-
Notifications
You must be signed in to change notification settings - Fork 24
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge pull request #157 from samuel-marsh/develop
Release v2.1.0
- Loading branch information
Showing
320 changed files
with
12,218 additions
and
2,445 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,3 +1,3 @@ | ||
| Version: 2.0.1 | ||
| Date: 2023-11-17 15:28:31 UTC | ||
| SHA: 2bf5f1166ee097878adef4e10d1a3923db44557b | ||
| Version: 2.1.0 | ||
| Date: 2024-02-23 19:16:02 UTC | ||
| SHA: 0d1bf8181d07c1754128b7edd9ae698c2d6cb22e |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -2,8 +2,8 @@ Package: scCustomize | |
| Type: Package | ||
| Title: Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing | ||
| Description: Collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using 'R'. 'scCustomize' aims to provide 1) Customized visualizations for aid in ease of use and to create more aesthetic and functional visuals. 2) Improve speed/reproducibility of common tasks/pieces of code in scRNA-seq analysis with a single or group of functions. For citation please use: Marsh SE (2021) "Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing" <doi:10.5281/zenodo.5706430> RRID:SCR_024675. | ||
| Version: 2.0.1 | ||
| Date: 2023-11-17 | ||
| Version: 2.1.0 | ||
| Date: 2024-02-21 | ||
| Authors@R: c( | ||
| person(given = "Samuel", family = "Marsh", email = "[email protected]", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-3012-6945")), | ||
| person(given = "Ming", family = "Tang", role = c("ctb"), email = "[email protected]"), | ||
|
|
@@ -38,7 +38,7 @@ Imports: | |
| patchwork, | ||
| pbapply, | ||
| purrr, | ||
| rlang (>= 1.0.1), | ||
| rlang (>= 1.1.3), | ||
| scales, | ||
| scattermore (>= 1.2), | ||
| SeuratObject (>= 5.0.0), | ||
|
|
@@ -48,6 +48,7 @@ Imports: | |
| tibble, | ||
| tidyr | ||
| Suggests: | ||
| BiocFileCache, | ||
| ComplexHeatmap, | ||
| dittoSeq, | ||
| DropletUtils, | ||
|
|
@@ -56,6 +57,7 @@ Suggests: | |
| knitr, | ||
| Nebulosa, | ||
| remotes, | ||
| reticulate, | ||
| rliger, | ||
| rmarkdown, | ||
| scuttle, | ||
|
|
@@ -66,4 +68,4 @@ License: GPL (>= 3) | |
| Encoding: UTF-8 | ||
| LazyData: true | ||
| Roxygen: list(markdown = TRUE) | ||
| RoxygenNote: 7.2.3 | ||
| RoxygenNote: 7.3.1 | ||
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,77 @@ | ||
| #%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% | ||
| #################### DEPRECATED FUNCTIONS #################### | ||
| #%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% | ||
|
|
||
| #' Deprecated functions `r lifecycle::badge("deprecated")` | ||
| #' | ||
| #' | ||
| #' @description | ||
| #' Use [FeatureScatter_scCustom()] instead of `Split_FeatureScatter()`. | ||
| #' | ||
| #' @export | ||
| #' @keywords internal | ||
| #' @rdname deprecated | ||
|
|
||
| Split_FeatureScatter <- function(...) { | ||
| lifecycle::deprecate_stop(when = "2.0.0", what = "Split_FeatureScatter()", with = "FeatureScatter_scCustom()") | ||
| } | ||
|
|
||
|
|
||
| #' @description | ||
| #' Use [Add_Mito_Ribo()] instead of `Add_Mito_Ribo_Seurat()`. | ||
| #' | ||
| #' @export | ||
| #' @keywords internal | ||
| #' @name deprecated | ||
|
|
||
| Add_Mito_Ribo_Seurat <- function(...) { | ||
| lifecycle::deprecate_stop(when = "2.1.0", what = "Add_Mito_Ribo_Seurat()", with = "Add_Mito_Ribo()") | ||
| } | ||
|
|
||
|
|
||
| #' @description | ||
| #' Use [Add_Mito_Ribo()] instead of `Add_Mito_Ribo_LIGER()`. | ||
| #' | ||
| #' @export | ||
| #' @keywords internal | ||
| #' @rdname deprecated | ||
|
|
||
| Add_Mito_Ribo_LIGER <- function(...) { | ||
| lifecycle::deprecate_stop(when = "2.1.0", what = "Add_Mito_Ribo_LIGER()", with = "Add_Mito_Ribo()") | ||
| } | ||
|
|
||
|
|
||
| #' @description | ||
| #' Use [Add_Cell_Complexity()] instead of `Add_Cell_Complexity_Seurat()`. | ||
| #' | ||
| #' @export | ||
| #' @keywords internal | ||
| #' @rdname deprecated | ||
|
|
||
| Add_Cell_Complexity_Seurat <- function(...) { | ||
| lifecycle::deprecate_stop(when = "2.1.0", what = "Add_Cell_Complexity_Seurat()", with = "Add_Cell_Complexity()") | ||
| } | ||
|
|
||
|
|
||
| #' @description | ||
| #' Use [Add_Cell_Complexity()] instead of `Add_Cell_Complexity_LIGER()`. | ||
| #' | ||
| #' @export | ||
| #' @keywords internal | ||
| #' @rdname deprecated | ||
|
|
||
| Add_Cell_Complexity_LIGER <- function(...) { | ||
| lifecycle::deprecate_stop(when = "2.1.0", what = "Add_Cell_Complexity_LIGER()", with = "Add_Cell_Complexity()") | ||
| } | ||
|
|
||
|
|
||
| #' @description | ||
| #' Use [Meta_Present()] instead of `Meta_Present_LIGER()`. | ||
| #' | ||
| #' @export | ||
| #' @keywords internal | ||
| #' @rdname deprecated | ||
|
|
||
| Meta_Present_LIGER <- function(...) { | ||
| lifecycle::deprecate_stop(when = "2.1.0", what = "Meta_Present_LIGER()", with = "Meta_Present()") | ||
| } |
Oops, something went wrong.