Merge pull request #205 from satijalab/develop

sctransform 0.4.2

Author: saketkc

.Rbuildignore

@@ -4,3 +4,4 @@
 ^supplement$
 ^scratch$
 ^revdep$
+.github

.github/workflows/rhub.yaml

@@ -0,0 +1,87 @@
+name: R-hub
+run-name: "${{ github.event.inputs.id }}: ${{ github.event.inputs.name || format('Manually run by {0}', github.triggering_actor) }}"
+
+on:
+  workflow_dispatch:
+    inputs:
+      config:
+        description: 'A comma separated list of R-hub platforms to use.'
+        type: string
+        default: 'linux,windows,macos'
+      name:
+        description: 'Run name. You can leave this empty now.'
+        type: string
+      id:
+        description: 'Unique ID. You can leave this empty now.'
+        type: string
+
+jobs:
+
+  setup:
+    runs-on: ubuntu-latest
+    outputs:
+      containers: ${{ steps.rhub-setup.outputs.containers }}
+      platforms: ${{ steps.rhub-setup.outputs.platforms }}
+
+    steps:
+    # NO NEED TO CHECKOUT HERE
+    - uses: r-hub/actions/setup@v1
+      with:
+        config: ${{ github.event.inputs.config }}
+      id: rhub-setup
+
+  linux-containers:
+    needs: setup
+    if: ${{ needs.setup.outputs.containers != '[]' }}
+    runs-on: ubuntu-latest
+    name: ${{ matrix.config.label }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config: ${{ fromJson(needs.setup.outputs.containers) }}
+    container:
+      image: ${{ matrix.config.container }}
+
+    steps:
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/platform-info@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/setup-deps@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/run-check@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+
+  other-platforms:
+    needs: setup
+    if: ${{ needs.setup.outputs.platforms != '[]' }}
+    runs-on: ${{ matrix.config.os }}
+    name: ${{ matrix.config.label }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config: ${{ fromJson(needs.setup.outputs.platforms) }}
+
+    steps:
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/setup-r@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}
+      - uses: r-hub/actions/platform-info@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/setup-deps@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}
+      - uses: r-hub/actions/run-check@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}

DESCRIPTION

@@ -1,11 +1,11 @@
 Package: sctransform
 Type: Package
 Title: Variance Stabilizing Transformations for Single Cell UMI Data
-Version: 0.4.1
-Date: 2023-10-18
+Version: 0.4.2
+Date: 2025-04-30
 Authors@R: c(
   person(given = "Christoph", family = "Hafemeister", email = "christoph.hafemeister@nyu.edu", role = "aut", comment = c(ORCID = "0000-0001-6365-8254")),
-  person(given = "Saket", family = "Choudhary", email = "schoudhary@nygenome.org", role = c("aut", "cre"), comment = c(ORCID = "0000-0001-5202-7633")),
+  person(given = "Saket", family = "Choudhary", email = "saketc@iitb.ac.in", role = c("aut", "cre"), comment = c(ORCID = "0000-0001-5202-7633")),
   person(given = "Rahul", family = "Satija", email = "rsatija@nygenome.org", role = "ctb", comment = c(ORCID = "0000-0001-9448-8833"))
   )
 Description: A normalization method for single-cell UMI count data using a 
@@ -42,4 +42,4 @@ Suggests:
   knitr
 Enhances:
   glmGamPoi
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.2

NAMESPACE

@@ -27,6 +27,7 @@ importFrom(dplyr,mutate)
 importFrom(dplyr,n)
 importFrom(dplyr,pull)
 importFrom(dplyr,summarise)
+importFrom(future,nbrOfWorkers)
 importFrom(future.apply,future_lapply)
 importFrom(graphics,abline)
 importFrom(graphics,par)

NEWS.md

@@ -1,6 +1,13 @@
 # News
 All notable changes will be documented in this file.
 
+## [0.4.2] - 2025-04-30
+
+### Fixed
+
+- Fixed citation orcid
+- Fix for future_lapply when using a single core [#201](https://github.com/satijalab/sctransform/issues/201)
+
 ## [0.4.1] - 2023-10-18
 
 ### Fixed 

R/differential_expression.R

@@ -20,12 +20,18 @@
 #'
 #' @import Matrix
 #' @importFrom future.apply future_lapply
+#' @importFrom future nbrOfWorkers
 #' @importFrom stats model.matrix p.adjust pchisq
 #'
 compare_expression <- function(x, umi, group, val1, val2, method = 'LRT', bin_size = 256,
                                cell_attr = x$cell_attr, y = x$y, min_cells = 5,
                                weighted = TRUE, randomize = FALSE, verbosity = 2,
                                verbose = NULL, show_progress = NULL) {
+  if (nbrOfWorkers() == 1){
+    my.lapply <- function(X, FUN, future.seed = TRUE) lapply(X, FUN)
+  } else {
+    my.lapply <- future_lapply
+  }
   # Take care of deprecated arguments
   if (!is.null(verbose)) {
     warning("The 'verbose' argument is deprecated as of v0.3. Use 'verbosity' instead. (in sctransform::vst)", immediate. = TRUE, call. = FALSE)
@@ -93,15 +99,15 @@ compare_expression <- function(x, umi, group, val1, val2, method = 'LRT', bin_si
   for (i in 1:max_bin) {
     genes_bin <- genes[bin_ind == i]
     if (method == 't_test') {
-      bin_res <- future_lapply(
+      bin_res <- my.lapply(
         X = genes_bin, 
         FUN = function(gene) {model_comparison_ttest(y[gene, use_cells], group)},
         future.seed = TRUE)
     }
     if (method == 'LRT') {
       mu <- x$model_pars_fit[genes_bin, -1, drop=FALSE] %*% t(regressor_data)  # in log space
       y <- as.matrix(umi[genes_bin, use_cells])
-      bin_res <- future_lapply(
+      bin_res <- my.lapply(
         X = genes_bin, 
         FUN = function(gene) {
           model_comparison_lrt(y[gene, ], mu[gene, ], x$model_pars_fit[gene, 'theta'], group, weights)},
@@ -175,7 +181,7 @@ compare_expression <- function(x, umi, group, val1, val2, method = 'LRT', bin_si
       y_theta[o] <- 10 ^ ksmooth(x = x$genes_log_mean_step1, y = log10(x$model_pars[, 'theta']),
                                  x.points = y_log_mean, bandwidth = bw, kernel='normal')$y
       names(y_theta) <- genes_bin
-      bin_res <- future_lapply(
+      bin_res <- my.lapply(
         X = genes_bin, 
         FUN = function(gene) {
           return(model_comparison_lrt_free3(gene, y[gene, ], y_theta[gene], x$model_str, cell_attr, group, weights, randomize))

R/vst.R

@@ -94,6 +94,7 @@ NULL
 #'
 #' @import Matrix
 #' @importFrom future.apply future_lapply
+#' @importFrom future nbrOfWorkers
 #' @importFrom MASS theta.ml theta.mm glm.nb negative.binomial
 #' @importFrom stats glm glm.fit df.residual ksmooth model.matrix as.formula approx density poisson var bw.SJ
 #' @importFrom utils txtProgressBar setTxtProgressBar capture.output
@@ -602,7 +603,12 @@ get_model_pars <- function(genes_step1, bin_size, umi, model_str, cells_step1,
     index_lst <- split(index_vec, ceiling(index_vec/genes_per_worker))
 
     # the index list will have at most n_workers entries, each one defining which genes to work on
-    par_lst <- future_lapply(
+    if (nbrOfWorkers() == 1){
+      my.lapply <- function(X, FUN, future.seed = TRUE) lapply(X, FUN)
+    } else {
+      my.lapply <- future_lapply
+    }
+    par_lst <- my.lapply(
       X = index_lst,
       FUN = function(indices) {
         umi_bin_worker <- umi_bin[indices, , drop = FALSE]
@@ -692,6 +698,7 @@ get_model_pars <- function(genes_step1, bin_size, umi, model_str, cells_step1,
 }
 
 get_model_pars_nonreg <- function(genes, bin_size, model_pars_fit, regressor_data, umi, model_str_nonreg, cell_attr, verbosity) {
+  
   bin_ind <- ceiling(x = 1:length(x = genes) / bin_size)
   max_bin <- max(bin_ind)
   if (verbosity > 1) {
@@ -702,9 +709,14 @@ get_model_pars_nonreg <- function(genes, bin_size, model_pars_fit, regressor_dat
     genes_bin <- genes[bin_ind == i]
     mu <- tcrossprod(model_pars_fit[genes_bin, -1, drop=FALSE], regressor_data)
     umi_bin <- as.matrix(umi[genes_bin, ])
+    if (nbrOfWorkers() == 1){
+      my.lapply <- function(X, FUN, future.seed = TRUE) lapply(X, FUN)
+    } else {
+      my.lapply <- future_lapply
+    }
     model_pars_nonreg[[i]] <- do.call(
       rbind,
-      future_lapply(X = genes_bin,
+      my.lapply(X = genes_bin,
                     FUN = function(gene) {
                       fam <- negative.binomial(theta = model_pars_fit[gene, 'theta'], link = 'log')
                       y <- umi_bin[gene, ]

README.md

@@ -21,13 +21,13 @@ Running sctransform:
 ```r
 # Runnning sctransform on a UMI matrix
 normalized_data <- sctransform::vst(umi_count_matrix)$y
-# v2 regularization
-normalized_data <- sctransform::vst(umi_count_matrix, vst.flavor="v2")$y
+# v1 regularization
+normalized_data <- sctransform::vst(umi_count_matrix, vst.flavor="v1")$y
 
 # Runnning sctransform on a Seurat object
 seurat_object <- Seurat::SCTransform(seurat_object)
-#v2 regularization
-seurat_object <- Seurat::SCTransform(seurat_object, vst.flavor="v2")
+# v1 regularization
+seurat_object <- Seurat::SCTransform(seurat_object, vst.flavor="v1")
 ```
 
 ## Help
@@ -39,7 +39,7 @@ Available vignettes:
 
 - [Variance stabilizing transformation](https://htmlpreview.github.io/?https://github.com/satijalab/sctransform/blob/supp_html/supplement/variance_stabilizing_transformation.html)  
 - [Using sctransform in Seurat](https://htmlpreview.github.io/?https://github.com/satijalab/sctransform/blob/supp_html/supplement/seurat.html)
-- [Examples of how to perform normalization, feature selection, integration, and differential expression with sctransform v2 regularization](https://satijalab.org/seurat/articles/sctransform_v2_vignette.html)
+- [Examples of how to perform normalization, feature selection, integration, and differential expression with sctransform v2 regularization](https://satijalab.org/seurat/articles/sctransform_vignette)
 
 
 Please use [the issue tracker](https://github.com/satijalab/sctransform/issues) if you encounter a problem

inst/CITATION

@@ -3,8 +3,8 @@ citHeader("To cite sctransform in publications, please use:")
 bibentry(bibtype = "article",
   author = c(person(given = "Christoph", family = "Hafemeister", email = "christoph.hafemeister@nyu.edu", role = "aut",
   comment = c(ORCID = "0000-0001-6365-8254")),
-  person(given = "Rahul", family = "Satija", email = "rsatija@nygenome.org", role = c("aut", "ctb"), comment = c(ORCID = "000
-  -0001-9448-8833"))),
+  person(given = "Rahul", family = "Satija", email = "rsatija@nygenome.org", role = c("aut", "ctb"),
+  comment = c(ORCID = "0000-0001-9448-8833"))),
   title = "Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression",
   journal = "Genome Biology",
   year = "2019",
@@ -16,7 +16,7 @@ bibentry(bibtype = "article",
 )
 
 bibentry(bibtype = "article",
-  author = c(person(given = "Saket", family = "Choudhary", email = "schoudhary@nygenome.org", role = c("aut", "cre"), comment = c(ORCID = "0000-0001-5202-7633")),
+  author = c(person(given = "Saket", family = "Choudhary", email = "saketc@iitb.ac.in", role = c("aut", "cre"), comment = c(ORCID = "0000-0001-5202-7633")),
   person(given = "Rahul", family = "Satija", email = "rsatija@nygenome.org", role = c("aut", "ctb"), comment = c(ORCID = "0000-0001-9448-8833"))),
   title = "Comparison and evaluation of statistical error models for scRNA-seq",
   journal = "Genome Biology",

revdep/README.md

@@ -1,49 +1,37 @@
 # Platform
 
-|field    |value                                          |
-|:--------|:----------------------------------------------|
-|version  |R version 4.3.1 (2023-06-16)                   |
-|os       |Ubuntu 20.04.6 LTS                             |
-|system   |x86_64, linux-gnu                              |
-|ui       |RStudio                                        |
-|language |(EN)                                           |
-|collate  |en_US.UTF-8                                    |
-|ctype    |en_US.UTF-8                                    |
-|tz       |America/New_York                               |
-|date     |2023-09-18                                     |
-|rstudio  |2023.03.1+446 Cherry Blossom (server)          |
-|pandoc   |3.1.3 @ /home/choudharys/miniconda3/bin/pandoc |
+|field    |value                                                         |
+|:--------|:-------------------------------------------------------------|
+|version  |R version 4.5.0 (2025-04-11)                                  |
+|os       |Ubuntu 24.04.2 LTS                                            |
+|system   |x86_64, linux-gnu                                             |
+|ui       |RStudio                                                       |
+|language |en_GB:en                                                      |
+|collate  |en_GB.UTF-8                                                   |
+|ctype    |en_GB.UTF-8                                                   |
+|tz       |Asia/Kolkata                                                  |
+|date     |2025-04-30                                                    |
+|rstudio  |2024.12.1+563 Kousa Dogwood (desktop)                         |
+|pandoc   |3.6.4 @ /data/miniconda3/bin/pandoc                           |
+|quarto   |1.5.57 @ /usr/lib/rstudio/resources/app/bin/quarto/bin/quarto |
 
 # Dependencies
 
-|package       |old   |new        |Δ  |
-|:-------------|:-----|:----------|:--|
-|sctransform   |0.3.5 |0.4.0      |*  |
-|digest        |NA    |0.6.33     |*  |
-|dplyr         |NA    |1.1.3      |*  |
-|future        |NA    |1.33.0     |*  |
-|future.apply  |NA    |1.11.0     |*  |
-|ggplot2       |NA    |3.4.3      |*  |
-|gtable        |NA    |0.3.4      |*  |
-|labeling      |NA    |0.4.3      |*  |
-|matrixStats   |NA    |1.0.0      |*  |
-|parallelly    |NA    |1.36.0     |*  |
-|Rcpp          |NA    |1.0.11     |*  |
-|RcppArmadillo |NA    |0.12.6.4.0 |*  |
-|rlang         |NA    |1.1.1      |*  |
-|vctrs         |NA    |0.6.3      |*  |
-|viridisLite   |NA    |0.4.2      |*  |
+|package     |old |new        |Δ  |
+|:-----------|:---|:----------|:--|
+|sctransform |NA  |0.4.1.9003 |*  |
 
 # Revdeps
 
-## Failed to check (6)
+## Failed to check (7)
 
-|package |version |error |warning |note |
-|:-------|:-------|:-----|:-------|:----|
-|CAMML   |?       |      |        |     |
-|EWCE    |?       |      |        |     |
-|muscat  |?       |      |        |     |
-|RESET   |?       |      |        |     |
-|Seurat  |?       |      |        |     |
-|VAM     |?       |      |        |     |
+|package  |version |error |warning |note |
+|:--------|:-------|:-----|:-------|:----|
+|CAMML    |?       |      |        |     |
+|EWCE     |?       |      |        |     |
+|muscat   |?       |      |        |     |
+|RESET    |?       |      |        |     |
+|SCdeconR |?       |      |        |     |
+|Seurat   |?       |      |        |     |
+|VAM      |?       |      |        |     |