From b221b347e9ea98af8f0d99b2ace3ec669de604f8 Mon Sep 17 00:00:00 2001 From: Astrid Deschenes Date: Mon, 22 Feb 2021 18:32:34 -0500 Subject: [PATCH] Update links to github in vignette --- vignettes/CNVMetrics.Rmd | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/vignettes/CNVMetrics.Rmd b/vignettes/CNVMetrics.Rmd index 3947cdb..8256c62 100644 --- a/vignettes/CNVMetrics.Rmd +++ b/vignettes/CNVMetrics.Rmd @@ -35,8 +35,8 @@ set.seed(121444) # Licensing -The `r Githubpkg("adeschen/CNVMetrics")` package and the underlying -`r Githubpkg("adeschen/CNVMetrics")` code are distributed under the +The `r Githubpkg("KrasnitzLab/CNVMetrics")` package and the underlying +`r Githubpkg("KrasnitzLab/CNVMetrics")` code are distributed under the Artistic license 2.0. You are free to use and redistribute this software. # Introduction @@ -71,7 +71,7 @@ tumor CNV profiles may reveal genomic determinants of metastasis. Similarly, patient-derived xenograft or organoid models of cancer are expected to recapitulate CNV patterns of the tumor tissue of origin [@Gendoo2019]. -The `r Githubpkg("adeschen/CNVMetrics")` package calculates metrics to +The `r Githubpkg("KrasnitzLab/CNVMetrics")` package calculates metrics to estimate the level of similarity between copy number profiles. Some metrics are calculated using the _CNV status calls_ (amplification/deletion status) while others are based on the level of amplification/deletion. Finally, a @@ -81,7 +81,7 @@ sample-to-sample heatmaps. # Installation To install the latest version accessible on the -[CNVMetrics Github Website](https://github.com/adeschen/CNVMetrics/releases "CNVMetrics Github Site"), the `r CRANpkg("devtools")` package is required. +[CNVMetrics Github Website](https://github.com/KrasnitzLab/CNVMetrics "CNVMetrics Github Site"), the `r CRANpkg("devtools")` package is required. ```{r installDemo01, eval=FALSE} ## Load required package @@ -92,7 +92,7 @@ devtools::install_github('KrasnitzLab/CNVMetrics') ``` It is also possible to install an official release. The list of available -releases is posted on the [CNVMetrics Release Website](https://github.com/adeschen/CNVMetrics/releases "CNVMetrics Release Site"). +releases is posted on the [CNVMetrics Release Website](https://github.com/KrasnitzLab/CNVMetrics/releases "CNVMetrics Release Site"). ```{r installDemo02, eval=FALSE} @@ -107,7 +107,7 @@ devtools::install_github('KrasnitzLab/CNVMetrics', ref = "v0.1.4") # Workflow for metrics calculated using _CNV status calls_ The following figure gives an overview of the capabilities of -`r Githubpkg("adeschen/CNVMetrics")` to calculate metrics using the +`r Githubpkg("KrasnitzLab/CNVMetrics")` to calculate metrics using the _CNV status calls_ (amplification/deletion status): @@ -268,7 +268,7 @@ plotOverlapMetric(metric, type = "AMPLIFICATION", # Metrics using the _CNV status calls_ This survey represents the similarity measures that are implemented in -`r Githubpkg("adeschen/CNVMetrics")` package. Those metrics are calculated +`r Githubpkg("KrasnitzLab/CNVMetrics")` package. Those metrics are calculated using the _CNV status calls_. The size of the amplified/deleted regions as well as the size of the overlapping of regions are always in base paired. @@ -301,7 +301,7 @@ value is 1. # Metrics using the level of amplification/deletion This survey represents the similarity measures that are implemented in -`r Githubpkg("adeschen/CNVMetrics")` package. +`r Githubpkg("KrasnitzLab/CNVMetrics")` package. TODO