fix README

stemangiola · Jul 31, 2023 · e092048 · e092048
1 parent b99992c
commit e092048
Show file tree

Hide file tree

Showing 8 changed files with 9 additions and 12 deletions.
diff --git a/README.Rmd b/README.Rmd
@@ -18,7 +18,7 @@ Website: [tidySingleCellExperiment](https://stemangiola.github.io/tidySingleCell
 
 Please also have a look at 
 
-- [tidySummarizedExperiment]((https://stemangiola.github.io/tidySummarizedExperiment/) for tidy manipulation of SummarizedExperiment objects)
+- [tidySummarizedExperiment](https://stemangiola.github.io/tidySummarizedExperiment/) for tidy manipulation of SummarizedExperiment objects)
 - [tidyseurat](https://stemangiola.github.io/tidyseurat/) for tidy manipulation of Seurat objects
 - [tidybulk](https://stemangiola.github.io/tidybulk/) for tidy bulk RNA-seq data analysis
 - [tidygate](https://github.com/stemangiola/tidygate) for adding custom gate information to your tibble 
@@ -27,7 +27,7 @@ Please also have a look at
 
 # Introduction
 
-tidySingleCellExperiment provides a bridge between Bioconductor single-cell packages [@amezquita2019orchestrating] and the tidyverse [@wickham2019welcome]. It creates an invisible layer that enables viewing the
+tidySingleCellExperiment provides a bridge between Bioconductor single-cell packages [@amezquita2019orchestrating] and the tidyverse [@wickham2019welcome]. It enables viewing the
 Bioconductor *SingleCellExperiment* object as a tidyverse tibble, and provides SingleCellExperiment-compatible *dplyr*, *tidyr*, *ggplot* and *plotly* functions. This allows users to get the best of both Bioconductor and tidyverse worlds.
 
 ## Functions/utilities available

diff --git a/README.md b/README.md
@@ -15,7 +15,8 @@ Website:
 
 Please also have a look at
 
-- [tidySummarizedExperiment]((https://stemangiola.github.io/tidySummarizedExperiment/)%20for%20tidy%20manipulation%20of%20SummarizedExperiment%20objects)
+- [tidySummarizedExperiment](https://stemangiola.github.io/tidySummarizedExperiment/)
+  for tidy manipulation of SummarizedExperiment objects)
 - [tidyseurat](https://stemangiola.github.io/tidyseurat/) for tidy
   manipulation of Seurat objects
 - [tidybulk](https://stemangiola.github.io/tidybulk/) for tidy bulk
@@ -29,11 +30,11 @@ Please also have a look at
 
 tidySingleCellExperiment provides a bridge between Bioconductor
 single-cell packages \[@amezquita2019orchestrating\] and the tidyverse
-\[@wickham2019welcome\]. It creates an invisible layer that enables
-viewing the Bioconductor *SingleCellExperiment* object as a tidyverse
-tibble, and provides SingleCellExperiment-compatible *dplyr*, *tidyr*,
-*ggplot* and *plotly* functions. This allows users to get the best of
-both Bioconductor and tidyverse worlds.
+\[@wickham2019welcome\]. It enables viewing the Bioconductor
+*SingleCellExperiment* object as a tidyverse tibble, and provides
+SingleCellExperiment-compatible *dplyr*, *tidyr*, *ggplot* and *plotly*
+functions. This allows users to get the best of both Bioconductor and
+tidyverse worlds.
 
 ## Functions/utilities available
 
@@ -288,10 +289,6 @@ pbmc_small_pca <-
     ## TRUE, : You're computing too large a percentage of total singular values, use a
     ## standard svd instead.
 
-    ## Warning in (function (A, nv = 5, nu = nv, maxit = 1000, work = nv + 7, reorth =
-    ## TRUE, : did not converge--results might be invalid!; try increasing work or
-    ## maxit
-
 ``` r
 pbmc_small_pca
 ```

diff --git a/man/figures/pc_plot-1.png b/man/figures/pc_plot-1.png
diff --git a/man/figures/plot2-1.png b/man/figures/plot2-1.png
diff --git a/man/figures/unnamed-chunk-10-1.png b/man/figures/unnamed-chunk-10-1.png
diff --git a/man/figures/unnamed-chunk-15-1.png b/man/figures/unnamed-chunk-15-1.png
diff --git a/man/figures/unnamed-chunk-16-1.png b/man/figures/unnamed-chunk-16-1.png
diff --git a/man/figures/unnamed-chunk-19-1.png b/man/figures/unnamed-chunk-19-1.png