Package: PanViz 1.9.1
Luca Anholt
PanViz: Integrating Multi-Omic Network Data With Summay-Level GWAS Data
This pacakge integrates data from the Kyoto Encyclopedia of Genes and Genomes (KEGG) with summary-level genome-wide association (GWAS) data, such as that provided by the GWAS Catalog or GWAS Central databases, or a user's own study or dataset, in order to produce biological networks, termed IMONs (Integrated Multi-Omic Networks). IMONs can be used to analyse trait-specific polymorphic data within the context of biochemical and metabolic reaction networks, providing greater biological interpretability for GWAS data.
Authors:
PanViz_1.9.1.tar.gz
PanViz_1.9.1.zip(r-4.5)PanViz_1.9.1.zip(r-4.4)PanViz_1.9.1.zip(r-4.3)
PanViz_1.9.1.tgz(r-4.4-any)PanViz_1.9.1.tgz(r-4.3-any)
PanViz_1.9.1.tar.gz(r-4.5-noble)PanViz_1.9.1.tar.gz(r-4.4-noble)
PanViz_1.9.1.tgz(r-4.4-emscripten)PanViz_1.9.1.tgz(r-4.3-emscripten)
PanViz.pdf |PanViz.html✨
PanViz/json (API)
| # Install 'PanViz' in R: |
| install.packages('PanViz', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/lucaanholt/panviz/issues
- er_snp_vector - Summary-level GWAS data vector for estrogen-receptor positive breast cancer
On BioConductor:PanViz-1.9.0(bioc 3.21)PanViz-1.7.0(bioc 3.20)
genomewideassociationreactomemetabolomicssnpgraphandnetworknetworkkegg
Last updated 5 days agofrom:37bd166048. Checks:ERROR: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | FAIL | Dec 18 2024 |
| R-4.5-win | ERROR | Dec 18 2024 |
| R-4.5-linux | ERROR | Dec 18 2024 |
| R-4.4-win | ERROR | Dec 18 2024 |
| R-4.4-mac | ERROR | Dec 18 2024 |
| R-4.3-win | ERROR | Dec 18 2024 |
| R-4.3-mac | ERROR | Dec 18 2024 |
Exports:decompose_IMONget_grouped_IMONget_IMONGWAS_data_reader
Dependencies:askpassclicolorspacecpp11curldata.tabledplyreasycsvfansiformatRfutile.loggerfutile.optionsgenericsgluehttrigraphjsonlitelambda.rlatticelifecyclemagrittrMatrixmimeopensslpillarpkgconfigpurrrR6RColorBrewerrentrezrlangstringistringrsystibbletidyrtidyselectutf8vctrswithrXML
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| adj_list_to_igraph | adj_list_to_igraph |
| adj_to_G | adjl_to_G |
| adjl_to_G_grouped | adjl_to_G_grouped |
| colour network by categorical group levels | colour_IMON |
| dbSNP_query_check | dbSNP_query_check |
| dbSNP query clean up function | dbSNP_query_clean |
| decompose_IMON | decompose_IMON |
| ego_IMON | ego_IMON |
| Summary-level GWAS data vector for estrogen-receptor positive breast cancer (EFO_1000649) | er_snp_vector |
| get IMON with SNP and or all network vertices coloured by group variables (either studies or phenotypes) | get_grouped_IMON |
| get_IMON | get_IMON |
| GWAS_data_reader | GWAS_data_reader |
| multi_hex_col_mix | multi_hex_col_mix |
| NCBI_clean | NCBI_clean |
| NCBI_clean_2 | NCBI_clean_2 |
| NCBI_dbSNP_query | NCBI_dbSNP_query |
| reaction_cleanup | reaction_cleanup |
| Retry function | retry |
| set_base_graph_attributes | set_base_graph_attributes |
| snp grouping by chosen categorical variable | set_snp_grouping |
| snp_gene_chr_match | snp_gene_chr_match |
| Fast vectorised SNP to gene chromosome number and genomic location mapping | snp_gene_map |
