Dependency analysis on package tximport

General information

Bioconductor link link
Package version1.24.0
Number of strong dependencies3
Number of all dependencies164
Number of parent packages3
Max heaviness from parent packages1
Total heaviness from parent packages3
Number of parent packages (including Suggests and Enhances)17

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Imports Suggests methods stats utils grDevices graphics tools grid stats4 splines parallel glue magrittr rlang R6 lattice jsonlite digest cli crayon ellipsis lifecycle withr fansi tibble pillar pkgconfig vctrs utf8 Rcpp stringr stringi evaluate yaml fastmap bit64 bit BiocGenerics S4Vectors IRanges GenomeInfoDb GenomicRanges RCurl XVector Biobase GenomeInfoDbData bitops zlibbioc SummarizedExperiment MatrixGenerics Matrix DelayedArray matrixStats locfit highr xfun rappdirs progress hms prettyunits purrr tidyselect ggplot2 RColorBrewer gtable isoband MASS mgcv scales nlme farver labeling munsell viridisLite colorspace AnnotationDbi DBI RSQLite Biostrings KEGGREST blob memoise plogr XML httr png cachem BiocParallel curl mime openssl futile.logger snow codetools BH askpass lambda.r futile.options sys formatR Rhdf5lib rhdf5filters limma bslib htmltools jquerylib knitr tinytex sass base64enc fs clipr vroom cpp11 tzdb brio callr desc pkgload praise processx ps waldo rprojroot rstudioapi diffobj rematch2 abind gtools qvalue svMisc SingleCellExperiment reshape2 plyr genefilter geneplotter RcppArmadillo annotate survival xtable GenomicFeatures BiocIO rtracklayer biomaRt Rsamtools GenomicAlignments restfulr BiocFileCache xml2 Rhtslib rjson dbplyr dplyr filelock assertthat generics 0 2 4 Imported methods 0 50 100 Required packages 0 20 40 60 80 Heaviness from parents utils stats methods tximportData matrixStats jsonlite rhdf5 limma Matrix edgeR knitr rmarkdown readr testthat fishpond DESeq2 TxDb.Hsapiens.UCSC.hg19.knownGene In total 3 packages are required directly or indirectly (164) when installing 'tximport' (1.24.0) Imports Suggests Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'tximport' Imported functions


Dependency table

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

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on tximport
utils Imports 5 0 0 0 1
stats Imports 1 0 0 0 1
methods Imports 1 0 0 0 1
TxDb.Hsapiens.UCSC.hg19.knownGene Suggests No object is imported into the namespace of tximport. 97 95
DESeq2 Suggests No object is imported into the namespace of tximport. 93 91
fishpond Suggests No object is imported into the namespace of tximport. 66 64
testthat Suggests No object is imported into the namespace of tximport. 36 34
readr Suggests No object is imported into the namespace of tximport. 31 29
rmarkdown Suggests No object is imported into the namespace of tximport. 27 25
knitr Suggests No object is imported into the namespace of tximport. 12 10
edgeR Suggests No object is imported into the namespace of tximport. 10 8
Matrix Suggests No object is imported into the namespace of tximport. 7 5
rhdf5 Suggests No object is imported into the namespace of tximport. 3 3
limma Suggests No object is imported into the namespace of tximport. 5 3
tximportData Suggests No object is imported into the namespace of tximport. 0 1
matrixStats Suggests No object is imported into the namespace of tximport. 0 1
jsonlite Suggests No object is imported into the namespace of tximport. 1 1

Analysis was done with pkgndep.