Package: BiocSet 1.21.0
Kayla Morrell
BiocSet: Representing Different Biological Sets
BiocSet displays different biological sets in a triple tibble format. These three tibbles are `element`, `set`, and `elementset`. The user has the abilty to activate one of these three tibbles to perform common functions from the dplyr package. Mapping functionality and accessing web references for elements/sets are also available in BiocSet.
Authors:
BiocSet_1.21.0.tar.gz
BiocSet_1.21.0.zip(r-4.5)BiocSet_1.21.0.zip(r-4.4)BiocSet_1.21.0.zip(r-4.3)
BiocSet_1.21.0.tgz(r-4.4-any)BiocSet_1.21.0.tgz(r-4.3-any)
BiocSet_1.21.0.tar.gz(r-4.5-noble)BiocSet_1.21.0.tar.gz(r-4.4-noble)
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BiocSet.pdf |BiocSet.html✨
BiocSet/json (API)
NEWS
| # Install 'BiocSet' in R: |
| install.packages('BiocSet', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:BiocSet-1.21.0(bioc 3.21)BiocSet-1.20.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 22 days agofrom:263c319c6b. Checks:OK: 5 ERROR: 2. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 19 2024 |
| R-4.5-win | OK | Nov 19 2024 |
| R-4.5-linux | OK | Nov 19 2024 |
| R-4.4-win | OK | Nov 19 2024 |
| R-4.4-mac | ERROR | Nov 19 2024 |
| R-4.3-win | OK | Nov 19 2024 |
| R-4.3-mac | ERROR | Nov 19 2024 |
Exports:arrange_elementarrange_elementsetarrange_setBiocSetBiocSet_from_elementsetBiocSet_from_GeneSetCollectioncoercedata.frame_from_elementdata.frame_from_elementsetdata.frame_from_setes_activatees_elementes_elementsetes_setexportfilter_elementfilter_elementsetfilter_setGeneSetCollection_from_BiocSetgo_setsimportintersect_singlekegg_setsleft_join_elementleft_join_elementsetleft_join_setmap_add_elementmap_add_setmap_multiplemap_setmap_uniquemetadatametadata<-mutate_elementmutate_elementsetmutate_setOBOSetoboset_element_ancestorsoboset_element_childrenoboset_element_parentsoboset_set_ancestorsoboset_set_childrenoboset_set_parentsselect_elementselect_elementsetselect_setsummarise_elementsummarise_elementsetsummarise_settibble_from_elementtibble_from_elementsettibble_from_setunion_singleurl_refurl_ref_elementurl_ref_set
Dependencies:AnnotationDbiaskpassBiobaseBiocGenericsBiocIOBiostringsbitbit64blobcachemclicpp11crayoncurlDBIdplyrfansifastmapgenericsGenomeInfoDbGenomeInfoDbDatagluehttrIRangesjsonliteKEGGRESTlifecyclemagrittrmemoisemimeontologyIndexopensslpillarpkgconfigplogrplyrpngpurrrR6RcpprlangRSQLiteS4VectorsstringistringrsystibbletidyrtidyselectUCSC.utilsutf8vctrswithrXVectorzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| BiocSet class | BiocSet BiocSet-class BiocSet_from_elementset es_element es_element,BiocSet-method es_elementset es_elementset,BiocSet-method es_set es_set,BiocSet-method show,BiocSet-method |
| as("BiocSet", "list") | coerce coerce,BiocSet,list-method |
| Functions applied to elements in a 'BiocSet' object | arrange_element data.frame_from_element element_funs filter_element left_join_element mutate_element select_element summarise_element tibble_from_element |
| Functions applied to elementsets in a 'BiocSet' object | arrange_elementset data.frame_from_elementset elementset_funs filter_elementset left_join_elementset mutate_elementset select_elementset summarise_elementset tibble_from_elementset |
| GeneSetCollection | BiocSet_from_GeneSetCollection genesetcollection GeneSetCollection_from_BiocSet |
| Importing/exporting | export,BiocSet,GMTFile,ANY-method export,BiocSet,OBOFile,ANY-method import import,GMTFile,ANY,ANY-method import,OBOFile,ANY,ANY-method |
| Intersect on a single 'BiocSet' object | intersect_single |
| Functions for mapping elements in the element tibble to different id types | mapping_element map_add_element map_multiple map_unique |
| Functions for mapping sets in the set tibble to different id types | go_sets kegg_sets mapping_set map_add_set map_set |
| Functions to display relationships of an 'OBOSet' object | oboset_element_ancestors oboset_element_children oboset_element_parents oboset_set_ancestors oboset_set_children oboset_set_parents obo_relations |
| OBOSet class | OBOSet OBOSet-class |
| Functions applied to sets in a 'BiocSet' object | arrange_set data.frame_from_set filter_set left_join_set mutate_set select_set set_funs summarise_set tibble_from_set |
| Union on a single 'BiocSet' object | union_single |
| Functions to access reference urls for different identifiers | url_ref url_ref_element url_ref_set |
