Dataset: IFNg | Dataset cancer.ds (GSE16873) | ID mapping files | Molecule (or gene) IDs to glyphs IDs in SBGN-ML files: | Molecule (or gene) IDs to KEGG ortholog IDs | Molecule (or gene) IDs to pathway IDs
Package: SBGNview.data 1.26.0
Weijun Luo
SBGNview.data: Supporting datasets for SBGNview package
This package contains: 1. A microarray gene expression dataset from a human breast cancer study. 2. A RNA-Seq gene expression dataset from a mouse study on IFNG knockout. 3. ID mapping tables between gene IDs and SBGN-ML file glyph IDs. 4. Percent of orthologs detected in other species of the genes in a pathway. Cutoffs of this percentage for defining if a pathway exists in another species. 5. XML text of SBGN-ML files for all pre-collected pathways.
Authors:
SBGNview.data_1.26.0.tar.gz
SBGNview.data_1.26.0.tar.gz(r-4.7-any)SBGNview.data_1.26.0.tar.gz(r-4.6-any)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
SBGNview.data/json (API)
| # Install 'SBGNview.data' in R: |
| install.packages('SBGNview.data', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- cancer.ds - A demo microarray dataset from a cancer study
- chebi_compound.name - Mapping table between two types of IDs
- chebi_kegg - Mapping table between two types of IDs
- chebi_metacyc.SBGN - Mapping table between two types of IDs
- chebi_pathway.id - Mapping table between two types of IDs
- chebi_pathwayCommons - Mapping table between two types of IDs
- compound.name_kegg - Mapping table between two types of IDs
- compound.name_pathway.id - Mapping table between two types of IDs
- compound.name_pathwayCommons - Mapping table between two types of IDs
- ENZYME_pathway.id - Mapping table between two types of IDs
- hsa_ENTREZID_pathwayCommons - Mapping table between two types of IDs
- hsa_KO_ENTREZID - Mapping table between two types of IDs
- hsa_pathwayCommons_ENSEMBL - Mapping table between two types of IDs
- IFNg - RNA-Seq result from a mouse IFNG knockout experiment
- kegg_pathwayCommons - Mapping table between two types of IDs
- KO_pathway.id - Mapping table between two types of IDs
- KO_pathwayCommons - Mapping table between two types of IDs
- mmu_KO_ENSEMBL - Mapping table between two types of IDs
- mmu_KO_ENTREZID - Mapping table between two types of IDs
- mmu_pathwayCommons_ENSEMBL - Mapping table between two types of IDs
- mmu_pathwayCommons_ENTREZID - Mapping table between two types of IDs
- pathway.completeness.cutoff.info - Cutoffs of pathway completeness used for defining existance of pathway in a species
- pathway.species.pct_Mapped - Pathway completeness in a species
- pathwayCommons_SYMBOL - Mapping table between two types of IDs
- sbgn.xmls - XML code of a SBGN-ML file
- SYMBOL_pathway.id - Mapping table between two types of IDs
On BioConductor:SBGNview.data-1.27.0(data/experiment 3.24)SBGNview.data-1.26.0(data/experiment 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
experimentdatacancerdatabreastcancerdatamicroarraydatageornaseqdatadatapkg
Last updated from:b1663a69ae (on RELEASE_3_23). Checks:1 ERROR, 2 NOTE, 1 OK. Indexed: no.
This is a data package. Data packages may be large and do not get checked across all platforms.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 143 | ||
| linux-devel | NOTE | 225 | ||
| source / vignettes | OK | 734 | ||
| linux-release | NOTE | 199 |
Exports:
Dependencies:base64encbookdownbslibcachemclidigestevaluatefastmapfontawesomefshighrhtmltoolsjquerylibjsonliteknitrlifecyclememoisemimeR6rappdirsrlangrmarkdownsasstinytexxfunyaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| A demo microarray dataset from a cancer study | cancer.ds |
| RNA-Seq result from a mouse IFNG knockout experiment | IFNg |
| Mapping table between two types of IDs | chebi_compound.name chebi_kegg chebi_metacyc.SBGN chebi_pathway.id chebi_pathwayCommons compound.name_kegg compound.name_pathway.id compound.name_pathwayCommons ENZYME_pathway.id hsa_ENTREZID_pathwayCommons hsa_KO_ENTREZID hsa_pathwayCommons_ENSEMBL kegg_pathwayCommons KO_pathway.id KO_pathwayCommons mapping mmu_KO_ENSEMBL mmu_KO_ENTREZID mmu_pathwayCommons_ENSEMBL mmu_pathwayCommons_ENTREZID pathwayCommons_SYMBOL SYMBOL_pathway.id |
| Cutoffs of pathway completeness used for defining existance of pathway in a species | pathway.completeness.cutoff.info |
| Pathway completeness in a species | pathway.species.pct_Mapped |
| XML code of a SBGN-ML file | sbgn.xmls |
