Dependency analysis on package maftools

General information

Bioconductor link link
Package version2.12.0
Number of strong dependencies15
Number of all dependencies127
Number of parent packages8
Max heaviness from parent packages8
Total heaviness from parent packages12
Number of parent packages (including Suggests and Enhances)24
Max co-heaviness from parent packages ("survival" and "grDevices")1

Dependency heatmap

In the following dependency heatmap, rows are the parent packages of maftools 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 maftools.

Adjust heatmap size:
Base packages Other packages Imports LinkingTo Suggests methods utils stats graphics grDevices grid splines tools stats4 parallel zlibbioc Matrix lattice BiocGenerics S4Vectors IRanges XVector GenomeInfoDb RCurl GenomeInfoDbData bitops glue crayon Biobase yaml magrittr rlang R6 GenomicRanges matrixStats SummarizedExperiment MatrixGenerics DelayedArray stringr stringi lifecycle codetools evaluate highr xfun colorspace RColorBrewer gtable scales farver labeling munsell viridisLite digest Biostrings rtracklayer Rsamtools XML GenomicAlignments BiocIO restfulr BiocParallel Rhtslib rjson futile.logger snow BH lambda.r futile.options formatR ellipsis tibble vctrs pillar fansi pkgconfig cli utf8 R.oo R.methodsS3 abind bslib htmltools jquerylib jsonlite knitr tinytex sass base64enc fastmap fs rappdirs tidyr dplyr purrr tidyselect cpp11 generics BSgenome pkgmaker registry rngtools cluster gridBase foreach doParallel ggplot2 reshape2 BiocManager xtable withr assertthat iterators isoband MASS mgcv plyr Rcpp nlme 0 2 4 Imported methods 0 20 40 60 Required packages 0 20 40 Heaviness from parents grDevices methods RColorBrewer DNAcopy data.table Rhtslib survival zlibbioc curl mclust R.utils berryFunctions S4Vectors IRanges knitr GenomicRanges Biostrings pheatmap RaggedExperiment rmarkdown BSgenome MultiAssayExperiment BSgenome.Hsapiens.UCSC.hg19 NMF In total 15 packages are required directly or indirectly (127) when installing 'maftools' (2.12.0) Imports LinkingTo Suggests Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'maftools' Imported functions The whole namespace is imported Package is listed in 'Imports' but namespace is not imported


Dependency table

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

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 maftools: number of required packages that can be reduced if moving parent package to Suggests of maftools.

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on maftools
survival Imports The whole set of functions/methods/classes from parent package is imported to the namespace of maftools. 9 8
RColorBrewer Imports The whole set of functions/methods/classes from parent package is imported to the namespace of maftools. 0 1
DNAcopy Imports The whole set of functions/methods/classes from parent package is imported to the namespace of maftools. 0 1
data.table Imports The whole set of functions/methods/classes from parent package is imported to the namespace of maftools. 1 1
Rhtslib Imports Parent package is listed in Imports of maftools but no object from parent package is imported. 1 1
grDevices Imports 5 0 0 0 0
methods Imports The whole set of functions/methods/classes from parent package is imported to the namespace of maftools. 0 0
zlibbioc LinkingTo Parent package is listed in LinkingTo of maftools but no object from parent package is imported. 0 0
NMF Suggests No object is imported into the namespace of maftools. 59 50
MultiAssayExperiment Suggests No object is imported into the namespace of maftools. 45 37
BSgenome.Hsapiens.UCSC.hg19 Suggests No object is imported into the namespace of maftools. 46 37
BSgenome Suggests No object is imported into the namespace of maftools. 45 36
rmarkdown Suggests No object is imported into the namespace of maftools. 27 24
RaggedExperiment Suggests No object is imported into the namespace of maftools. 25 17
Biostrings Suggests No object is imported into the namespace of maftools. 17 12
pheatmap Suggests No object is imported into the namespace of maftools. 18 12
GenomicRanges Suggests No object is imported into the namespace of maftools. 15 11
knitr Suggests No object is imported into the namespace of maftools. 12 10
R.utils Suggests No object is imported into the namespace of maftools. 5 4
IRanges Suggests No object is imported into the namespace of maftools. 7 4
S4Vectors Suggests No object is imported into the namespace of maftools. 6 3
berryFunctions Suggests No object is imported into the namespace of maftools. 6 2
curl Suggests No object is imported into the namespace of maftools. 0 1
mclust Suggests No object is imported into the namespace of maftools. 4 1

Analysis was done with pkgndep.