Package: gemma.R 3.1.6

Ogan Mancarci

gemma.R: A wrapper for Gemma's Restful API to access curated gene expression data and differential expression analyses

Low- and high-level wrappers for Gemma's RESTful API. They enable access to curated expression and differential expression data from over 10,000 published studies. Gemma is a web site, database and a set of tools for the meta-analysis, re-use and sharing of genomics data, currently primarily targeted at the analysis of gene expression profiles.

Authors:Javier Castillo-Arnemann [aut], Jordan Sicherman [aut], Ogan Mancarci [cre, aut], Guillaume Poirier-Morency [aut]

gemma.R_3.1.6.tar.gz
gemma.R_3.1.6.zip(r-4.5)gemma.R_3.1.6.zip(r-4.4)gemma.R_3.1.6.zip(r-4.3)
gemma.R_3.1.6.tgz(r-4.4-any)gemma.R_3.1.6.tgz(r-4.3-any)
gemma.R_3.1.6.tar.gz(r-4.5-noble)gemma.R_3.1.6.tar.gz(r-4.4-noble)
gemma.R_3.1.6.tgz(r-4.4-emscripten)gemma.R_3.1.6.tgz(r-4.3-emscripten)
gemma.R.pdf |gemma.R.html✨
gemma.R/json (API)
NEWS

# Install 'gemma.R' in R:
install.packages('gemma.R', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/pavlidislab/gemma.r/issues

On BioConductor:gemma.R-3.1.5(bioc 3.20)gemma.R-3.0.6(bioc 3.19)

bioconductor-package

38 exports 2.50 score 63 dependencies

Last updated 20 days agofrom:610f89799b

Exports:filter_propertiesforget_gemma_memoisedgemma_callgemma_kablegemma_memoiseget_all_pagesget_child_termsget_dataset_annotationsget_dataset_designget_dataset_differential_expression_analysesget_dataset_expressionget_dataset_expression_for_genesget_dataset_objectget_dataset_platformsget_dataset_processed_expressionget_dataset_quantitation_typesget_dataset_raw_expressionget_dataset_samplesget_datasetsget_datasets_by_idsget_differential_expression_valuesget_gene_go_termsget_gene_locationsget_gene_probesget_genesget_platform_annotationsget_platform_datasetsget_platform_element_genesget_platforms_by_idsget_result_setsget_taxaget_taxon_datasetsmake_designsearch_annotationssearch_datasetssearch_gemmaset_gemma_userupdate_result

Dependencies:abindaskpassassertthatbase64encBiobaseBiocGenericsbitbit64cachemclicpp11crayoncurldata.tableDelayedArraydigestdplyrfansifastmapgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesgluehttrIRangesjsonlitelatticelifecyclelubridatemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpillarpkgconfigpurrrR.methodsS3R.ooR.utilsR6rappdirsrlangS4ArraysS4VectorsSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttimechangeUCSC.utilsutf8vctrswithrXVectorzlibbioc

Readme and manuals

Help Manual

Help pageTopics
Return all supported filter propertiesfilter_properties
Clear gemma.R cacheforget_gemma_memoised
Custom gemma callgemma_call
Create printable tables out of gemma.R outputsgemma_kable
Enable and disable memoisation of gemma.R functionsgemma_memoise
gemma.R package: Access curated gene expression data and differential expression analysesgemma.R-package gemma.R
Get all pages of a paginated callget_all_pages
Return child terms of a termget_child_terms
Retrieve the annotations of a datasetget_dataset_annotations
Retrieve the design of a datasetget_dataset_design
Retrieve annotations and surface level stats for a dataset's differential analysesget_dataset_differential_expression_analyses
Retrieve the expression data matrix of a set of datasets and genesget_dataset_expression_for_genes
Compile gene expression data and metadataget_dataset_object
Retrieve the platforms of a datasetget_dataset_platforms
Retrieve processed expression data of a datasetget_dataset_processed_expression
Retrieve quantitation types of a datasetget_dataset_quantitation_types
Retrieve raw expression data of a datasetget_dataset_raw_expression
Retrieve the samples of a datasetget_dataset_samples
Retrieve all datasetsget_datasets
Retrieve datasets by their identifiersget_datasets_by_ids
Retrieve differential expression resultsget_differential_expression_values
Retrieve the GO terms associated to a geneget_gene_go_terms
Retrieve the physical locations of a given geneget_gene_locations
Retrieve the probes associated to a genes across all platformsget_gene_probes
Retrieve genes matching gene identifiersget_genes
Retrieve Platform Annotations by Gemmaget_platform_annotations
Retrieve all experiments using a given platformget_platform_datasets
Retrieve the genes associated to a probe in a given platformget_platform_element_genes
Retrieve all platforms matching a set of platform identifiersget_platforms_by_ids
Retrieve all result sets matching the provided criteriaget_result_sets
Get taxaget_taxa
Make simplified design framesmake_design
Search for annotation tagssearch_annotations
Search everything in Gemmasearch_gemma
Authentication by user nameset_gemma_user
Update resultupdate_result