Dependency analysis on package VariantAnnotation
General information
| Bioconductor link | link |
|---|---|
| Package version | 1.42.1 |
| Number of strong dependencies | 98 |
| Number of all dependencies | 152 |
| Number of parent packages | 20 |
| Max heaviness from parent packages | 26 |
| Total heaviness from parent packages | 27 |
Number of parent packages (including Suggests and Enhances) | 31 |
| Max co-heaviness from parent packages ("GenomicFeatures" and "AnnotationDbi") | 25 |
Dependency heatmap
In the following dependency heatmap, rows are the parent packages of VariantAnnotation 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 VariantAnnotation.
Dependency table
"Import" information is from the NAMESPACE file of VariantAnnotation.
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 VariantAnnotation: number of required packages that can be reduced if moving parent package to Suggests of VariantAnnotation.
| Parent package | Field | imports | importMethods | importClasses | Required packages | Heaviness from parent on VariantAnnotation |
|---|---|---|---|---|---|---|
| methods | Depends | The whole set of functions/methods/classes from parent package is imported to the namespace of VariantAnnotation. | 0 | 0 | ||
| MatrixGenerics | Depends | 1 | 0 | 0 | 2 | 0 |
| BiocGenerics | Depends | The whole set of functions/methods/classes from parent package is imported to the namespace of VariantAnnotation. | 4 | 0 | ||
| GenomeInfoDb | Depends | The whole set of functions/methods/classes from parent package is imported to the namespace of VariantAnnotation. | 11 | 0 | ||
| GenomicRanges | Depends | The whole set of functions/methods/classes from parent package is imported to the namespace of VariantAnnotation. | 15 | 0 | ||
| SummarizedExperiment | Depends | The whole set of functions/methods/classes from parent package is imported to the namespace of VariantAnnotation. | 24 | 0 | ||
| Rsamtools | Depends | The whole set of functions/methods/classes from parent package is imported to the namespace of VariantAnnotation. | 29 | 0 | ||
| GenomicFeatures | Imports | 4 | 7 | 1 | 96 | 26 |
| BSgenome | Imports | 0 | 0 | 1 | 45 | 1 |
| utils | Imports | 3 | 0 | 0 | 0 | 0 |
| zlibbioc | Imports | The whole set of functions/methods/classes from parent package is imported to the namespace of VariantAnnotation. | 0 | 0 | ||
| DBI | Imports | 0 | 9 | 0 | 1 | 0 |
| Biobase | Imports | 3 | 0 | 1 | 5 | 0 |
| S4Vectors | Imports | The whole set of functions/methods/classes from parent package is imported to the namespace of VariantAnnotation. | 6 | 0 | ||
| IRanges | Imports | The whole set of functions/methods/classes from parent package is imported to the namespace of VariantAnnotation. | 7 | 0 | ||
| XVector | Imports | 2 | 0 | 0 | 10 | 0 |
| Biostrings | Imports | 6 | 4 | 2 | 17 | 0 |
| AnnotationDbi | Imports | 0 | 8 | 1 | 44 | 0 |
| rtracklayer | Imports | 2 | 0 | 0 | 44 | 0 |
| Rhtslib | LinkingTo | Parent package is listed in LinkingTo of VariantAnnotation but no object from parent package is imported. |
1 | 0 | ||
| AnnotationHub | Suggests | No object is imported into the namespace of VariantAnnotation. | 85 | 22 | ||
| BiocStyle | Suggests | No object is imported into the namespace of VariantAnnotation. | 30 | 15 | ||
| ggplot2 | Suggests | No object is imported into the namespace of VariantAnnotation. | 37 | 14 | ||
| snpStats | Suggests | No object is imported into the namespace of VariantAnnotation. | 12 | 3 | ||
| SIFT.Hsapiens.dbSNP132 | Suggests | No object is imported into the namespace of VariantAnnotation. | 99 | 2 | ||
| SIFT.Hsapiens.dbSNP137 | Suggests | No object is imported into the namespace of VariantAnnotation. | 99 | 2 | ||
| PolyPhen.Hsapiens.dbSNP131 | Suggests | No object is imported into the namespace of VariantAnnotation. | 99 | 2 | ||
| RUnit | Suggests | No object is imported into the namespace of VariantAnnotation. | 3 | 1 | ||
| SNPlocs.Hsapiens.dbSNP.20101109 | Suggests | No object is imported into the namespace of VariantAnnotation. | 16 | 1 | ||
| BSgenome.Hsapiens.UCSC.hg19 | Suggests | No object is imported into the namespace of VariantAnnotation. | 46 | 1 | ||
| TxDb.Hsapiens.UCSC.hg19.knownGene | Suggests | No object is imported into the namespace of VariantAnnotation. | 97 | 1 | ||
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 VariantAnnotation | Co-heaviness as Jaccard coeffcient |
|---|---|---|---|
| AnnotationDbi | GenomicFeatures | 25 | 0.49 |
Analysis was done with pkgndep.