update README, fix misspelling

bioinfocz · Sep 13, 2024 · 0d04599 · 0d04599
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diff --git a/README.Rmd b/README.Rmd
@@ -22,10 +22,10 @@ knitr::opts_chunk$set(
 [![Overview and outputs](https://img.shields.io/badge/Overview%20&%20outputs-vignette("pipeline_overview")-informational)](https://bioinfocz.github.io/scdrake/articles/pipeline_overview.html)
 [![Pipeline diagram](https://img.shields.io/badge/Pipeline%20diagram-Show-informational)](https://github.com/bioinfocz/scdrake/blob/main/diagrams/README.md)
 ![License](https://img.shields.io/github/license/bioinfocz/scdrake)
-[![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
+[![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-stable-green.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)
 [![Docker Image CI](https://github.com/bioinfocz/scdrake/actions/workflows/docker-ci.yml/badge.svg?branch=main)](https://github.com/bioinfocz/scdrake/actions/workflows/docker-ci.yml)
 
-`{scdrake}` is a scalable and reproducible pipeline for secondary analysis of droplet-based single-cell RNA-seq data.
+`{scdrake}` is a scalable and reproducible pipeline for secondary analysis of droplet-based single-cell RNA-seq data (scRNA-seq) and spot-based spatial transcriptomics data (SRT).
 `{scdrake}` is an R package built on top of the `{drake}` package, a [Make](https://www.gnu.org/software/make)-like pipeline
 toolkit for [R language](https://www.r-project.org).
 
@@ -34,9 +34,13 @@ The main features of the `{scdrake}` pipeline are:
 - Import of scRNA-seq data:
   [10x Genomics Cell Ranger](https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
   output, delimited table, or `SingleCellExperiment` object.
-- Quality control and filtering of cells and genes, removal of empty droplets.
+- Import of SRT data:
+  [10x Genomics Space Ranger](https://www.10xgenomics.com/support/software/space-ranger/latest/getting-started/what-is-space-ranger)
+  output, delimited table, or `SingleCellExperiment` object, and tissue positions file as in Space ranger.
+- Quality control and filtering of cells/spots and genes, removal of empty droplets.
 - Higly variable genes detection, cell cycle scoring, normalization, clustering, and dimensionality reduction.
-- Cell type annotation.
+- Spatially variable genes detection (for SRT data)
+- Cell type annotation using reference sets, cell type annotation using user-provided marker genes.
 - Integration of multiple datasets.
 - Computation of cluster markers and differentially expressed genes between clusters (denoted as "contrasts").
 - Rich graphical and HTML outputs based on customizable RMarkdown documents.
@@ -378,7 +382,7 @@ By contributing to this project, you agree to abide by its terms.
 ### Funding
 
 This work was supported by [ELIXIR CZ](https://www.elixir-czech.cz) research infrastructure project
-(MEYS Grant No: LM2018131) including access to computing and storage facilities.
+(MEYS Grant No: LM2018131 and LM2023055) including access to computing and storage facilities.
 
 ### Software and methods used by `{scdrake}`
 
@@ -402,4 +406,4 @@ Many things are used by `{scdrake}`, but these are really worth mentioning:
 - The code is styled automatically thanks to `{styler}`.
 - The documentation is formatted thanks to `{devtools}` and `{roxygen2}`.
 
-This package was developed using `{biocthis}`.
+This package was developed using `{biocthis}`.
diff --git a/README.md b/README.md
@@ -13,12 +13,13 @@ outputs](https://img.shields.io/badge/Overview%20&%20outputs-vignette(%22pipelin
 diagram](https://img.shields.io/badge/Pipeline%20diagram-Show-informational)](https://github.com/bioinfocz/scdrake/blob/main/diagrams/README.md)
 ![License](https://img.shields.io/github/license/bioinfocz/scdrake)
 [![Lifecycle:
-experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
+experimental](https://img.shields.io/badge/lifecycle-stable-green.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)
 [![Docker Image
 CI](https://github.com/bioinfocz/scdrake/actions/workflows/docker-ci.yml/badge.svg?branch=main)](https://github.com/bioinfocz/scdrake/actions/workflows/docker-ci.yml)
 
 `{scdrake}` is a scalable and reproducible pipeline for secondary
-analysis of droplet-based single-cell RNA-seq data. `{scdrake}` is an R
+analysis of droplet-based single-cell RNA-seq data (scRNA-seq) and
+spot-based spatial transcriptomics data (SRT). `{scdrake}` is an R
 package built on top of the `{drake}` package, a
 [Make](https://www.gnu.org/software/make)-like pipeline toolkit for [R
 language](https://www.r-project.org).
@@ -28,11 +29,17 @@ The main features of the `{scdrake}` pipeline are:
 -   Import of scRNA-seq data: [10x Genomics Cell
     Ranger](https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
     output, delimited table, or `SingleCellExperiment` object.
--   Quality control and filtering of cells and genes, removal of empty
-    droplets.
+-   Import of SRT data: [10x Genomics Space
+    Ranger](https://www.10xgenomics.com/support/software/space-ranger/latest/getting-started/what-is-space-ranger)
+    output, delimited table, or `SingleCellExperiment` object, and
+    tissue positions file as in Space ranger.
+-   Quality control and filtering of cells/spots and genes, removal of
+    empty droplets.
 -   Higly variable genes detection, cell cycle scoring, normalization,
     clustering, and dimensionality reduction.
--   Cell type annotation.
+-   Spatially variable genes detection (for SRT data)
+-   Cell type annotation using reference sets, cell type annotation
+    using user-provided marker genes.
 -   Integration of multiple datasets.
 -   Computation of cluster markers and differentially expressed genes
     between clusters (denoted as “contrasts”).
@@ -341,6 +348,7 @@ website of the current development version.
 -   General information:
     -   Pipeline overview: `vignette("pipeline_overview")`
     -   FAQ & Howtos: `vignette("scdrake_faq")`
+    -   Spatial extension: `vignette("scdrake_spatial")`
     -   Command line interface (CLI): `vignette("scdrake_cli")`
     -   Config files (internals): `vignette("scdrake_config")`
     -   Environment variables: `vignette("scdrake_envvars")`
@@ -352,8 +360,9 @@ website of the current development version.
         -   Stage `01_input_qc`: reading in data, filtering, quality
             control -\> `vignette("stage_input_qc")`
         -   Stage `02_norm_clustering`: normalization, HVG selection,
-            dimensionality reduction, clustering, cell type annotation
-            -\> `vignette("stage_norm_clustering")`
+            SVG selection, dimensionality reduction, clustering,
+            (manual) cell type annotation -\>
+            `vignette("stage_norm_clustering")`
     -   Integration pipeline:
         -   Stage `01_integration`: reading in data and integration -\>
             `vignette("stage_integration")`
@@ -436,8 +445,8 @@ contributing to this project, you agree to abide by its terms.
 ### Funding
 
 This work was supported by [ELIXIR CZ](https://www.elixir-czech.cz)
-research infrastructure project (MEYS Grant No: LM2018131) including
-access to computing and storage facilities.
+research infrastructure project (MEYS Grant No: LM2018131 and LM2023055)
+including access to computing and storage facilities.
 
 ### Software and methods used by `{scdrake}`
 

diff --git a/_pkgdown.yml b/_pkgdown.yml
@@ -29,7 +29,7 @@ navbar:
       text: Integration pipeline guide
       href: articles/scdrake_integration.html
     spatial:
-      text: Spatial extention
+      text: Spatial extension
       href: articles/scdrake_spatial.html
     faq:
       text: FAQ & Howtos

diff --git a/vignettes/_vignette_signpost.Rmd b/vignettes/_vignette_signpost.Rmd
@@ -10,6 +10,7 @@
 - General information:
   - Pipeline overview: `vignette("pipeline_overview")`
   - FAQ & Howtos: `vignette("scdrake_faq")`
+  - Spatial extension: `vignette("scdrake_spatial")`
   - Command line interface (CLI): `vignette("scdrake_cli")`
   - Config files (internals): `vignette("scdrake_config")`
   - Environment variables: `vignette("scdrake_envvars")`
@@ -19,7 +20,7 @@
 - Pipelines and stages:
   - Single-sample pipeline:
     - Stage `01_input_qc`: reading in data, filtering, quality control -> `vignette("stage_input_qc")`
-    - Stage `02_norm_clustering`: normalization, HVG selection, dimensionality reduction, clustering, cell type annotation
+    - Stage `02_norm_clustering`: normalization, HVG selection, SVG selection, dimensionality reduction, clustering, (manual) cell type annotation
       -> `vignette("stage_norm_clustering")`
   - Integration pipeline:
     - Stage `01_integration`: reading in data and integration -> `vignette("stage_integration")`

diff --git a/vignettes/scdrake_spatial.Rmd b/vignettes/scdrake_spatial.Rmd
@@ -1,13 +1,13 @@
 ---
-title: "Spatial extention"
+title: "Spatial extension"
 date: "`r glue::glue('<sup>Document generated: {format(Sys.time(), \"%Y-%m-%d %H:%M:%S %Z%z</sup>\")}')`"
 package: scdrake
 output:
   BiocStyle::html_document:
     toc: true
     toc_float: true
 vignette: >
-  %\VignetteIndexEntry{Spatial extention}
+  %\VignetteIndexEntry{Spatial extension}
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}  
 ---
@@ -21,13 +21,13 @@ This vignette should serve as a supplement to other vignettes, as `vignette("sta
 
 ***
 
-## Spatial extention functions
+## Spatial exsention functions
 
 ***
 
 ### Spatial visualization
 
-For (`01_input_qc`) and (`02_norm_clustering`) of the single-sample pipeline we now offer visualization of tissue, as pseudo tissue spot visualization. Spatial extention will add spot coordinates (array_col and array_row) from SpaceRanger tissue_possitions.csv file, and will filter away all spots, that are by SpaceRanger labeled as not in tissue. Visualization function are implemented from the [Giotto package](https://drieslab.github.io/Giotto_website/). Visualization is automatically used for quality control and dimension reduction results.    
+For (`01_input_qc`) and (`02_norm_clustering`) of the single-sample pipeline we now offer visualization of tissue, as pseudo tissue spot visualization. Spatial extension will add spot coordinates (array_col and array_row) from SpaceRanger tissue_possitions.csv file, and will filter away all spots, that are by SpaceRanger labeled as not in tissue. Visualization function are implemented from the [Giotto package](https://drieslab.github.io/Giotto_website/). Visualization is automatically used for quality control and dimension reduction results.
 
 ***
 

diff --git a/vignettes/stage_input_qc.Rmd b/vignettes/stage_input_qc.Rmd
@@ -120,7 +120,7 @@ INPUT_QC_REPORT_RMD_FILE: "Rmd/single_sample/01_input_qc.Rmd"
 
 **Type:** character scalar
 
-A path to RMarkdown file used for HTML report of this pipeline stage. For spatial extention, the default RMarkdown file is `01_input_qc_spatial.Rmd`
+A path to RMarkdown file used for HTML report of this pipeline stage. For spatial extension, the default RMarkdown file is `01_input_qc_spatial.Rmd`
 
 ***
 
@@ -143,7 +143,7 @@ You can also negate the selection by specifying `negate: true`.
 
 ***
 
-#### Spatial extention
+#### Spatial extension
 
 
 ```yaml

diff --git a/vignettes/stage_norm_clustering.Rmd b/vignettes/stage_norm_clustering.Rmd
@@ -117,7 +117,7 @@ several `{scdrake}` functions.
 
 ***
 
-#### Spatial extention
+#### Spatial extension
 
 
 ```yaml
-Original file line number
+Diff line change
@@ Expand Up / @@ -117,7 +117,7 @@ several `{scdrake}` functions. @@
     ***
-    #### Spatial extention
+    #### Spatial extension
     ```yaml
@@ Expand Down @@