Dependency analysis on package methylPipe

General information

Bioconductor link link
Package version1.30.0
Number of strong dependencies149
Number of all dependencies157
Number of parent packages19
Max heaviness from parent packages103
Total heaviness from parent packages109
Number of parent packages (including Suggests and Enhances)23
Max co-heaviness from parent packages ("Gviz" and "data.table")1

Dependency heatmap

In the following dependency heatmap, rows are the parent packages of methylPipe and columns are the dependency packages that each parent package brings in. On the right side of the heatmap, there are three barplot annotations: 1. number of imported functions/S4 methods/S4 classes from parent packages; 2. number of dependency packages from each parent package; 3. heaviness of each parent package on methylPipe.

Adjust heatmap size:
Base packages Other packages Depends Imports Suggests methods utils stats graphics stats4 tools grDevices grid parallel splines BiocGenerics S4Vectors bitops IRanges RCurl GenomeInfoDbData GenomeInfoDb XVector zlibbioc GenomicRanges crayon MatrixGenerics Biobase Matrix DelayedArray matrixStats lattice Biostrings BiocParallel Rhtslib futile.logger snow codetools BH lambda.r futile.options formatR Rsamtools SummarizedExperiment yaml rtracklayer GenomicAlignments XML BiocIO restfulr rjson glue AnnotationDbi BSgenome stringr httr DBI RSQLite KEGGREST curl rlang png R6 magrittr stringi jsonlite mime openssl bit64 blob memoise pkgconfig Rcpp plogr vctrs askpass cli bit cachem fastmap sys RColorBrewer biomaRt GenomicFeatures digest progress BiocFileCache rappdirs xml2 hms prettyunits dbplyr dplyr filelock lifecycle ellipsis assertthat pillar purrr tibble tidyselect withr generics fansi utf8 evaluate highr xfun limma gtools caTools KernSmooth ensembldb biovizBase latticeExtra AnnotationFilter ProtGenerics scales Hmisc dichromat VariantAnnotation jpeg lazyeval farver labeling munsell viridisLite survival Formula ggplot2 cluster rpart nnet foreign gtable gridExtra data.table htmlTable viridis htmltools base64enc colorspace isoband MASS mgcv knitr checkmate htmlwidgets rstudioapi nlme backports mhsmm geneplotter mvtnorm annotate xtable 0 5 10 Imported methods 0 50 100 Required packages 0 50 100 Heaviness from parents methods grDevices graphics stats utils GenomicRanges SummarizedExperiment Rsamtools parallel data.table BiocGenerics marray S4Vectors gplots IRanges GenomeInfoDb Biostrings GenomicAlignments Gviz knitr BSgenome.Hsapiens.UCSC.hg18 MethylSeekR TxDb.Hsapiens.UCSC.hg18.knownGene In total 149 packages are required directly or indirectly (157) when installing 'methylPipe' (1.30.0) Depends Imports Suggests Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'methylPipe' Imported functions The whole namespace is imported


Dependency table

"Import" information is from the NAMESPACE file of methylPipe.

imports: number of imported functions/objects; importMethods: number of imported S4 methods; importClasses: number of imported S4 classes.

Required packages: number of strong dependency packages for each of the parent package (or in other words, number of dependency packages the parent package brings in).

Heaviness from parent on methylPipe: number of required packages that can be reduced if moving parent package to Suggests of methylPipe.

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on methylPipe
methods Depends The whole set of functions/methods/classes from parent package is imported to the namespace of methylPipe. 0 0
grDevices Depends 2 0 0 0 0
graphics Depends 11 0 0 0 0
stats Depends 9 0 0 0 0
utils Depends 1 0 0 0 0
GenomicRanges Depends The whole set of functions/methods/classes from parent package is imported to the namespace of methylPipe. 15 0
SummarizedExperiment Depends The whole set of functions/methods/classes from parent package is imported to the namespace of methylPipe. 24 0
Rsamtools Depends The whole set of functions/methods/classes from parent package is imported to the namespace of methylPipe. 29 0
Gviz Imports The whole set of functions/methods/classes from parent package is imported to the namespace of methylPipe. 142 103
gplots Imports 1 0 0 7 4
marray Imports 1 0 0 6 2
parallel Imports 4 0 0 0 0
data.table Imports 1 0 0 1 0
BiocGenerics Imports 6 0 0 4 0
S4Vectors Imports The whole set of functions/methods/classes from parent package is imported to the namespace of methylPipe. 6 0
IRanges Imports The whole set of functions/methods/classes from parent package is imported to the namespace of methylPipe. 7 0
GenomeInfoDb Imports 3 0 0 11 0
Biostrings Imports The whole set of functions/methods/classes from parent package is imported to the namespace of methylPipe. 17 0
GenomicAlignments Imports 4 0 0 38 0
MethylSeekR Suggests No object is imported into the namespace of methylPipe. 78 6
BSgenome.Hsapiens.UCSC.hg18 Suggests No object is imported into the namespace of methylPipe. 46 1
TxDb.Hsapiens.UCSC.hg18.knownGene Suggests No object is imported into the namespace of methylPipe. 97 1
knitr Suggests No object is imported into the namespace of methylPipe. 12 0

Analysis was done with pkgndep.