pull

Merge branch 'master' of github.com:Melbourne-COVID-Predict/jascap

# Conflicts:
#	NAMESPACE

NAMESPACE

@@ -18,6 +18,7 @@ export(annotation_consensus)
 export(annotation_label_transfer)
 export(calculate_pseudobulk)
 export(cell_cycle_scoring)
+export(clean_cellxgene_cell_types)
 export(convert_gene_names)
 export(create_pseudobulk)
 export(delete_lines_with_word)
@@ -52,6 +53,7 @@ export(normalise_abundance_seurat_SCT)
 export(preprocessing_output)
 export(pseudobulk_merge)
 export(read_data_container)
+export(reference_annotation_to_consensus)
 export(reference_label_coarse_id)
 export(reference_label_fine_id)
 export(remove_dead_scuttle)
@@ -60,7 +62,6 @@ export(remove_empty_DropletUtils)
 export(run_targets_pipeline)
 export(score_cell_cycle_seurat)
 export(se_add_dispersion)
-export(seurat_to_ligand_receptor_count)
 export(split_summarized_experiment)
 export(target_append)
 export(test_differential_abundance_hpc)
@@ -73,7 +74,6 @@ import(broom)
 import(crew)
 import(crew.cluster)
 import(dplyr)
-import(future.apply)
 import(ggplot2)
 import(ggupset)
 import(here)
@@ -85,31 +85,13 @@ import(tidySingleCellExperiment)
 import(tidySummarizedExperiment)
 import(tidyseurat)
 importFrom(AnnotationDbi,mapIds)
-importFrom(CellChat,aggregateNet)
-importFrom(CellChat,computeExpr_LR)
-importFrom(CellChat,computeExpr_agonist)
-importFrom(CellChat,computeExpr_coreceptor)
-importFrom(CellChat,computeRegionDistance)
-importFrom(CellChat,createCellChat)
-importFrom(CellChat,filterCommunication)
-importFrom(CellChat,identifyOverExpressedGenes)
-importFrom(CellChat,identifyOverExpressedInteractions)
-importFrom(CellChat,projectData)
-importFrom(CellChat,scPalette)
-importFrom(CellChat,searchPair)
-importFrom(CellChat,setIdent)
-importFrom(CellChat,subsetCommunication)
-importFrom(CellChat,subsetDB)
-importFrom(CellChat,subsetData)
-importFrom(CellChat,triMean)
 importFrom(DropletUtils,barcodeRanks)
 importFrom(DropletUtils,emptyDrops)
 importFrom(EnsDb.Hsapiens.v86,EnsDb.Hsapiens.v86)
 importFrom(HDF5Array,loadHDF5SummarizedExperiment)
 importFrom(HDF5Array,saveHDF5SummarizedExperiment)
 importFrom(Matrix,Matrix)
 importFrom(Matrix,colSums)
-importFrom(RColorBrewer,brewer.pal)
 importFrom(S4Vectors,cbind)
 importFrom(S4Vectors,metadata)
 importFrom(S4Vectors,split)
@@ -147,22 +129,18 @@ importFrom(SummarizedExperiment,rowData)
 importFrom(callr,r)
 importFrom(celldex,BlueprintEncodeData)
 importFrom(celldex,MonacoImmuneData)
-importFrom(circlize,colorRamp2)
-importFrom(cowplot,as_grob)
 importFrom(crew,crew_controller_local)
 importFrom(data.table,":=")
 importFrom(digest,digest)
 importFrom(dplyr,"%>%")
 importFrom(dplyr,across)
-importFrom(dplyr,add_count)
 importFrom(dplyr,as_tibble)
 importFrom(dplyr,bind_rows)
 importFrom(dplyr,case_when)
 importFrom(dplyr,count)
 importFrom(dplyr,distinct)
 importFrom(dplyr,filter)
 importFrom(dplyr,group_by)
-importFrom(dplyr,if_else)
 importFrom(dplyr,join_by)
 importFrom(dplyr,left_join)
 importFrom(dplyr,mutate)
@@ -176,16 +154,10 @@ importFrom(dplyr,tibble)
 importFrom(dplyr,tribble)
 importFrom(dplyr,with_groups)
 importFrom(edgeR,estimateDisp)
-importFrom(future,nbrOfWorkers)
 importFrom(future,tweak)
 importFrom(glue,glue)
-importFrom(grid,grid.grab)
-importFrom(gridGraphics,grid.echo)
 importFrom(here,here)
 importFrom(ids,random_id)
-importFrom(igraph,graph_from_adjacency_matrix)
-importFrom(igraph,in_circle)
-importFrom(igraph,layout_)
 importFrom(lme4,findbars)
 importFrom(magrittr,"%$%")
 importFrom(magrittr,"%>%")
@@ -194,31 +166,22 @@ importFrom(magrittr,extract2)
 importFrom(magrittr,not)
 importFrom(magrittr,set_names)
 importFrom(methods,show)
-importFrom(methods,slot)
-importFrom(patchwork,wrap_elements)
-importFrom(pbapply,pbsapply)
 importFrom(purrr,compact)
 importFrom(purrr,imap)
 importFrom(purrr,map)
 importFrom(purrr,map2)
-importFrom(purrr,map2_dbl)
 importFrom(purrr,map_chr)
 importFrom(purrr,map_int)
 importFrom(purrr,rep_along)
 importFrom(purrr,safely)
 importFrom(purrr,set_names)
-importFrom(purrr,when)
 importFrom(readr,read_csv)
 importFrom(readr,write_lines)
-importFrom(reshape2,melt)
 importFrom(rlang,enquo)
 importFrom(rlang,is_symbolic)
 importFrom(rlang,parse_expr)
 importFrom(rlang,quo_is_symbolic)
-importFrom(rlang,quo_name)
 importFrom(rlang,sym)
-importFrom(scales,rescale)
-importFrom(scales,viridis_pal)
 importFrom(scater,isOutlier)
 importFrom(scuttle,logNormCounts)
 importFrom(scuttle,perCellQCMetrics)
@@ -238,6 +201,7 @@ importFrom(targets,tar_config_get)
 importFrom(targets,tar_option_set)
 importFrom(targets,tar_script)
 importFrom(tibble,as_tibble)
+importFrom(tibble,deframe)
 importFrom(tibble,enframe)
 importFrom(tibble,rowid_to_column)
 importFrom(tibble,tibble)