Dependency analysis on package GenomicFeatures

General information

Bioconductor link link
Package version1.48.3
Number of strong dependencies96
Number of all dependencies136
Number of parent packages19
Max heaviness from parent packages25
Total heaviness from parent packages48
Number of parent packages (including Suggests and Enhances)43
Max co-heaviness from parent packages ("biomaRt" and "AnnotationDbi")11

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Depends Imports Suggests methods utils stats graphics stats4 tools grDevices parallel grid BiocGenerics S4Vectors IRanges bitops RCurl GenomeInfoDbData zlibbioc GenomeInfoDb XVector crayon Biostrings Biobase glue GenomicRanges rlang BiocParallel Rhtslib yaml futile.logger snow codetools BH lambda.r futile.options formatR DBI bit64 blob pkgconfig Rcpp plogr bit vctrs cli fastmap XML Rsamtools SummarizedExperiment MatrixGenerics Matrix DelayedArray matrixStats lattice memoise cachem jsonlite R6 GenomicAlignments BiocIO restfulr rjson RSQLite KEGGREST httr png curl mime openssl askpass sys AnnotationDbi stringr magrittr stringi digest rappdirs hms ellipsis lifecycle generics progress BiocFileCache xml2 prettyunits dbplyr dplyr filelock assertthat pillar purrr tibble tidyselect withr fansi utf8 rtracklayer GenomicFeatures biomaRt BSgenome xfun evaluate highr lazyeval lubridate cpp11 bookdown knitr rmarkdown BiocManager htmltools jquerylib tinytex bslib base64enc sass fs AnnotationFilter ProtGenerics 0 5 10 Imported methods 0 50 100 Required packages 0 10 20 Heaviness from parents BiocGenerics S4Vectors IRanges GenomeInfoDb GenomicRanges AnnotationDbi methods utils stats tools DBI RCurl Biobase BiocIO XVector RSQLite Biostrings rtracklayer biomaRt pasillaBamSubset RUnit knitr AnnotationFilter RMariaDB Rsamtools BiocStyle GenomicAlignments org.Mm.eg.db org.Hs.eg.db BSgenome mirbase.db BSgenome.Hsapiens.UCSC.hg19 BSgenome.Celegans.UCSC.ce11 BSgenome.Dmelanogaster.UCSC.dm3 SNPlocs.Hsapiens.dbSNP144.GRCh38 FDb.UCSC.tRNAs TxDb.Hsapiens.UCSC.hg19.knownGene TxDb.Celegans.UCSC.ce11.ensGene TxDb.Dmelanogaster.UCSC.dm3.ensGene TxDb.Mmusculus.UCSC.mm10.knownGene TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts TxDb.Hsapiens.UCSC.hg38.knownGene ensembldb In total 96 packages are required directly or indirectly (136) when installing 'GenomicFeatures' (1.48.3) Depends Imports Suggests Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'GenomicFeatures' Imported functions Imported S4 methods Imported S4 classes The whole namespace is imported


Dependency table

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

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on GenomicFeatures
BiocGenerics Depends The whole set of functions/methods/classes from parent package is imported to the namespace of GenomicFeatures. 4 0
S4Vectors Depends The whole set of functions/methods/classes from parent package is imported to the namespace of GenomicFeatures. 6 0
IRanges Depends The whole set of functions/methods/classes from parent package is imported to the namespace of GenomicFeatures. 7 0
GenomeInfoDb Depends The whole set of functions/methods/classes from parent package is imported to the namespace of GenomicFeatures. 11 0
GenomicRanges Depends The whole set of functions/methods/classes from parent package is imported to the namespace of GenomicFeatures. 15 0
AnnotationDbi Depends The whole set of functions/methods/classes from parent package is imported to the namespace of GenomicFeatures. 44 0
biomaRt Imports 8 0 0 70 25
rtracklayer Imports 10 0 0 44 23
methods Imports The whole set of functions/methods/classes from parent package is imported to the namespace of GenomicFeatures. 0 0
utils Imports 7 0 0 0 0
stats Imports 1 0 0 0 0
tools Imports 2 0 0 0 0
DBI Imports 0 8 0 1 0
RCurl Imports 1 0 0 2 0
Biobase Imports 1 0 0 5 0
BiocIO Imports 1 0 2 8 0
XVector Imports The whole set of functions/methods/classes from parent package is imported to the namespace of GenomicFeatures. 10 0
RSQLite Imports 2 0 0 17 0
Biostrings Imports 3 0 3 17 0
BiocStyle Suggests No object is imported into the namespace of GenomicFeatures. 30 15
ensembldb Suggests No object is imported into the namespace of GenomicFeatures. 100 5
knitr Suggests No object is imported into the namespace of GenomicFeatures. 12 4
RMariaDB Suggests No object is imported into the namespace of GenomicFeatures. 20 3
AnnotationFilter Suggests No object is imported into the namespace of GenomicFeatures. 17 2
BSgenome.Hsapiens.UCSC.hg19 Suggests No object is imported into the namespace of GenomicFeatures. 46 2
BSgenome.Celegans.UCSC.ce11 Suggests No object is imported into the namespace of GenomicFeatures. 46 2
BSgenome.Dmelanogaster.UCSC.dm3 Suggests No object is imported into the namespace of GenomicFeatures. 46 2
SNPlocs.Hsapiens.dbSNP144.GRCh38 Suggests No object is imported into the namespace of GenomicFeatures. 46 2
FDb.UCSC.tRNAs Suggests No object is imported into the namespace of GenomicFeatures. 97 2
TxDb.Hsapiens.UCSC.hg19.knownGene Suggests No object is imported into the namespace of GenomicFeatures. 97 2
TxDb.Celegans.UCSC.ce11.ensGene Suggests No object is imported into the namespace of GenomicFeatures. 97 2
TxDb.Dmelanogaster.UCSC.dm3.ensGene Suggests No object is imported into the namespace of GenomicFeatures. 97 2
TxDb.Mmusculus.UCSC.mm10.knownGene Suggests No object is imported into the namespace of GenomicFeatures. 97 2
TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts Suggests No object is imported into the namespace of GenomicFeatures. 97 2
TxDb.Hsapiens.UCSC.hg38.knownGene Suggests No object is imported into the namespace of GenomicFeatures. 97 2
pasillaBamSubset Suggests No object is imported into the namespace of GenomicFeatures. 0 1
RUnit Suggests No object is imported into the namespace of GenomicFeatures. 3 1
org.Mm.eg.db Suggests No object is imported into the namespace of GenomicFeatures. 45 1
org.Hs.eg.db Suggests No object is imported into the namespace of GenomicFeatures. 45 1
BSgenome Suggests No object is imported into the namespace of GenomicFeatures. 45 1
mirbase.db Suggests No object is imported into the namespace of GenomicFeatures. 45 1
Rsamtools Suggests No object is imported into the namespace of GenomicFeatures. 29 0
GenomicAlignments Suggests No object is imported into the namespace of GenomicFeatures. 38 0

The following table lists pairs of parent packages with co-heaviness larger than 10. The co-heaviness measures the number of additional dependencies that two parent packages simultaneously import and are only imported by the two parents.

Note the co-heaviness from parents can be always easily observed in the dependency heatmap.

Parent 1 Parent 2 Co-heaviness on GenomicFeatures Co-heaviness as Jaccard coeffcient
AnnotationDbi biomaRt 11 0.306

Analysis was done with pkgndep.