New release

.github/workflows/unittest.yml

@@ -74,8 +74,9 @@ jobs:
         name: Unittest docker
         id: test-snapshot
         run: |
-          docker run --name run_tests -e CI=true $DOCKER_TAG
-          docker cp run_tests:/test_result.txt .
+          CONTAINER_NAME="run_tests_${{ github.run_id }}"
+          docker run --name "$CONTAINER_NAME" -e CI=true $DOCKER_TAG
+          docker cp "$CONTAINER_NAME":/test_result.txt .
 
       - 
         name: Check workflow result

DESCRIPTION

@@ -21,8 +21,10 @@ Imports:
     AnnotationHub,
     ape,
     ArrayExpress,
+    assertthat,
     aws.s3,
     base,
+    base64enc,
     batchelor,
     beeswarm,
     Biobase,
@@ -56,6 +58,7 @@ Imports:
     GGally,
     ggiraph,
     ggplot2,
+    ggprism,
     ggrepel,
     ggtext,
     glasso,
@@ -75,11 +78,14 @@ Imports:
     harmony,
     HiClimR,
     htmlwidgets,
+    httr,
     igraph,
     iheatmapr,
     IntNMF,
     irlba,
     isva,
+    jsonlite,
+    knitr,
     lazyeval,
     limma,
     magrittr,
@@ -156,6 +162,7 @@ Imports:
     SummarizedExperiment,
     survival,
     sva,
+    tidyprompt,
     tidyr,
     TileDBArray,
     tools,

NAMESPACE

@@ -13,12 +13,22 @@ export(MultiOmicsSAE)
 export(abbreviate_pheno)
 export(add_opacity)
 export(ai.ask)
+export(ai.ask_ellmer)
+export(ai.create_ellmer_chat)
+export(ai.create_image_gemini)
+export(ai.create_image_grok)
+export(ai.create_image_openai)
+export(ai.create_report)
 export(ai.genesets_keywords)
 export(ai.genesets_summary)
+export(ai.get_image_models)
 export(ai.get_models)
 export(ai.get_ollama_models)
 export(ai.get_remote_models)
 export(ai.model_is_available)
+export(ai.tool_get_current_time)
+export(ai.tool_get_expression)
+export(ai.tool_plot_volcano)
 export(alias2hugo)
 export(allSpecies)
 export(allSpecies.ANNOTHUB)
@@ -155,6 +165,7 @@ export(gsea.radarplot)
 export(gset.averageCLR)
 export(gset.averageFC)
 export(gset.cor)
+export(gset.fastFET)
 export(gset.fisher)
 export(gset.fisher2)
 export(gset.fitContrastsWithAllMethods)
@@ -279,8 +290,11 @@ export(mx.create_metabolite_sets)
 export(mx.detect_probetype)
 export(ngs.fitContrastsWithAllMethods)
 export(ngs.fitContrastsWithDESEQ2)
+export(ngs.fitContrastsWithDESEQ2.regress.covs)
 export(ngs.fitContrastsWithEDGER)
+export(ngs.fitContrastsWithEDGER.regress.covs)
 export(ngs.fitContrastsWithLIMMA)
+export(ngs.fitContrastsWithLIMMA.regress.covs)
 export(ngs.fitContrastsWithLIMMA.timeseries)
 export(ngs.fitContrastsWithTTEST)
 export(ngs.fitContrastsWithWILCOXON)
@@ -294,6 +308,7 @@ export(nnmCorrect2)
 export(nonnegative_transform)
 export(normalizeExpression)
 export(normalizeMultiOmics)
+export(normalizeOrganism)
 export(normalizeRLE)
 export(normalizeTMM)
 export(normalizeToControls)
@@ -500,13 +515,13 @@ export(rbind_sparse_matrix)
 export(read.as_matrix)
 export(read.gmt)
 export(read_Olink_NPX)
-export(read_Olink_samples)
 export(read_annot)
 export(read_contrasts)
 export(read_counts)
 export(read_files)
 export(read_h5_counts)
 export(read_samples)
+export(read_spectronaut)
 export(referenceNormalization)
 export(relevelFactorFirst)
 export(removeTechnicalEffects)
@@ -555,6 +570,7 @@ export(star.symbols)
 export(stratifyContrasts)
 export(strwrap2)
 export(substrmatch)
+export(sum_treps)
 export(superBC2)
 export(svaCorrect)
 export(svdImpute2)
@@ -584,12 +600,14 @@ export(wgcna.computeDistinctMatrix)
 export(wgcna.computeModuleEnrichment)
 export(wgcna.compute_multiomics)
 export(wgcna.createConsensusLayers)
+export(wgcna.create_report)
 export(wgcna.describeModules)
 export(wgcna.filterColors)
 export(wgcna.getConsensusGeneStats)
 export(wgcna.getConsensusTopGenesAndSets)
 export(wgcna.getGeneStats)
 export(wgcna.getModuleCrossGenes)
+export(wgcna.getMultiTopGenesAndSets)
 export(wgcna.getTopGenesAndSets)
 export(wgcna.matchColors)
 export(wgcna.pickSoftThreshold)
@@ -611,6 +629,7 @@ export(wgcna.plotModuleHubGenes)
 export(wgcna.plotModuleScores)
 export(wgcna.plotModuleSignificance)
 export(wgcna.plotModuleTraitHeatmap)
+export(wgcna.plotMultiDendroAndColors)
 export(wgcna.plotMultiEigengeneCorrelation)
 export(wgcna.plotPowerAnalysis)
 export(wgcna.plotPowerAnalysis_multi)