Overview | Installation and loading | Gene list functional enrichment analysis with gost | Enrichment analysis | Multiple queries | Visualization | Data sources and versions | Custom data sources with upload_GMT_file | Creating a Generic Enrichment Map (GEM) file for EnrichmentMap | Gene identifier conversion with gconvert | Mapping homologous genes across related organisms with gorth | SNP identifier conversion to gene name with gsnpense | Accessing archived versions or the beta release with set_base_url | Supported organisms and identifier namespaces | Citation | Need help? | References
Package: gprofiler2 0.2.4
Liis Kolberg
gprofiler2: Interface to the 'g:Profiler' Toolset
A toolset for functional enrichment analysis and visualization, gene/protein/SNP identifier conversion and mapping orthologous genes across species via 'g:Profiler' (<https://biit.cs.ut.ee/gprofiler/>). The main tools are: (1) 'g:GOSt' - functional enrichment analysis and visualization of gene lists; (2) 'g:Convert' - gene/protein/transcript identifier conversion across various namespaces; (3) 'g:Orth' - orthology search across species; (4) 'g:SNPense' - mapping SNP rs identifiers to chromosome positions, genes and variant effects. This package is an R interface corresponding to the 2019 update of 'g:Profiler' and provides access to 'g:Profiler' for versions 'e94_eg41_p11' and higher. See the package 'gProfileR' for accessing older versions from the 'g:Profiler' toolset.
Authors:
gprofiler2_0.2.4.tar.gz
gprofiler2_0.2.4.tar.gz(r-4.7-any)gprofiler2_0.2.4.tar.gz(r-4.6-any)
gprofiler2_0.2.4.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
gprofiler2/json (API)
| # Install 'gprofiler2' in R: |
| install.packages('gprofiler2', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated from:616daa073b. Checks:4 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 152 | ||
| source / vignettes | OK | 237 | ||
| linux-release-x86_64 | OK | 153 | ||
| wasm-release | OK | 127 |
Exports:gconvertget_base_urlget_tls_versionget_user_agentget_version_infogorthgostgostplotgprofiler_requestgsnpensemapViridispublish_gostplotpublish_gosttablerandom_queryset_base_urlset_tls_versionset_user_agentupload_GMT_file
Dependencies:askpassbase64encbitopsbslibcachemclicpp11crosstalkcurldata.tabledigestdplyrevaluatefarverfastmapfontawesomefsgenericsggplot2gluegridExtragtablehighrhtmltoolshtmlwidgetshttrisobandjquerylibjsonliteknitrlabelinglaterlazyevallifecyclemagrittrmemoisemimeopensslotelpillarpkgconfigplotlypromisespurrrR6rappdirsRColorBrewerRcppRCurlrlangrmarkdownS7sassscalesstringistringrsystibbletidyrtidyselecttinytexutf8vctrsviridisLitewithrxfunyaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Gene ID conversion. | gconvert |
| Get the current base URL. | get_base_url |
| Get the TLS version for SSL | get_tls_version |
| Get current user agent string. | get_user_agent |
| Get version info of g:Profiler data sources | get_version_info |
| Orthology search. | gorth |
| Gene list functional enrichment. | gost |
| Manhattan plot of functional enrichment results. | gostplot |
| Perform a g:Profiler API request | gprofiler_request |
| Convert SNP rs identifiers to genes. | gsnpense |
| Map vector of numeric values to Viridis color scale. | mapViridis |
| Create and save an annotated Manhattan plot of enrichment results. | publish_gostplot |
| Create and save a table with the functional enrichment analysis results. | publish_gosttable |
| Generate a random gene list for testing. | random_query |
| Set the base URL. | set_base_url |
| Set the TLS version to use for SSL | set_tls_version |
| Set custom user agent string. | set_user_agent |
| Upload custom annotations for functional enrichment analysis in g:GOSt. | upload_GMT_file |