Getting started | Installation | Loading the package | Accessing the SkeletalVis dataset | Exploring SkeletalVis | Searching all datasets for a gene of interest | Find a dataset of interest | Retrieve a dataset of interest | Filtering a dataset of interest | Volcano plots | Finding similar datasets | Plotting the similarities | Visualising OATargets data
Package: SkeletalVis 0.1.2
SkeletalVis: Exploration and Visualisation of Skeletal Transcriptomics Data
Allows search and visualisation of a collection of uniformly processed skeletal transcriptomic datasets. Includes methods to identify datasets where genes of interest are differentially expressed and find datasets with a similar gene expression pattern to a query dataset Soul J, Hardingham TE, Boot-Handford RP, Schwartz JM (2019) <doi:10.1093/bioinformatics/bty947>.
Authors:
SkeletalVis_0.1.2.tar.gz
SkeletalVis_0.1.2.zip(r-4.7)SkeletalVis_0.1.2.zip(r-4.6)SkeletalVis_0.1.2.zip(r-4.5)
SkeletalVis_0.1.2.tgz(r-4.6-any)SkeletalVis_0.1.2.tgz(r-4.5-any)
SkeletalVis_0.1.2.tar.gz(r-4.7-any)SkeletalVis_0.1.2.tar.gz(r-4.6-any)
SkeletalVis_0.1.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
SkeletalVis/json (API)
| # Install 'SkeletalVis' in R: |
| install.packages('SkeletalVis', repos = c('https://soulj.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/soulj/skeletalvis/issues
Datasets:
- query - Example gene expression dataset
Last updated from:8754e2a7bd. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 171 | ||
| source / vignettes | OK | 223 | ||
| linux-release-x86_64 | OK | 208 | ||
| macos-release-arm64 | OK | 184 | ||
| macos-oldrel-arm64 | OK | 181 | ||
| windows-devel | OK | 131 | ||
| windows-release | OK | 135 | ||
| windows-oldrel | OK | 106 | ||
| wasm-release | OK | 126 |
Exports:browse_skeletalvisexperiment_similarityget_comparisonsget_exp_tableget_experimentget_gene_fold_changesload_skeletalvisplot_similaritysearch_skeletalvisview_curated_oagenesview_networkview_prioritised_oagenesvolcano_plot
Dependencies:arrowaskpassassertthatbase64encbitbit64bslibcachemclicommonmarkcowplotcpp11crosstalkcurldata.tabledigestdplyrDTevaluatefarverfastmapfontawesomefsgenericsggplot2ggrepelgluegtablehighrhtmltoolshtmlwidgetshttpuvhttrigraphisobandjquerylibjsonliteknitrlabelinglaterlatticelazyevallifecyclemagrittrMatrixmemoisemimeminiUIopensslotelpbapplypillarpkgconfigplotlypromisespurrrR6rappdirsRColorBrewerRcpprlangrmarkdownS7sassscalesshinysourcetoolsstringistringrsystibbletidyrtidyselecttinytexutf8vctrsviridisLitevisNetworkwithrxfunxtableyaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Browse the skeletalvis database metadata | browse_skeletalvis |
| Get cosine similarity for a query dataset against the skeletalvis database | experiment_similarity |
| Retrieve metadata for the SkeletalVis database | get_comparisons |
| Retrieve the experiment table for the SkeletalVis database | get_exp_table |
| Get the gene differential expression results for an experiment of interest | get_experiment |
| Get gene differential expression results for genes of interest | get_gene_fold_changes |
| Load SkeletalVis data | load_skeletalvis |
| Plot ranked cosine similarity scores with top n labels | plot_similarity |
| Example gene expression dataset | query |
| Search for experiments in SkeletalVis | search_skeletalvis |
| View curated osteoarthritis associated genes | view_curated_oagenes |
| View the OATarget gene network | view_network |
| View prioritised osteoarthritis associated genes | view_prioritised_oagenes |
| Volcano Plot of Gene Expression Data | volcano_plot |
