Dependency analysis on package GenomicRanges

General information

Bioconductor link link
Package version1.48.0
Number of strong dependencies15
Number of all dependencies192
Number of parent packages9
Max heaviness from parent packages4
Total heaviness from parent packages7
Number of parent packages (including Suggests and Enhances)44

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Depends Imports Suggests utils methods stats graphics stats4 tools grDevices grid parallel splines BiocGenerics S4Vectors IRanges RCurl bitops GenomeInfoDbData zlibbioc XVector GenomeInfoDb crayon Biostrings Biobase lattice glue GenomicRanges jsonlite R6 yaml XML MatrixGenerics Matrix DelayedArray matrixStats rlang fastmap BiocParallel futile.logger snow codetools BH lambda.r futile.options formatR Rcpp httr png curl mime openssl askpass sys Rhtslib SummarizedExperiment Rsamtools DBI RSQLite KEGGREST bit64 blob memoise pkgconfig plogr bit vctrs cachem cli magrittr AnnotationDbi digest GenomicAlignments BiocIO restfulr rjson stringr stringi rappdirs rtracklayer ellipsis lifecycle pillar tibble withr fansi utf8 BiocFileCache dbplyr dplyr filelock assertthat purrr tidyselect generics biomaRt progress xml2 hms prettyunits GenomicFeatures BSgenome evaluate highr xfun htmltools base64enc xtable locfit knitr bslib jquerylib sass fs RColorBrewer scales farver labeling munsell viridisLite survival ggplot2 gtable colorspace isoband MASS mgcv nlme tinytex BiocManager lazyeval htmlwidgets genefilter geneplotter RcppArmadillo annotate limma graph Rgraphviz bookdown rmarkdown org.Hs.eg.db BiocVersion interactiveDisplayBase shiny DT httpuv fontawesome sourcetools later promises commonmark crosstalk DESeq2 hwriter statmod ensembldb biovizBase latticeExtra AnnotationFilter ProtGenerics Hmisc dichromat VariantAnnotation jpeg Formula cluster rpart nnet foreign gridExtra data.table htmlTable viridis checkmate rstudioapi backports 0 1 2 Imported methods 0 50 100 Required packages 0 50 100 Heaviness from parents methods stats4 BiocGenerics S4Vectors IRanges GenomeInfoDb utils stats XVector RNAseqData.HNRNPC.bam.chr14 pasillaBamSubset digest RUnit Biobase Matrix edgeR knitr KEGGgraph Biostrings SummarizedExperiment KEGGREST rmarkdown Rsamtools BiocStyle GenomicAlignments AnnotationDbi rtracklayer BSgenome hgu95av2probe hgu95av2.db BSgenome.Scerevisiae.UCSC.sacCer2 BSgenome.Hsapiens.UCSC.hg19 BSgenome.Mmusculus.UCSC.mm10 annotate AnnotationHub DESeq2 GenomicFeatures TxDb.Athaliana.BioMart.plantsmart22 TxDb.Dmelanogaster.UCSC.dm3.ensGene TxDb.Hsapiens.UCSC.hg19.knownGene TxDb.Mmusculus.UCSC.mm10.knownGene VariantAnnotation DEXSeq Gviz In total 15 packages are required directly or indirectly (192) when installing 'GenomicRanges' (1.48.0) Depends Imports Suggests Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'GenomicRanges' Imported functions The whole namespace is imported


Dependency table

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

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on GenomicRanges
GenomeInfoDb Depends The whole set of functions/methods/classes from parent package is imported to the namespace of GenomicRanges. 11 4
methods Depends The whole set of functions/methods/classes from parent package is imported to the namespace of GenomicRanges. 0 0
stats4 Depends 2 0 0 0 0
BiocGenerics Depends The whole set of functions/methods/classes from parent package is imported to the namespace of GenomicRanges. 4 0
S4Vectors Depends The whole set of functions/methods/classes from parent package is imported to the namespace of GenomicRanges. 6 0
IRanges Depends The whole set of functions/methods/classes from parent package is imported to the namespace of GenomicRanges. 7 0
XVector Imports The whole set of functions/methods/classes from parent package is imported to the namespace of GenomicRanges. 10 3
utils Imports 2 0 0 0 0
stats Imports 1 0 0 0 0
Gviz Suggests No object is imported into the namespace of GenomicRanges. 142 128
DEXSeq Suggests No object is imported into the namespace of GenomicRanges. 114 100
VariantAnnotation Suggests No object is imported into the namespace of GenomicRanges. 98 84
TxDb.Athaliana.BioMart.plantsmart22 Suggests No object is imported into the namespace of GenomicRanges. 97 83
TxDb.Dmelanogaster.UCSC.dm3.ensGene Suggests No object is imported into the namespace of GenomicRanges. 97 83
TxDb.Hsapiens.UCSC.hg19.knownGene Suggests No object is imported into the namespace of GenomicRanges. 97 83
TxDb.Mmusculus.UCSC.mm10.knownGene Suggests No object is imported into the namespace of GenomicRanges. 97 83
GenomicFeatures Suggests No object is imported into the namespace of GenomicRanges. 96 82
DESeq2 Suggests No object is imported into the namespace of GenomicRanges. 93 79
AnnotationHub Suggests No object is imported into the namespace of GenomicRanges. 85 71
annotate Suggests No object is imported into the namespace of GenomicRanges. 47 33
hgu95av2.db Suggests No object is imported into the namespace of GenomicRanges. 46 32
BSgenome.Scerevisiae.UCSC.sacCer2 Suggests No object is imported into the namespace of GenomicRanges. 46 32
BSgenome.Hsapiens.UCSC.hg19 Suggests No object is imported into the namespace of GenomicRanges. 46 32
BSgenome.Mmusculus.UCSC.mm10 Suggests No object is imported into the namespace of GenomicRanges. 46 32
BSgenome Suggests No object is imported into the namespace of GenomicRanges. 45 31
hgu95av2probe Suggests No object is imported into the namespace of GenomicRanges. 45 31
AnnotationDbi Suggests No object is imported into the namespace of GenomicRanges. 44 30
rtracklayer Suggests No object is imported into the namespace of GenomicRanges. 44 30
BiocStyle Suggests No object is imported into the namespace of GenomicRanges. 30 27
rmarkdown Suggests No object is imported into the namespace of GenomicRanges. 27 24
GenomicAlignments Suggests No object is imported into the namespace of GenomicRanges. 38 24
Rsamtools Suggests No object is imported into the namespace of GenomicRanges. 29 15
KEGGREST Suggests No object is imported into the namespace of GenomicRanges. 27 13
SummarizedExperiment Suggests No object is imported into the namespace of GenomicRanges. 24 10
knitr Suggests No object is imported into the namespace of GenomicRanges. 12 9
edgeR Suggests No object is imported into the namespace of GenomicRanges. 10 7
KEGGgraph Suggests No object is imported into the namespace of GenomicRanges. 13 6
Matrix Suggests No object is imported into the namespace of GenomicRanges. 7 4
Biostrings Suggests No object is imported into the namespace of GenomicRanges. 17 3
RNAseqData.HNRNPC.bam.chr14 Suggests No object is imported into the namespace of GenomicRanges. 0 1
pasillaBamSubset Suggests No object is imported into the namespace of GenomicRanges. 0 1
digest Suggests No object is imported into the namespace of GenomicRanges. 1 1
RUnit Suggests No object is imported into the namespace of GenomicRanges. 3 1
Biobase Suggests No object is imported into the namespace of GenomicRanges. 5 1

Analysis was done with pkgndep.