Package: tidyCoverage 1.3.0

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-1.3.0(bioc 3.21)tidyCoverage-1.2.0(bioc 3.20)

software sequencing coverage

5.90 score 20 stars 6 scripts 116 downloads 10 exports 81 dependencies

Last updated 2 months agofrom:defcab5566. Checks:OK: 5 NOTE: 2. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Dec 19 2024
R-4.5-win	NOTE	Dec 19 2024
R-4.5-linux	NOTE	Dec 19 2024
R-4.4-win	OK	Dec 19 2024
R-4.4-mac	OK	Dec 19 2024
R-4.3-win	OK	Dec 19 2024
R-4.3-mac	OK	Dec 19 2024

Exports:aggregate as_tibble coarsen CoverageExperiment expand geom_aggrcoverage geom_coverage scale_x_genome scale_y_coverage show

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

Introduction to tidyCoverage

Rendered fromtidyCoverage.Rmdusingknitr::rmarkdownon Dec 19 2024.

Last update: 2024-07-11
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
Plotting functions	geom_aggrcoverage geom_coverage ggplot-tidyCoverage scale_x_genome scale_y_coverage
show	print.AggregatedCoverage print.CoverageExperiment show show,AggregatedCoverage-method show,CoverageExperiment-method tbl_format_header.tidyAggregatedCoverage tbl_format_header.tidyCoverageExperiment