Merge pull request #87 from william-hutchison/fix-installation

Fix installation

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: HPCell
 Title: Massively-parallel R native pipeline for single-cell analysis
-Version: 0.3.8
+Version: 0.3.11
 Authors@R: c(person("Stefano", "Mangiola", email = "[email protected]",
                   role = c("aut", "cre")),
                   person("Jiayi", "Si", email = "[email protected]",
@@ -15,7 +15,8 @@ Remotes:
     sqjin/CellChat,
     satijalab/seurat@seurat5,
     satijalab/seurat-data@seurat5,
-    seurat-data/azimuth@master
+    satijalab/azimuth@master,
+    mojaveazure/seurat-disk@master
 Biarch: true
 Imports:
   targets,
@@ -75,7 +76,15 @@ Imports:
   ggupset, 
   here, 
   qs,
-  ensembldb
+  ensembldb,
+  Azimuth,
+  DelayedArray,
+  HDF5Array, 
+  SeuratObject,
+  SingleCellExperiment, 
+  biomaRt, 
+  lme4, 
+  tidyselect
 Suggests: 
     testthat(>= 3.0.0), 
     scRNAseq,

NAMESPACE

@@ -105,6 +105,7 @@ importFrom(Matrix,colSums)
 importFrom(S4Vectors,cbind)
 importFrom(S4Vectors,metadata)
 importFrom(S4Vectors,split)
+importFrom(Seurat,Assays)
 importFrom(Seurat,CellCycleScoring)
 importFrom(Seurat,CreateAssayObject)
 importFrom(Seurat,CreateSeuratObject)
@@ -147,7 +148,6 @@ importFrom(celldex,MonacoImmuneData)
 importFrom(crew,crew_controller_local)
 importFrom(data.table,":=")
 importFrom(digest,digest)
-importFrom(dplyr,"%>%")
 importFrom(dplyr,as_tibble)
 importFrom(dplyr,case_when)
 importFrom(dplyr,count)
@@ -186,14 +186,14 @@ importFrom(purrr,map)
 importFrom(purrr,map2)
 importFrom(purrr,map_chr)
 importFrom(purrr,map_int)
-importFrom(purrr,rep_along)
 importFrom(purrr,safely)
 importFrom(purrr,set_names)
 importFrom(readr,write_lines)
 importFrom(rlang,enquo)
 importFrom(rlang,is_symbolic)
 importFrom(rlang,parse_expr)
 importFrom(rlang,quo_is_symbolic)
+importFrom(rlang,rep_along)
 importFrom(rlang,sym)
 importFrom(scater,isOutlier)
 importFrom(scuttle,logNormCounts)

R/differential_expression.R

@@ -15,7 +15,7 @@
 #' @importFrom dplyr distinct
 #' @importFrom dplyr filter
 #' @importFrom dplyr pull
-#' @importFrom dplyr enframe
+#' @importFrom tibble enframe
 #' @importFrom purrr map
 #' @importFrom purrr map_int
 #' @importFrom stringr str_subset

R/functions.R

@@ -289,14 +289,15 @@ empty_droplet_threshold<- function(input_read_RNA_assay,
 #' @importFrom celldex BlueprintEncodeData
 #' @importFrom celldex MonacoImmuneData
 #' 
-#' # Seurat
 #' @importFrom Seurat CreateAssayObject
 #' @importFrom Seurat SCTransform
 #' @importFrom Seurat CreateSeuratObject
 #' @importFrom Seurat VariableFeatures
 #' @importFrom Seurat FindTransferAnchors
 #' @importFrom Seurat MapQuery
 #' @importFrom Seurat as.SingleCellExperiment
+#' @importFrom Seurat Assays
+#' @importFrom SeuratObject RenameAssays
 #' @import Seurat
 #' 
 #' @importFrom scuttle logNormCounts
@@ -315,8 +316,6 @@ empty_droplet_threshold<- function(input_read_RNA_assay,
 #' @importFrom stringr str_detect
 #' @importFrom tidyr nest
 #' @importFrom S4Vectors cbind
-#' @importFrom S4Vectors Assays
-#' @importFrom S4Vectors RenameAssays
 #' 
 #' @export
 annotation_label_transfer <- function(input_read_RNA_assay,
@@ -1072,9 +1071,12 @@ non_batch_variation_removal <- function(input_read_RNA_assay,
 #'
 #' @return Processed and filter_empty_droplets dataset.
 #'
-#' @importFrom dplyr left_join filter select
+#' @importFrom dplyr filter
+#' @importFrom dplyr select
+#' @importFrom dplyr left_join  
 #' @import SeuratObject
-#' @importFrom SummarizedExperiment left_join assay assay<-
+#' @importFrom SummarizedExperiment assay
+#' @importFrom SummarizedExperiment assay<-
 #' @import tidySingleCellExperiment 
 #' @import tidyseurat
 #' @importFrom magrittr not

R/modules_grammar_hpc.R

@@ -460,7 +460,6 @@ get_single_cell.HPCell = function(input_hpc, target_input = "data_object", targe
 #'
 #' @name test_differential_abundance-HPCell-method
 #' @rdname test_differential_abundance
-#' @inherit tidybulk::test_differential_abundance
 #'
 #' @importFrom tidybulk test_differential_abundance
 #' @exportMethod test_differential_abundance

R/tranform_assay.R

@@ -66,7 +66,6 @@ transform_assay.HPCell = function(
 #' @importFrom glue glue
 #' @importFrom digest digest
 #' @importFrom stats density
-#' @importFrom stats which.max
 #'
 #' @export
 transform_utility  = function(input_read_RNA_assay, transform_fx, external_path, container_type) {

R/utilities.R

@@ -808,7 +808,6 @@ is_strong_evidence = function(single_cell_data, cell_annotation_azimuth_l2, cell
 #'
 #' This function takes cell type annotations from multiple datasets (Azimuth, Monaco, Blueprint) and harmonizes them into a consensus annotation. The function utilizes predefined mappings between cell type labels in these datasets to generate standardized cell types across references.
 #'
-#' @importFrom dplyr %>%
 #' @importFrom dplyr mutate
 #' @importFrom dplyr case_when
 #' @importFrom dplyr left_join
@@ -825,12 +824,12 @@ is_strong_evidence = function(single_cell_data, cell_annotation_azimuth_l2, cell
 #'
 #' @examples
 #' # Example usage:
-#' tibble(
+#' tibble::tibble(
 #'   azimuth_predicted.celltype.l2 = c("CD8 TEM", "NK", "CD4 Naive"),
 #'   monaco_first.labels.fine = c("Effector memory CD8 T cells", "Natural killer cells", "Naive CD4 T cells"),
 #'   blueprint_first.labels.fine = c("CD8+ Tem", "NK cells", "Naive B-cells")
-#' ) %>%
-#'   mutate(consensus = reference_annotation_to_consensus(
+#' ) |>
+#'   dplyr::mutate(consensus = reference_annotation_to_consensus(
 #'     azimuth_predicted.celltype.l2, monaco_first.labels.fine, blueprint_first.labels.fine))
 #' 
 #' @note This function is designed to harmonize specific cell types, especially T cells, B cells, monocytic cells, and innate lymphoid cells (ILCs), across reference datasets.
@@ -2321,10 +2320,7 @@ add_tier_inputs <- function(command, arguments_to_tier, i) {
 #' @param chunk_size The size of each chunk. Defaults to 100.
 #' @return A tibble with the features and their corresponding chunk numbers.
 #' @importFrom dplyr tibble
-#' @importFrom purrr rep_along
-#' @importFrom purrr ceiling
-#' @importFrom purrr seq_len
-#' @importFrom purrr length
+#' @importFrom rlang rep_along
 #' @importFrom magrittr divide_by
 #' 
 #' 
@@ -2649,7 +2645,6 @@ check_for_name_value_conflicts <- function(...) {
 #' # $packages
 #' # [1] "tidySummarizedExperiment" "HPCell"
 #' 
-#' @importFrom stats substitute
 #' @noRd
 expand_tiered_arguments <- function(lst, tiers, argument_to_replace, tiered_args) {
   # Check if the argument to replace exists in the list
@@ -2767,7 +2762,6 @@ write_HDF5_array_safe = function(normalized_rna, name, directory){
 #' @import DelayedArray
 #' @importFrom DelayedArray blockApply
 #' @importFrom methods as
-#' @importFrom stats as.numeric
 #' @importFrom utils capture.output
 #'
 #' @examples

README.md

@@ -50,7 +50,7 @@ The key features of HPCell include:
 ## Installation
 
 ``` r
-remote::install_github("MangiolaLaboratory/HPCell")
+remotes::install_github("MangiolaLaboratory/HPCell")
 ```
 
 ## The input

README.rmd

@@ -35,7 +35,7 @@ The key features of HPCell include:
 
 ```{r, eval=FALSE}
 
-remote::install_github("MangiolaLaboratory/HPCell")
+remotes::install_github("MangiolaLaboratory/HPCell")
 
 ```