diff --git a/README.md b/README.md index 422b086..6266296 100644 --- a/README.md +++ b/README.md @@ -69,14 +69,9 @@ Download the latest release and then install it using: `install.packages("", repos = NULL, type="source")` -The latest release can also be directly installed from github, using the `devtools` package: - -`devtools::install_github("bartongroup/rats", ref="master")` - -2. For testing purposes (bug resolutions, new features), you can install the ongoing developmental version from Github: -`devtools::install_github("bartongroup/rats", ref="development")` -Developmental versions are works in progress and will not be archived in snapshots. For reproducible/publishable analyses, -**always use a release version**, NOT a developmental version. +2. For testing purposes (bug resolutions, new features), you can install the ongoing developmental version from Github, (you will also need to have the `devtools` package installed): +`devtools::install_github("bartongroup/rats")` +Developmental versions are works in progress and will not be archived. For publishable analyses, **always use a release version**, NOT a developmental version. ### Differential Transcript Usage diff --git a/inst/doc/intro.Rmd b/inst/doc/intro.Rmd index 4a82f74..a9a42bc 100644 --- a/inst/doc/intro.Rmd +++ b/inst/doc/intro.Rmd @@ -67,10 +67,6 @@ Download the latest release and then install it using: `install.packages("", repos = NULL, type="source")` -Or install directly with the help of the [devtools](https://www.rstudio.com/products/rpackages/devtools/) package: - -`devtools::install_github("bartongroup/rats", ref="master")` - Release snapshots are labelled with even-ending version numbers (x.x.0/2/4/6/8). #### through Bioconductor @@ -79,9 +75,10 @@ Not available yet. #### developmental version -The most current developmental version of `rats` can be installed directly from the working copy on Github, using `devtools`: +The most current developmental version of `rats` can be installed directly from the working copy on Github, using the [devtools](https://www.rstudio.com/products/rpackages/devtools/) package +(which you will need to install first): -`devtools::install_github("bartongroup/rats", ref="development")` +`devtools::install_github("bartongroup/rats")` As this version represents active development, it can change at any moment. Features may be added, removed or changed without notice. **Do not rely on this version for reproducible analysis of important data!** diff --git a/inst/doc/intro.html b/inst/doc/intro.html index dc0422c..6d2f1ec 100644 --- a/inst/doc/intro.html +++ b/inst/doc/intro.html @@ -245,10 +245,6 @@

from Github

install.packages("<path/to/dowloaded/package>", repos = NULL, type="source")

-

Or install directly with the help of the devtools package:

- -

devtools::install_github("bartongroup/rats", ref="master")

-

Release snapshots are labelled with even-ending version numbers (x.x.0/2/4/6/8).

through Bioconductor

@@ -257,9 +253,10 @@

through Bioconductor

developmental version

-

The most current developmental version of rats can be installed directly from the working copy on Github, using devtools:

+

The most current developmental version of rats can be installed directly from the working copy on Github, using the devtools package +(which you will need to install first):

-

devtools::install_github("bartongroup/rats", ref="development")

+

devtools::install_github("bartongroup/rats")

As this version represents active development, it can change at any moment. Features may be added, removed or changed without notice. Do not rely on this version for reproducible analysis of important data! diff --git a/inst/doc/plots.html b/inst/doc/plots.html index 7cbc260..4a622bb 100644 --- a/inst/doc/plots.html +++ b/inst/doc/plots.html @@ -268,7 +268,7 @@

Isoform abundances for a given gene

plot_gene(mydtu, "MIX6", style="byisoform") -

plot of chunk unnamed-chunk-4

+

plot of chunk unnamed-chunk-4

Customisation of the gene plot

@@ -287,13 +287,13 @@

Change information layers

plot_gene(mydtu, "MIX6", style="byisoform", colourby="DTU", shapeby="replicate")
-

plot of chunk unnamed-chunk-5

+

plot of chunk unnamed-chunk-5

# For a less busy look, any of the information layers can be disabled.
 plot_gene(mydtu, "MIX6", style="byisoform", colourby="none", shapeby="none")
-

plot of chunk unnamed-chunk-5

+

plot of chunk unnamed-chunk-5

Change colour code

diff --git a/vignettes/intro.Rmd b/vignettes/intro.Rmd index 4a82f74..a9a42bc 100644 --- a/vignettes/intro.Rmd +++ b/vignettes/intro.Rmd @@ -67,10 +67,6 @@ Download the latest release and then install it using: `install.packages("", repos = NULL, type="source")` -Or install directly with the help of the [devtools](https://www.rstudio.com/products/rpackages/devtools/) package: - -`devtools::install_github("bartongroup/rats", ref="master")` - Release snapshots are labelled with even-ending version numbers (x.x.0/2/4/6/8). #### through Bioconductor @@ -79,9 +75,10 @@ Not available yet. #### developmental version -The most current developmental version of `rats` can be installed directly from the working copy on Github, using `devtools`: +The most current developmental version of `rats` can be installed directly from the working copy on Github, using the [devtools](https://www.rstudio.com/products/rpackages/devtools/) package +(which you will need to install first): -`devtools::install_github("bartongroup/rats", ref="development")` +`devtools::install_github("bartongroup/rats")` As this version represents active development, it can change at any moment. Features may be added, removed or changed without notice. **Do not rely on this version for reproducible analysis of important data!**