Merge branch 'default' into main

Author: ritamtbsilva

README.Rmd

@@ -17,12 +17,12 @@ knitr::opts_chunk$set(
 
 <!-- badges: start -->
 
-<!--![](https://img.shields.io/badge/status-development-yellowgreen)-->
+![](https://img.shields.io/badge/status-development-yellowgreen)
 [![Pkgdown](https://img.shields.io/badge/docs-pkgdown-blue.svg)](https://diseasetranscriptomicslab.github.io/markeR/)
 ![Minimal R Version](https://img.shields.io/badge/min%20R-4.5.0-blue.svg)
 [![codecov](https://codecov.io/gh/DiseaseTranscriptomicsLab/markeR/graph/badge.svg?token=7T1I4JCJG6)](https://codecov.io/gh/DiseaseTranscriptomicsLab/markeR)
-<!-- [![R-CMD-check](https://github.com/DiseaseTranscriptomicsLab/markeR/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/DiseaseTranscriptomicsLab/markeR/actions/workflows/R-CMD-check.yaml)-->
-<!-- [![Bioconductor Check](https://github.com/DiseaseTranscriptomicsLab/markeR/actions/workflows/bioc-check.yml/badge.svg)](https://github.com/DiseaseTranscriptomicsLab/markeR/actions/workflows/bioc-check.yml) -->
+[![R-CMD-check](https://github.com/DiseaseTranscriptomicsLab/markeR/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/DiseaseTranscriptomicsLab/markeR/actions/workflows/R-CMD-check.yaml)
+[![Bioconductor Check](https://github.com/DiseaseTranscriptomicsLab/markeR/actions/workflows/bioc-check.yml/badge.svg)](https://github.com/DiseaseTranscriptomicsLab/markeR/actions/workflows/bioc-check.yml)
 
 <!-- badges: end -->
 
@@ -57,20 +57,8 @@ The folder `inst/Paper/` is in the **paper** branch and contains all scripts and
 
 ## Installation 
 
+Install the latest development release of markeR from [GitHub](https://github.com/) with:
 
-Install the latest release from Bioconductor:
-
-```{r, eval=FALSE}
-# Install from Bioconductor
-if (!requireNamespace("BiocManager", quietly = TRUE))
-    install.packages("BiocManager")
-BiocManager::install("markeR")
-library(markeR)
-```
- 
-
-Or install the latest development release of `markeR` from [GitHub](https://github.com/) with:
-   
 ``` r
 # install.packages("devtools")
 devtools::install_github("DiseaseTranscriptomicsLab/markeR@*release")

README.md

@@ -5,14 +5,14 @@
 
 <!-- badges: start -->
 
-<!--![](https://img.shields.io/badge/status-development-yellowgreen)-->
-
+![](https://img.shields.io/badge/status-development-yellowgreen)
 [![Pkgdown](https://img.shields.io/badge/docs-pkgdown-blue.svg)](https://diseasetranscriptomicslab.github.io/markeR/)
 ![Minimal R
 Version](https://img.shields.io/badge/min%20R-4.5.0-blue.svg)
 [![codecov](https://codecov.io/gh/DiseaseTranscriptomicsLab/markeR/graph/badge.svg?token=7T1I4JCJG6)](https://codecov.io/gh/DiseaseTranscriptomicsLab/markeR)
-<!-- [![R-CMD-check](https://github.com/DiseaseTranscriptomicsLab/markeR/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/DiseaseTranscriptomicsLab/markeR/actions/workflows/R-CMD-check.yaml)-->
-<!-- [![Bioconductor Check](https://github.com/DiseaseTranscriptomicsLab/markeR/actions/workflows/bioc-check.yml/badge.svg)](https://github.com/DiseaseTranscriptomicsLab/markeR/actions/workflows/bioc-check.yml) -->
+[![R-CMD-check](https://github.com/DiseaseTranscriptomicsLab/markeR/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/DiseaseTranscriptomicsLab/markeR/actions/workflows/R-CMD-check.yaml)
+[![Bioconductor
+Check](https://github.com/DiseaseTranscriptomicsLab/markeR/actions/workflows/bioc-check.yml/badge.svg)](https://github.com/DiseaseTranscriptomicsLab/markeR/actions/workflows/bioc-check.yml)
 
 <!-- badges: end -->
 
@@ -58,18 +58,7 @@ analyses and figures. You can browse it
 
 ## Installation
 
-Install the latest release from Bioconductor:
-
-``` r
-# Install from Bioconductor
-if (!requireNamespace("BiocManager", quietly = TRUE))
-    install.packages("BiocManager")
-BiocManager::install("markeR")
-library(markeR)
-```
-
-Or install the latest development release of `markeR` from
-[GitHub](https://github.com/) with:
+Install the latest development release of markeR from [GitHub](https://github.com/) with:
 
 ``` r
 # install.packages("devtools")

vignettes/markeR.Rmd

@@ -53,16 +53,7 @@ The package is implemented with flexibility and extensibility as core design pri
 
 # Installation
 
-Install the latest release from Bioconductor:
-
-```{r, eval=FALSE}
-# Install from Bioconductor
-if (!requireNamespace("BiocManager", quietly = TRUE))
-  install.packages("BiocManager")
-BiocManager::install("markeR")
-```
-
-Or install the latest development release of `markeR` from [GitHub](https://github.com/) with:
+Install the latest development release of `markeR` from [GitHub](https://github.com/) with:
 
 ```r
 devtools::install_github("DiseaseTranscriptomicsLab/markeR@*release")