Package: derfinderPlot 1.47.0

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]

derfinderPlot_1.47.0.tar.gz
derfinderPlot_1.47.0.zip(r-4.7)derfinderPlot_1.47.0.zip(r-4.6)derfinderPlot_1.47.0.zip(r-4.5)
derfinderPlot_1.47.0.tgz(r-4.6-any)derfinderPlot_1.47.0.tgz(r-4.5-any)
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derfinderPlot_1.47.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
derfinderPlot/json (API)

# 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-1.47.0(bioc 3.24)derfinderPlot-1.46.0(bioc 3.23)

differentialexpression sequencing rnaseq software visualization immunooncology bioconductor derfinder

5.30 score 2 stars 9 scripts 561 downloads 1 mentions 4 exports 139 dependencies

Last updated from:3e8a612ad8. Checks:1 WARNING, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	277
linux-devel-x86_64	OK	557
source / vignettes	OK	418
linux-release-x86_64	OK	947
macos-release-arm64	OK	348
macos-oldrel-arm64	OK	433
windows-devel	OK	602
windows-release	OK	591
windows-oldrel	OK	797
wasm-release	OK	230

Exports:plotCluster plotOverview plotRegionCoverage vennRegions

Dependencies:abind AnnotationDbi AnnotationFilter askpass backports base64enc BH Biobase BiocBaseUtils BiocGenerics BiocIO BiocManager BiocParallel Biostrings biovizBase bit bit64 bitops blob BSgenome bslib bumphunter cachem checkmate cigarillo cli cluster codetools colorspace cpp11 crayon curl data.table DBI DelayedArray derfinder derfinderHelper dichromat digest doRNG ensembldb evaluate farver fastmap fontawesome foreach foreign formatR Formula fs futile.logger futile.options generics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicFiles GenomicRanges ggbio ggplot2 glue graph gridExtra gtable highr Hmisc htmlTable htmltools htmlwidgets httr IRanges isoband iterators jquerylib jsonlite KEGGREST knitr labeling lambda.r lattice lazyeval lifecycle limma locfit magrittr Matrix MatrixGenerics matrixStats memoise mime nnet openssl OrganismDbi pkgconfig plyr png ProtGenerics qvalue R6 rappdirs RBGL RColorBrewer Rcpp RCurl reshape2 restfulr Rhtslib rjson rlang rmarkdown rngtools rpart Rsamtools RSQLite rstudioapi rtracklayer S4Arrays S4Vectors S7 sass scales Seqinfo snow SparseArray statmod stringi stringr SummarizedExperiment sys tinytex UCSC.utils VariantAnnotation vctrs viridisLite withr xfun XML XVector yaml

Introduction to derfinderPlot

Rendered fromderfinderPlot.Rmdusingknitr::rmarkdown

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