment,BigWigFileList,GRangesList-method CoverageExperiment,BigWigFileList,list-method CoverageExperiment,list,GRanges-method CoverageExperiment,list,GRangesList-method CoverageExperiment,list,list-method CoverageExperiment,RleList,GRanges-method CoverageExperiment,RleList,GRangesList-method CoverageExperiment,RleList,list-method
Example 'CoverageExperiment' and 'AggregatedCoverage' objects	ac ce data
Expand a CoverageExperiment object	expand,CoverageExperiment expand,CoverageExperiment-method expand.CoverageExperiment
show	print.AggregatedCoverage print.CoverageExperiment show show,AggregatedCoverage-method show,CoverageExperiment-method tbl_format_header.tidyAggregatedCoverage tbl_format_header.tidyCoverageExperiment