Dependency analysis on package fishpond

General information

Bioconductor link link
Package version2.2.0
Number of strong dependencies66
Number of all dependencies211
Number of parent packages17
Max heaviness from parent packages35
Total heaviness from parent packages40
Number of parent packages (including Suggests and Enhances)36
Max co-heaviness from parent packages ("SingleCellExperiment" and "SummarizedExperiment")4

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Imports Suggests methods utils stats graphics tools grDevices stats4 grid splines parallel BiocGenerics S4Vectors glue IRanges RCurl GenomeInfoDbData bitops rlang R6 GenomeInfoDb XVector zlibbioc lattice Biobase Rcpp magrittr pkgconfig vctrs cli crayon Matrix matrixStats digest lifecycle MatrixGenerics GenomicRanges DelayedArray tibble withr ellipsis fansi pillar stringi utf8 SummarizedExperiment stringr gtable MASS scales farver labeling munsell RColorBrewer viridisLite colorspace ggplot2 isoband mgcv nlme plyr reshape2 jsonlite fastmap mime cachem Biostrings DBI RSQLite KEGGREST curl httr bit64 blob memoise plogr png openssl bit askpass sys yaml rappdirs AnnotationDbi XML BiocParallel futile.logger snow codetools BH lambda.r futile.options formatR BiocFileCache BiocIO rtracklayer biomaRt Rsamtools dbplyr dplyr filelock GenomicAlignments restfulr progress xml2 Rhtslib assertthat purrr tidyselect generics rjson hms prettyunits evaluate htmltools base64enc GenomicFeatures AnnotationFilter ProtGenerics lazyeval highr xfun bslib jquerylib sass fs xtable ensembldb knitr rstudioapi shiny httpuv fontawesome sourcetools later promises commonmark survival htmlwidgets tinytex brio callr desc pkgload praise processx ps waldo rprojroot diffobj rematch2 emdbook RcppEigen RcppNumerical coda bbmle numDeriv bdsmatrix mvtnorm impute shinyFiles openxlsx GSA zip genefilter locfit geneplotter RcppArmadillo annotate tximport AnnotationHub BiocManager BiocVersion interactiveDisplayBase DT crosstalk BSgenome biovizBase latticeExtra Hmisc dichromat VariantAnnotation jpeg Formula cluster rpart nnet foreign gridExtra data.table htmlTable viridis checkmate backports 0 5 10 Imported methods 0 50 100 Required packages 0 20 40 60 80 Heaviness from parents graphics stats utils methods matrixStats jsonlite abind Rcpp gtools svMisc S4Vectors IRanges Matrix GenomicRanges SummarizedExperiment SingleCellExperiment qvalue macrophage tximportData data.table limma GenomeInfoDb knitr pheatmap rmarkdown testthat apeglm AnnotationDbi org.Hs.eg.db samr DESeq2 GenomicFeatures ensembldb EnsDb.Hsapiens.v86 tximeta Gviz In total 66 packages are required directly or indirectly (211) when installing 'fishpond' (2.2.0) Imports Suggests Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'fishpond' 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 fishpond.

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on fishpond
qvalue Imports Parent package is listed in Imports of fishpond but no object from parent package is imported. 44 35
jsonlite Imports 1 0 0 1 1
abind Imports Parent package is listed in Imports of fishpond but no object from parent package is imported. 2 1
gtools Imports 1 0 0 3 1
svMisc Imports 1 0 0 4 1
SingleCellExperiment Imports 1 0 0 25 1
graphics Imports 8 0 0 0 0
stats Imports 8 0 0 0 0
utils Imports 6 0 0 0 0
methods Imports 3 0 0 0 0
matrixStats Imports 4 0 0 0 0
Rcpp Imports The whole set of functions/methods/classes from parent package is imported to the namespace of fishpond. 2 0
S4Vectors Imports 3 0 0 6 0
IRanges Imports 1 0 0 7 0
Matrix Imports 6 0 0 7 0
GenomicRanges Imports 11 0 0 15 0
SummarizedExperiment Imports 13 0 0 24 0
Gviz Suggests No object is imported into the namespace of fishpond. 142 84
tximeta Suggests No object is imported into the namespace of fishpond. 123 79
EnsDb.Hsapiens.v86 Suggests No object is imported into the namespace of fishpond. 101 57
ensembldb Suggests No object is imported into the namespace of fishpond. 100 56
GenomicFeatures Suggests No object is imported into the namespace of fishpond. 96 52
DESeq2 Suggests No object is imported into the namespace of fishpond. 93 37
samr Suggests No object is imported into the namespace of fishpond. 49 24
org.Hs.eg.db Suggests No object is imported into the namespace of fishpond. 45 20
AnnotationDbi Suggests No object is imported into the namespace of fishpond. 44 19
rmarkdown Suggests No object is imported into the namespace of fishpond. 27 15
testthat Suggests No object is imported into the namespace of fishpond. 36 14
apeglm Suggests No object is imported into the namespace of fishpond. 36 9
knitr Suggests No object is imported into the namespace of fishpond. 12 5
macrophage Suggests No object is imported into the namespace of fishpond. 0 1
tximportData Suggests No object is imported into the namespace of fishpond. 0 1
data.table Suggests No object is imported into the namespace of fishpond. 1 1
limma Suggests No object is imported into the namespace of fishpond. 5 1
pheatmap Suggests No object is imported into the namespace of fishpond. 18 1
GenomeInfoDb Suggests No object is imported into the namespace of fishpond. 11 0

Analysis was done with pkgndep.