Package: derfinderPlot 1.41.0

Leonardo Collado-Torres

derfinderPlot: Plotting functions for derfinder

This package provides plotting functions for results from the derfinder package. This helps separate the graphical dependencies required for making these plots from the core functionality of derfinder.

Authors:Leonardo Collado-Torres [aut, cre], Andrew E. Jaffe [aut], Jeffrey T. Leek [aut, ths]

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derfinderPlot.pdf |derfinderPlot.html✨
derfinderPlot/json (API)
NEWS

# Install 'derfinderPlot' in R:

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

Bug tracker:https://github.com/leekgroup/derfinderplot/issues

On BioConductor:derfinderPlot-1.41.0(bioc 3.21)derfinderPlot-1.40.0(bioc 3.20)

differentialexpression sequencing rnaseq software visualization immunooncology bioconductor derfinder

5.00 score 2 stars 5 scripts 342 downloads 1 mentions 4 exports 164 dependencies

Last updated 3 months agofrom:b8a1580108. Checks:9 OK. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Mar 24 2025
R-4.5-win	OK	Mar 24 2025
R-4.5-mac	OK	Mar 24 2025
R-4.5-linux	OK	Mar 24 2025
R-4.4-win	OK	Mar 24 2025
R-4.4-mac	OK	Mar 24 2025
R-4.4-linux	OK	Mar 24 2025
R-4.3-win	OK	Mar 24 2025
R-4.3-mac	OK	Mar 24 2025

Exports:plotCluster plotOverview plotRegionCoverage vennRegions

Dependencies:abind AnnotationDbi AnnotationFilter askpass backports base64enc BH Biobase BiocFileCache BiocGenerics BiocIO BiocManager BiocParallel biomaRt Biostrings biovizBase bit bit64 bitops blob BSgenome bslib bumphunter cachem checkmate cli cluster codetools colorspace cpp11 crayon curl data.table DBI dbplyr DelayedArray derfinder derfinderHelper dichromat digest doRNG dplyr ensembldb evaluate fansi farver fastmap filelock fontawesome forcats foreach foreign formatR Formula fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicFiles GenomicRanges GGally ggbio ggplot2 ggstats glue graph gridExtra gtable highr Hmisc hms htmlTable htmltools htmlwidgets httr httr2 IRanges isoband iterators jquerylib jsonlite KEGGREST knitr labeling lambda.r lattice lazyeval lifecycle limma locfit magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell nlme nnet openssl OrganismDbi patchwork pillar pkgconfig plogr plyr png prettyunits progress ProtGenerics purrr qvalue R6 rappdirs RBGL RColorBrewer Rcpp RCurl reshape2 restfulr Rhtslib rjson rlang rmarkdown rngtools rpart Rsamtools RSQLite rstudioapi rtracklayer S4Arrays S4Vectors sass scales snow SparseArray statmod stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tinytex txdbmaker UCSC.utils utf8 VariantAnnotation vctrs viridis viridisLite withr xfun XML xml2 XVector yaml

Introduction to derfinderPlot

Leonardo Collado-Torres

Rendered fromderfinderPlot.Rmdusingknitr::rmarkdownon Mar 24 2025.

Last update: 2024-12-12
Started: 2014-09-24

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Plot the coverage information surrounding a region cluster	plotCluster
Plot a karyotype overview of the genome with the identified regions	plotOverview
Makes plots for every region while summarizing the annotation	plotRegionCoverage
Venn diagram for annotated regions given the genomic state	vennRegions