Merge branch 'master' of github.com:stemangiola/HCAquery

Author: stemangiola

.github/workflows/check-bioc.yml

@@ -243,7 +243,8 @@ jobs:
               dir('check', 'tar.gz$', full.names = TRUE),
               `quit-with-status` = TRUE,
               `no-check-R-ver` = TRUE,
-              `no-check-bioc-help` = TRUE
+              `no-check-bioc-help` = TRUE,
+              `new-package` = TRUE
           )
         shell: Rscript {0}
 

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: CuratedAtlasQueryR
 Title: Queries the Human Cell Atlas
-Version: 0.4.3
+Version: 0.99.1
 Authors@R: c(
     person(
         "Stefano",
@@ -90,23 +90,13 @@ Imports:
     tibble,
     utils,
     dbplyr (>= 2.3.0),
-    duckdb
+    duckdb,
+    stringr
 Suggests:
-    here,
-    stringr,
-    tidyseurat,
     zellkonverter,
-    scMerge,
-    DelayedArray,
-    openssl,
-    cellxgenedp,
-    celldex,
-    SingleR,
     rmarkdown,
     knitr,
     testthat,
-    tidySingleCellExperiment,
-    ggplot2,
     basilisk,
     arrow,
     reticulate
@@ -130,3 +120,11 @@ URL: https://github.com/stemangiola/CuratedAtlasQueryR
 BugReports: https://github.com/stemangiola/CuratedAtlasQueryR/issues
 VignetteBuilder: knitr
 Roxygen: list(markdown = TRUE)
+Collate: 
+    'utils.R'
+    'counts.R'
+    'dev.R'
+    'metadata.R'
+    'seurat.R'
+    'unharmonised.R'
+    'zzz.R'

NAMESPACE

@@ -5,13 +5,13 @@ export(get_SingleCellExperiment)
 export(get_metadata)
 export(get_seurat)
 export(get_unharmonised_metadata)
-import(Seurat)
-import(dbplyr)
 importFrom(BiocGenerics,cbind)
 importFrom(DBI,dbConnect)
+importFrom(DBI,dbDisconnect)
 importFrom(HDF5Array,HDF5RealizationSink)
 importFrom(HDF5Array,loadHDF5SummarizedExperiment)
 importFrom(S4Vectors,DataFrame)
+importFrom(Seurat,as.SingleCellExperiment)
 importFrom(SeuratObject,as.Seurat)
 importFrom(SeuratObject,as.sparse)
 importFrom(SingleCellExperiment,SingleCellExperiment)
@@ -25,19 +25,22 @@ importFrom(cli,cli_abort)
 importFrom(cli,cli_alert_info)
 importFrom(cli,cli_alert_success)
 importFrom(cli,cli_alert_warning)
+importFrom(cli,hash_sha256)
+importFrom(dbplyr,remote_con)
 importFrom(dplyr,as_tibble)
 importFrom(dplyr,collect)
 importFrom(dplyr,filter)
-importFrom(dplyr,full_join)
+importFrom(dplyr,group_by)
 importFrom(dplyr,inner_join)
 importFrom(dplyr,mutate)
 importFrom(dplyr,pull)
+importFrom(dplyr,summarise)
 importFrom(dplyr,tbl)
-importFrom(dplyr,tibble)
 importFrom(dplyr,transmute)
 importFrom(duckdb,duckdb)
 importFrom(glue,glue)
 importFrom(httr,GET)
+importFrom(httr,HEAD)
 importFrom(httr,modify_url)
 importFrom(httr,parse_url)
 importFrom(httr,progress)
@@ -47,13 +50,17 @@ importFrom(methods,as)
 importFrom(purrr,imap)
 importFrom(purrr,keep)
 importFrom(purrr,map)
+importFrom(purrr,map_chr)
+importFrom(purrr,map_dbl)
 importFrom(purrr,map_int)
 importFrom(purrr,pmap_chr)
 importFrom(purrr,reduce)
 importFrom(purrr,set_names)
-importFrom(purrr,transpose)
+importFrom(purrr,walk)
 importFrom(rlang,.data)
 importFrom(stats,setNames)
+importFrom(stringr,str_remove_all)
+importFrom(stringr,str_replace_all)
 importFrom(tibble,column_to_rownames)
 importFrom(tools,R_user_dir)
 importFrom(utils,head)