@@ -21,7 +21,7 @@ before_install:

   - Rscript -e 'install.packages("devtools")'

   - Rscript -e 'devtools::install_version("xgboost", version = "0.90.0.2", repos = "http://cran.us.r-project.org")'

   - pip install --upgrade pip

-  - pip install scipy scrublet scanpy scanorama scgen bbknn

+  - pip install scipy scrublet scanpy scanorama bbknn

 install:

 - R -e 'devtools::install_deps(dep = TRUE, upgrade="never")'

@@ -31,11 +31,9 @@ addons:

     packages:

       - libv8-dev

-r_build_args: "--no-build-vignettes"

-r_check_args: "--no-vignettes --no-build-vignettes --as-cran"

+r_check_args: "--as-cran"

 r_github_packages:

   - jimhester/lintr

-  - campbio/celda

 notifications:

   slack:

     secure: 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

@@ -1,6 +1,6 @@

 Package: singleCellTK

 Type: Package

-Title: Interactive Analysis of Single Cell RNA-Seq Data

+Title: Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

 Version: 1.7.6

 Author: David Jenkins

 Authors@R: c(person(given="David", family="Jenkins", email="dfj@bu.edu", role=c("aut","cre"),

@@ -20,12 +20,9 @@ Depends:

     SingleCellExperiment,

     DelayedArray,

     Biobase

-Description: Run common single cell analysis directly through your browser

-    including differential expression, downsampling analysis, and clustering.

+Description: Run common single cell analysis in the R console or directly through your browser. Includes many functions for import, quality control, normalization, batch correction, clustering, differential expression, and visualization..

 License: MIT + file LICENSE

 Encoding: UTF-8

-cache:

-  - packages: true

 biocViews: SingleCell, GeneExpression, DifferentialExpression, Alignment,

     Clustering, ImmunoOncology

 LazyData: TRUE

@@ -123,7 +120,6 @@ Remotes:

     rz2333/mnormt@1.5-6,

     joshua-d-campbell/liger,

     joshua-d-campbell/shiny-directory-input,

-    campbio/celda@RELEASE_3_11

 VignetteBuilder: knitr

 URL: https://compbiomed.github.io/sctk_docs/

 BugReports: https://github.com/compbiomed/singleCellTK/issues

@@ -89,9 +89,10 @@

 #' There are no known R solutions at present. Refer \url{https://github.com/rstudio/reticulate/issues/209}

 #' @return A \code{SingleCellExperiment} object.

 #' @examples

+#' \dontrun{

 #' sce <- importAnnData(sampleDirs = system.file("extdata/annData_pbmc_3k", package = "singleCellTK"),

 #'                      sampleNames = 'pbmc3k_20by20')

-

+#' }

 #' @export

 importAnnData <- function(sampleDirs = NULL,

                           sampleNames = NULL,

new file mode 100644

@@ -0,0 +1,84 @@

+

+#' Imports samples from different sources and compiles them into a list of SCE objects

+#' @param allImportEntries object containing the sources and parameters of all the samples being imported (from the UI)

+#' @return A list of \link[SingleCellExperiment]{SingleCellExperiment} object containing

+#' the droplet or cell data or both,depending on the dataType that users provided.

+#' @export

+importMultipleSources <- function(allImportEntries) {

+  sceObjs <- list()

+  for (entry in allImportEntries$samples) {

+    if (entry$type == "cellRanger2") {

+      if (is.null(entry$params$cellRangerDirs)) {

+        newSce <- importCellRangerV2Sample(

+          dataDir = entry$params$dataDir,

+          sampleName = entry$params$sampleName,

+        )

+      } else {

+        newSce <- importCellRangerV2(

+          cellRangerDirs = entry$params$cellRangerDirs,

+          sampleDirs = entry$params$sampleDirs,

+          sampleNames = entry$params$sampleNames,

+        )

+      }

+      

+    } else if (entry$type == "cellRanger3") {

+      if (is.null(entry$params$cellRangerDirs)) {

+        newSce <- importCellRangerV3Sample(

+          dataDir = entry$params$dataDir,

+          sampleName = entry$params$sampleName,

+        )

+      } else {

+        newSce <- importCellRangerV3(

+          cellRangerDirs = entry$params$cellRangerDirs,

+          sampleDirs = entry$params$sampleDirs,

+          sampleNames = entry$params$sampleNames,

+        )

+      }

+    } else if (entry$type == "starSolo") {

+      newSce <- importSTARsolo(

+        STARsoloDirs = entry$params$STARsoloDirs,

+        samples = entry$params$amples

+      )

+    } else if (entry$type == "busTools") {

+      newSce <- importBUStools(

+        BUStoolsDirs = entry$params$BUStoolsDirs,

+        samples = entry$params$samples,

+      )

+    } else if (entry$type == "seqc") {

+      newSce <- importSEQC(

+        seqcDirs = entry$params$seqcDirs,

+        samples = entry$params$samples,

+        prefix = entry$params$prefix,

+      )

+    } else if (entry$type == "optimus") {

+      newSce <- importOptimus(

+        OptimusDirs = entry$params$OptimusDirs,

+        samples = entry$params$samples

+      )

+    } else if (entry$type == "files") {

+      newSce <- importFromFiles(assayFile = entry$params$assayFile,

+                                annotFile = entry$params$annotFile,

+                                featureFile = entry$params$featureFile,

+                                assayName = entry$params$assayName)

+    } else if (entry$type == "example") {

+      newSce <- importExampleData(dataset = entry$params$dataset)

+    } else if (entry$type == "rds") {

+      importedrds <- readRDS(entry$params$rdsFile)

+      if (base::inherits(importedrds, "SummarizedExperiment")) {

+        newSce <- importedrds

+      } else if (base::inherits(importedrds, "Seurat")) {

+        newSce <- convertSeuratToSCE(importedrds)

+      } else {

+        stop("The '.rds' file should contain a 'SingleCellExperiment' or 'Seurat' object.")

+      }

+    }

+    sceObjs = c(sceObjs, list(newSce))

+  }

+  

+  return(combineSCE(sceList = sceObjs,

+                    by.r = NULL,

+                    by.c = Reduce(intersect, lapply(sceObjs, function(x) { colnames(colData(x))})),

+                    combined = T)

+  )

+}

+

@@ -393,87 +393,3 @@ qcInputProcess <- function(preproc,

     stop(paste0("'", preproc, "' not supported."))

 }

-

-#' Imports samples from different sources and compiles them into a list of SCE objects

-#' @param allImportEntries object containing the sources and parameters of all the samples being imported (from the UI)

-#' @return A list of \link[SingleCellExperiment]{SingleCellExperiment} object containing

-#' the droplet or cell data or both,depending on the dataType that users provided.

-#' @export

-importMultipleSources <- function(allImportEntries) {

-  sceObjs <- list()

-  for (entry in allImportEntries$samples) {

-    if (entry$type == "cellRanger2") {

-      if (is.null(entry$params$cellRangerDirs)) {

-        newSce <- importCellRangerV2Sample(

-          dataDir = entry$params$dataDir,

-          sampleName = entry$params$sampleName,

-        )

-      } else {

-        newSce <- importCellRangerV2(

-          cellRangerDirs = entry$params$cellRangerDirs,

-          sampleDirs = entry$params$sampleDirs,

-          sampleNames = entry$params$sampleNames,

-        )

-      }

-

-    } else if (entry$type == "cellRanger3") {

-      if (is.null(entry$params$cellRangerDirs)) {

-        newSce <- importCellRangerV3Sample(

-          dataDir = entry$params$dataDir,

-          sampleName = entry$params$sampleName,

-        )

-      } else {

-        newSce <- importCellRangerV3(

-          cellRangerDirs = entry$params$cellRangerDirs,

-          sampleDirs = entry$params$sampleDirs,

-          sampleNames = entry$params$sampleNames,

-        )

-      }

-    } else if (entry$type == "starSolo") {

-      newSce <- importSTARsolo(

-        STARsoloDirs = entry$params$STARsoloDirs,

-        samples = entry$params$amples

-      )

-    } else if (entry$type == "busTools") {

-      newSce <- importBUStools(

-        BUStoolsDirs = entry$params$BUStoolsDirs,

-        samples = entry$params$samples,

-      )

-    } else if (entry$type == "seqc") {

-      newSce <- importSEQC(

-        seqcDirs = entry$params$seqcDirs,

-        samples = entry$params$samples,

-        prefix = entry$params$prefix,

-      )

-    } else if (entry$type == "optimus") {

-      newSce <- importOptimus(

-        OptimusDirs = entry$params$OptimusDirs,

-        samples = entry$params$samples

-      )

-    } else if (entry$type == "files") {

-      newSce <- importFromFiles(assayFile = entry$params$assayFile,

-                                annotFile = entry$params$annotFile,

-                                featureFile = entry$params$featureFile,

-                                assayName = entry$params$assayName)

-    } else if (entry$type == "example") {

-      newSce <- withConsoleMsgRedirect(importExampleData(dataset = entry$params$dataset))

-    } else if (entry$type == "rds") {

-      importedrds <- readRDS(entry$params$rdsFile)

-      if (base::inherits(importedrds, "SummarizedExperiment")) {

-        newSce <- importedrds

-      } else if (base::inherits(importedrds, "Seurat")) {

-        newSce <- convertSeuratToSCE(importedrds)

-      } else {

-        shiny::showNotification("The '.rds' file should contain a 'SingleCellExperiment' or 'Seurat' object.", type = "error")

-      }

-    }

-    sceObjs = c(sceObjs, list(newSce))

-  }

-

-  return(combineSCE(sceList = sceObjs,

-                    by.r = NULL,

-                    by.c = Reduce(intersect, lapply(sceObjs, function(x) { colnames(colData(x))})),

-                    combined = T)

-         )

-}

-

@@ -13,8 +13,8 @@ exportSCE(

 )

 }

 \arguments{

-\item{inSCE}{A \link[SingleCellExperiment]{SingleCellExperiment} object 

-that contains the data. QC metrics are stored in colData of the 

+\item{inSCE}{A \link[SingleCellExperiment]{SingleCellExperiment} object

+that contains the data. QC metrics are stored in colData of the

 singleCellExperiment object.}

 \item{samplename}{Sample name. This will be used as name of subdirectories

@@ -22,7 +22,7 @@ and the prefix of flat file output. Default is 'sample'.}

 \item{directory}{Output directory. Default is './'.}

-\item{type}{Type of data. The type of data stored in SingleCellExperiment object. 

+\item{type}{Type of data. The type of data stored in SingleCellExperiment object.

 It can be 'Droplets'(raw droplets matrix) or 'Cells' (cells matrix).}

 \item{format}{The format of output. It currently supports flat files, rds files

@@ -29,7 +29,7 @@ cell count matrix data}

 \item{dataType}{Type of the input data. It can be one of "Droplet", "Cell" or "Both".}

 }

 \value{

-A \link[SingleCellExperiment]{SingleCellExperiment} object which combines all 

+A \link[SingleCellExperiment]{SingleCellExperiment} object which combines all

 objects in sceList. The colData is merged.

 }

 \description{

@@ -25,7 +25,7 @@ getSceParams(

 \item{samplename}{The sample name of the \link[SingleCellExperiment]{SingleCellExperiment} objects.}

-\item{writeYAML}{Whether output yaml file to store parameters. Default if TRUE. If FALSE, 

+\item{writeYAML}{Whether output yaml file to store parameters. Default if TRUE. If FALSE,

 return character object.}

 }

 \description{

@@ -55,6 +55,8 @@ Additionally there might be errors in converting some python objects in the unst

 There are no known R solutions at present. Refer \url{https://github.com/rstudio/reticulate/issues/209}

 }

 \examples{

+\dontrun{

 sce <- importAnnData(sampleDirs = system.file("extdata/annData_pbmc_3k", package = "singleCellTK"),

                      sampleNames = 'pbmc3k_20by20')

 }

+}

@@ -1,5 +1,5 @@

 % Generated by roxygen2: do not edit by hand

-% Please edit documentation in R/sctkQCUtils.R

+% Please edit documentation in R/importMultipleSources.R

 \name{importMultipleSources}

 \alias{importMultipleSources}

 \title{Imports samples from different sources and compiles them into a list of SCE objects}

@@ -59,6 +59,9 @@ test_that(desc = "Testing importOptimus", {

 }) 

 test_that(desc = "Testing importAnnData", {

+  if (!reticulate::py_module_available("anndata")){

+    skip("'anndata' not available. Skipping testing importAnnData")

+  }

   sce <- importAnnData(sampleDirs = system.file("extdata/annData_pbmc_3k", package = "singleCellTK"),

                        sampleNames = 'pbmc3k_20by20')

   expect_true(validObject(sce))