From 0b6aefcdd16042560eb6403ab9bf118f4c4021bf Mon Sep 17 00:00:00 2001 From: Kent Riemondy Date: Wed, 3 Apr 2024 09:28:57 -0600 Subject: [PATCH] bump version, redoc, and update news --- DESCRIPTION | 4 ++-- NEWS | 5 ++++- man/cbmc_m.Rd | 2 +- man/cbmc_ref.Rd | 2 +- man/downrefs.Rd | 2 +- man/human_genes_10x.Rd | 2 +- man/mouse_genes_10x.Rd | 2 +- man/pbmc_matrix_small.Rd | 2 +- man/pbmc_meta.Rd | 2 +- man/pbmc_vargenes.Rd | 2 +- tests/testthat/test_gsea.R | 1 + 11 files changed, 15 insertions(+), 11 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 8d3be11f..e3a1fb92 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: clustifyr Title: Classifier for Single-cell RNA-seq Using Cell Clusters -Version: 1.15.1 +Version: 1.15.2 Description: Package designed to aid in classifying cells from single-cell RNA sequencing data using external reference data (e.g., bulk RNA-seq, scRNA-seq, microarray, gene lists). A variety of correlation based methods and gene list enrichment methods are provided to assist cell @@ -87,7 +87,7 @@ VignetteBuilder: ByteCompile: true Encoding: UTF-8 Roxygen: list(markdown = TRUE) -RoxygenNote: 7.3.0 +RoxygenNote: 7.3.1 LazyData: true Config/Needs/website: pkgdown, diff --git a/NEWS b/NEWS index 27b0c73c..a0973919 100644 --- a/NEWS +++ b/NEWS @@ -52,4 +52,7 @@ Changes in version 1.7.3 (2022-03-09) + Maintainer change Changes in version 1.15.1 (2023-10-31) -+ Replace `Seurat` dependency with `SeuratObject` \ No newline at end of file ++ Replace `Seurat` dependency with `SeuratObject` + +Changes in version 1.15.2 (2024-04-03) ++ Add support for Seurat version 5 objects diff --git a/man/cbmc_m.Rd b/man/cbmc_m.Rd index 7c4cfba7..22d91557 100644 --- a/man/cbmc_m.Rd +++ b/man/cbmc_m.Rd @@ -22,8 +22,8 @@ Other data: \code{\link{downrefs}}, \code{\link{human_genes_10x}}, \code{\link{mouse_genes_10x}}, -\code{\link{pbmc_markers_M3Drop}}, \code{\link{pbmc_markers}}, +\code{\link{pbmc_markers_M3Drop}}, \code{\link{pbmc_matrix_small}}, \code{\link{pbmc_meta}}, \code{\link{pbmc_vargenes}} diff --git a/man/cbmc_ref.Rd b/man/cbmc_ref.Rd index b3a77784..fb52df60 100644 --- a/man/cbmc_ref.Rd +++ b/man/cbmc_ref.Rd @@ -22,8 +22,8 @@ Other data: \code{\link{downrefs}}, \code{\link{human_genes_10x}}, \code{\link{mouse_genes_10x}}, -\code{\link{pbmc_markers_M3Drop}}, \code{\link{pbmc_markers}}, +\code{\link{pbmc_markers_M3Drop}}, \code{\link{pbmc_matrix_small}}, \code{\link{pbmc_meta}}, \code{\link{pbmc_vargenes}} diff --git a/man/downrefs.Rd b/man/downrefs.Rd index f93cb9e3..3bf25a34 100644 --- a/man/downrefs.Rd +++ b/man/downrefs.Rd @@ -22,8 +22,8 @@ Other data: \code{\link{cbmc_ref}}, \code{\link{human_genes_10x}}, \code{\link{mouse_genes_10x}}, -\code{\link{pbmc_markers_M3Drop}}, \code{\link{pbmc_markers}}, +\code{\link{pbmc_markers_M3Drop}}, \code{\link{pbmc_matrix_small}}, \code{\link{pbmc_meta}}, \code{\link{pbmc_vargenes}} diff --git a/man/human_genes_10x.Rd b/man/human_genes_10x.Rd index 0b3e6cfb..074602ff 100644 --- a/man/human_genes_10x.Rd +++ b/man/human_genes_10x.Rd @@ -22,8 +22,8 @@ Other data: \code{\link{cbmc_ref}}, \code{\link{downrefs}}, \code{\link{mouse_genes_10x}}, -\code{\link{pbmc_markers_M3Drop}}, \code{\link{pbmc_markers}}, +\code{\link{pbmc_markers_M3Drop}}, \code{\link{pbmc_matrix_small}}, \code{\link{pbmc_meta}}, \code{\link{pbmc_vargenes}} diff --git a/man/mouse_genes_10x.Rd b/man/mouse_genes_10x.Rd index a685dcea..6f2e4d0f 100644 --- a/man/mouse_genes_10x.Rd +++ b/man/mouse_genes_10x.Rd @@ -22,8 +22,8 @@ Other data: \code{\link{cbmc_ref}}, \code{\link{downrefs}}, \code{\link{human_genes_10x}}, -\code{\link{pbmc_markers_M3Drop}}, \code{\link{pbmc_markers}}, +\code{\link{pbmc_markers_M3Drop}}, \code{\link{pbmc_matrix_small}}, \code{\link{pbmc_meta}}, \code{\link{pbmc_vargenes}} diff --git a/man/pbmc_matrix_small.Rd b/man/pbmc_matrix_small.Rd index faf20a1a..d2eed8e4 100644 --- a/man/pbmc_matrix_small.Rd +++ b/man/pbmc_matrix_small.Rd @@ -23,8 +23,8 @@ Other data: \code{\link{downrefs}}, \code{\link{human_genes_10x}}, \code{\link{mouse_genes_10x}}, -\code{\link{pbmc_markers_M3Drop}}, \code{\link{pbmc_markers}}, +\code{\link{pbmc_markers_M3Drop}}, \code{\link{pbmc_meta}}, \code{\link{pbmc_vargenes}} } diff --git a/man/pbmc_meta.Rd b/man/pbmc_meta.Rd index 87be2671..a08e6edf 100644 --- a/man/pbmc_meta.Rd +++ b/man/pbmc_meta.Rd @@ -23,8 +23,8 @@ Other data: \code{\link{downrefs}}, \code{\link{human_genes_10x}}, \code{\link{mouse_genes_10x}}, -\code{\link{pbmc_markers_M3Drop}}, \code{\link{pbmc_markers}}, +\code{\link{pbmc_markers_M3Drop}}, \code{\link{pbmc_matrix_small}}, \code{\link{pbmc_vargenes}} } diff --git a/man/pbmc_vargenes.Rd b/man/pbmc_vargenes.Rd index 75d6980c..4d79040c 100644 --- a/man/pbmc_vargenes.Rd +++ b/man/pbmc_vargenes.Rd @@ -23,8 +23,8 @@ Other data: \code{\link{downrefs}}, \code{\link{human_genes_10x}}, \code{\link{mouse_genes_10x}}, -\code{\link{pbmc_markers_M3Drop}}, \code{\link{pbmc_markers}}, +\code{\link{pbmc_markers_M3Drop}}, \code{\link{pbmc_matrix_small}}, \code{\link{pbmc_meta}} } diff --git a/tests/testthat/test_gsea.R b/tests/testthat/test_gsea.R index f20973df..5cfe9505 100644 --- a/tests/testthat/test_gsea.R +++ b/tests/testthat/test_gsea.R @@ -4,6 +4,7 @@ context("run_gsea") shush <- function(...) { capture.output(..., file = nullfile()) } + test_that("output is correctly formatted", { data("pbmc_vargenes")