1. scone
  2. README.md
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Update README

Davide Risso authored on 06/05/2021 10:43:14
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README.md
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1 1 
 ## SCONE ##
2 2
3 
-[![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active)
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-[![Build Status](https://travis-ci.org/YosefLab/scone.svg?branch=master)](https://travis-ci.org/YosefLab/scone)
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-[![Coverage](https://codecov.io/gh/YosefLab/scone/branch/master/graph/badge.svg)](https://codecov.io/gh/YosefLab/scone)
3 
+<!-- badges: start -->
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+[![Lifecycle: stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)
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+[![BioC status](http://www.bioconductor.org/shields/build/release/bioc/scone.svg)](https://bioconductor.org/checkResults/release/bioc-LATEST/scone)
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+[![R-CMD-check](https://github.com/YosefLab/scone/workflows/R-CMD-check-bioc/badge.svg)](https://github.com/YosefLab/scone/actions)
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+<!-- badges: end -->
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+
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 ### Single-Cell Overview of Normalized Expression data ###
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8 11 
 SCONE (Single-Cell Overview of Normalized Expression), a package for single-cell RNA-seq data quality control (QC) and normalization. This data-driven framework uses summaries of expression data to assess the efficacy of normalization workflows.
... ... 
@@ -17,17 +20,15 @@ if (!requireNamespace("BiocManager", quietly=TRUE))
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 BiocManager::install("scone")
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 ```
19 22
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-Note that SCONE is currently in Bioconductor devel and hence requires R-devel (>= 3.4).
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-
22 23 
 ### Install from Github ###
23 24
24 
-Usually not recommended. SCONE is under active development. To download the development version of the package, use the `devtools` package.
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+Usually not recommended. To download the development version of the package, use
25 26
26 27 
 ```{r}
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-library(devtools)
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-install_github("YosefLab/scone")
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+BiocManager::install("YosefLab/scone")
29 29 
 ```
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 ### Install for R 3.3 ###
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33 33 
 You can download the latest release of SCONE for R 3.3 [here](https://github.com/YosefLab/scone/releases/tag/v0.99.0).
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+This is useful only for reproducing old results.
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replace BiocInstaller biocLite mentions with BiocManager

LiNk-NY authored on 30/08/2018 17:55:57
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@@ -12,8 +12,9 @@ SCONE (Single-Cell Overview of Normalized Expression), a package for single-cell
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 We recommend installation of the package via bioconductor.
13 13
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 ```{r}
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-source("https://bioconductor.org/biocLite.R")
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-biocLite("scone")
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+if (!requireNamespace("BiocManager", quietly=TRUE))
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+    install.packages("BiocManager")
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+BiocManager::install("scone")
17 18 
 ```
18 19
19 20 
 Note that SCONE is currently in Bioconductor devel and hence requires R-devel (>= 3.4).
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Update README.md

Davide Risso authored on 29/03/2017 18:43:22 • GitHub committed on 29/03/2017 18:43:22
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@@ -7,16 +7,26 @@
7 7
8 8 
 SCONE (Single-Cell Overview of Normalized Expression), a package for single-cell RNA-seq data quality control (QC) and normalization. This data-driven framework uses summaries of expression data to assess the efficacy of normalization workflows.
9 9
10 
-### To Install ###
10 
+### Install from Bioconductor ###
11 11
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-The easiest way to install the package is to type in R
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+We recommend installation of the package via bioconductor.
13 13
14 14 
 ```{r}
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 source("https://bioconductor.org/biocLite.R")
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-biocLite("devtools")
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-biocLite("YosefLab/scone", dependencies=TRUE)
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+biocLite("scone")
18 17 
 ```
19 18
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-Note that SCONE is currently under consideration in Bioconductor and hence requires R-devel (>= 3.4) and Bioconductor devel.
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+Note that SCONE is currently in Bioconductor devel and hence requires R-devel (>= 3.4).
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+
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+### Install from Github ###
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+
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+Usually not recommended. SCONE is under active development. To download the development version of the package, use the `devtools` package.
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+
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+```{r}
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+library(devtools)
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+install_github("YosefLab/scone")
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+```
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+
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+### Install for R 3.3 ###
21 31
22 32 
 You can download the latest release of SCONE for R 3.3 [here](https://github.com/YosefLab/scone/releases/tag/v0.99.0).
Browse code

Update README.md

Davide Risso authored on 29/03/2017 18:36:51 • GitHub committed on 29/03/2017 18:36:51
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README.md
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1 1 
 ## SCONE ##
2 2
3 
-[![Project Status: WIP - Initial development is in progress, but there has not yet been a stable, usable release suitable for the public.](http://www.repostatus.org/badges/latest/wip.svg)](http://www.repostatus.org/#wip)
3 
+[![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active)
4 4 
 [![Build Status](https://travis-ci.org/YosefLab/scone.svg?branch=master)](https://travis-ci.org/YosefLab/scone)
5 5 
 [![Coverage](https://codecov.io/gh/YosefLab/scone/branch/master/graph/badge.svg)](https://codecov.io/gh/YosefLab/scone)
6 6 
 ### Single-Cell Overview of Normalized Expression data ###
Browse code

Update README.md

Davide Risso authored on 28/11/2016 18:46:08 • GitHub committed on 28/11/2016 18:46:08
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README.md
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@@ -17,4 +17,6 @@ biocLite("devtools")
17 17 
 biocLite("YosefLab/scone", dependencies=TRUE)
18 18 
 ```
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-Note that SCONE requires R (>= 3.3) and Bioconductor (>= 3.3). You can download the latest version of R from [CRAN](https://cran.r-project.org). To update Bioconductor to its latest release, follow the instructions [here](https://www.bioconductor.org/install/#update-bioconductor-packages).
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+Note that SCONE is currently under consideration in Bioconductor and hence requires R-devel (>= 3.4) and Bioconductor devel.
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+
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+You can download the latest release of SCONE for R 3.3 [here](https://github.com/YosefLab/scone/releases/tag/v0.99.0).
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Update README.md

Davide Risso authored on 15/07/2016 19:06:17 • GitHub committed on 15/07/2016 19:06:17
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2 2
3 3 
 [![Project Status: WIP - Initial development is in progress, but there has not yet been a stable, usable release suitable for the public.](http://www.repostatus.org/badges/latest/wip.svg)](http://www.repostatus.org/#wip)
4 4 
 [![Build Status](https://travis-ci.org/YosefLab/scone.svg?branch=master)](https://travis-ci.org/YosefLab/scone)
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-
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+[![Coverage](https://codecov.io/gh/YosefLab/scone/branch/master/graph/badge.svg)](https://codecov.io/gh/YosefLab/scone)
6 6 
 ### Single-Cell Overview of Normalized Expression data ###
7 7
8 8 
 SCONE (Single-Cell Overview of Normalized Expression), a package for single-cell RNA-seq data quality control (QC) and normalization. This data-driven framework uses summaries of expression data to assess the efficacy of normalization workflows.
Browse code

Update README.md

Davide Risso authored on 15/07/2016 17:25:17 • GitHub committed on 15/07/2016 17:25:17
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README.md
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1 1 
 ## SCONE ##
2 2
3 3 
 [![Project Status: WIP - Initial development is in progress, but there has not yet been a stable, usable release suitable for the public.](http://www.repostatus.org/badges/latest/wip.svg)](http://www.repostatus.org/#wip)
4 
+[![Build Status](https://travis-ci.org/YosefLab/scone.svg?branch=master)](https://travis-ci.org/YosefLab/scone)
4 5
5 6 
 ### Single-Cell Overview of Normalized Expression data ###
6 7
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Update README.md

Davide Risso authored on 08/07/2016 16:53:17 • GitHub committed on 08/07/2016 16:53:17
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README.md
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@@ -16,3 +16,4 @@ biocLite("devtools")
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 biocLite("YosefLab/scone", dependencies=TRUE)
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 ```
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+Note that SCONE requires R (>= 3.3) and Bioconductor (>= 3.3). You can download the latest version of R from [CRAN](https://cran.r-project.org). To update Bioconductor to its latest release, follow the instructions [here](https://www.bioconductor.org/install/#update-bioconductor-packages).
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Update README.md

Michael authored on 15/06/2016 03:09:54 • GitHub committed on 15/06/2016 03:09:54
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4 4
5 5 
 ### Single-Cell Overview of Normalized Expression data ###
6 6
7 
-scone is a package to compare and rank the performance of different normalization schemes in real single-cell RNA-seq datasets.
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+SCONE (Single-Cell Overview of Normalized Expression), a package for single-cell RNA-seq data quality control (QC) and normalization. This data-driven framework uses summaries of expression data to assess the efficacy of normalization workflows.
8 8
9 9 
 ### To Install ###
10 10
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Update README.md

Davide Risso authored on 09/06/2016 16:36:26
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1 1 
 ## SCONE ##
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+
3 
+[![Project Status: WIP - Initial development is in progress, but there has not yet been a stable, usable release suitable for the public.](http://www.repostatus.org/badges/latest/wip.svg)](http://www.repostatus.org/#wip)
4 
+
2 5 
 ### Single-Cell Overview of Normalized Expression data ###
3 6
4 7 
 scone is a package to compare and rank the performance of different normalization schemes in real single-cell RNA-seq datasets.
5 8
6 
-[![Project Status: WIP - Initial development is in progress, but there has not yet been a stable, usable release suitable for the public.](http://www.repostatus.org/badges/latest/wip.svg)](http://www.repostatus.org/#wip)
7 
-
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 ### To Install ###
9 10
10 11 
 The easiest way to install the package is to type in R
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Update README.md

Davide Risso authored on 09/06/2016 16:35:42
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README.md
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1 1 
 ## SCONE ##
2 2 
 ### Single-Cell Overview of Normalized Expression data ###
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-============
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-Private Repo containing SCONE R Package
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-
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+scone is a package to compare and rank the performance of different normalization schemes in real single-cell RNA-seq datasets.
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8 6 
 [![Project Status: WIP - Initial development is in progress, but there has not yet been a stable, usable release suitable for the public.](http://www.repostatus.org/badges/latest/wip.svg)](http://www.repostatus.org/#wip)
9 7
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-
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 ### To Install ###
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-	# Clone the GitHub repo:
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-	git clone https://github.com/YosefLab/scone.git
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-
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-	# Install via command line:
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-	R CMD INSTALL scone
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-
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-	# You may get errors if dependencies are not installed prior to scone installation.
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-	# Install SCDE dependency at http://hms-dbmi.github.io/scde/package.html
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-	# Install RUVSeq dependency using
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-	source("https://bioconductor.org/biocLite.R")
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-	biocLite("RUVSeq")
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+The easiest way to install the package is to type in R
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+
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+```{r}
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+source("https://bioconductor.org/biocLite.R")
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+biocLite("devtools")
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+biocLite("YosefLab/scone", dependencies=TRUE)
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+```
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+
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Merge branch 'master' of https://github.com/YosefLab/scone

Davide Risso authored on 03/05/2016 01:05:38
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Mention callr.org/install

Henrik Bengtsson authored on 27/04/2016 19:18:31
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@@ -15,7 +15,9 @@ Private Repo containing SCONE R Package
15 15 
 	git clone https://github.com/YosefLab/scone.git
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 	# Install via command line:
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-	R CMD INSTALL scone
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+	R CMD INSTALL scone
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+
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 	# You may get errors if dependencies are not installed prior to scone installation.
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 	# Install SCDE dependency at http://hms-dbmi.github.io/scde/package.html
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 	# Install clusterCells dependency using devtools::install_github('epurdom/clusterCells')
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+	# Alternative: source("http://callr.org/install#hms-dbmi/scde,epurdom/clusterCells")
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Update README.md

Davide Risso authored on 05/04/2016 01:03:22
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@@ -6,6 +6,9 @@ Private Repo containing SCONE R Package
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7 7 
 ---------------------------------------
8 8
9 
+[![Project Status: WIP - Initial development is in progress, but there has not yet been a stable, usable release suitable for the public.](http://www.repostatus.org/badges/latest/wip.svg)](http://www.repostatus.org/#wip)
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+
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+
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 ### To Install ###
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 	# Clone the GitHub repo:
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Added compactness measure for stability evaluation.

mbcole authored on 18/02/2016 21:46:48
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 	R CMD INSTALL scone
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 	# You may get errors if dependencies are not installed prior to scone installation.
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 	# Install SCDE dependency at http://hms-dbmi.github.io/scde/package.html
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-	# Install RUVSeq dependency using devtools::install_github('drisso/RUVSeq')
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+	# Install clusterCells dependency using devtools::install_github('epurdom/clusterCells')
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Update README.md

Bioconductor version of RUVSeq is good

Michael authored on 16/02/2016 23:29:12
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@@ -15,4 +15,6 @@ Private Repo containing SCONE R Package
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 	R CMD INSTALL scone
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 	# You may get errors if dependencies are not installed prior to scone installation.
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 	# Install SCDE dependency at http://hms-dbmi.github.io/scde/package.html
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-	# Install RUVSeq dependency using devtools::install_github('drisso/RUVSeq')
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+	# Install RUVSeq dependency using
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+	source("https://bioconductor.org/biocLite.R")
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+	biocLite("RUVSeq")
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Updated README in dev

mbcole authored on 14/02/2016 02:04:35
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@@ -11,4 +11,8 @@ Private Repo containing SCONE R Package
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 	# Clone the GitHub repo:
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 	git clone https://github.com/YosefLab/scone.git
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-	...
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+	# Install via command line:
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+	R CMD INSTALL scone
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+	# You may get errors if dependencies are not installed prior to scone installation.
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+	# Install SCDE dependency at http://hms-dbmi.github.io/scde/package.html
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+	# Install RUVSeq dependency using devtools::install_github('drisso/RUVSeq')
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Update README.md

Michael authored on 11/02/2016 01:32:34
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README.md
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@@ -15,3 +15,4 @@ Private Repo containing SCONE R Package
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 	R CMD INSTALL scone
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 	# You may get errors if dependencies are not installed prior to scone installation.
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 	# Install SCDE dependency at http://hms-dbmi.github.io/scde/package.html
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+	# Install RUVSeq dependency using devtools::install_github('drisso/RUVSeq')
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Update README.md

Michael authored on 08/02/2016 19:27:46
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README.md
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@@ -14,3 +14,4 @@ Private Repo containing SCONE R Package
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 	# Install via command line:
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 	R CMD INSTALL scone
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 	# You may get errors if dependencies are not installed prior to scone installation.
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+	# Install SCDE dependency at http://hms-dbmi.github.io/scde/package.html
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Update README.md

Michael authored on 08/02/2016 19:21:01
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README.md
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@@ -11,4 +11,6 @@ Private Repo containing SCONE R Package
11 11 
 	# Clone the GitHub repo:
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 	git clone https://github.com/YosefLab/scone.git
13 13
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-	...
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+	# Install via command line:
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+	R CMD INSTALL scone
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+	# You may get errors if dependencies are not installed prior to scone installation.
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Update README.md

mbcole authored on 05/02/2016 02:41:06
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11 11 
 	# Clone the GitHub repo:
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 	git clone https://github.com/YosefLab/scone.git
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+
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+	...
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Modified README

mbcole authored on 05/02/2016 02:37:06
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README.md
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 ## SCONE ##
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-### Single-Cell Overview of Normalized Expression ###
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+### Single-Cell Overview of Normalized Expression data ###
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 ============
4 4
5 5 
 Private Repo containing SCONE R Package
Browse code

Update README.md

mbcole authored on 05/02/2016 02:17:17
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-# scone
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+## SCONE ##
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+### Single-Cell Overview of Normalized Expression ###
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+============
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+
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+Private Repo containing SCONE R Package
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+
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+---------------------------------------
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+
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+### To Install ###
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+
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+	# Clone the GitHub repo:
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+	git clone https://github.com/YosefLab/scone.git
Browse code

first commit

Michael Cole authored on 05/02/2016 02:01:28
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+# scone