fix: fixed unavailable URLS, related to showteeth#29

Author: m-jahn

README.Rmd

@@ -270,7 +270,7 @@ basic_coverage +
 
 ##### Load the data
 
-The DNA-seq data used here are from [Copy number work flow](http://bioconductor.org/help/course-materials/2014/SeattleOct2014/B02.2.3_CopyNumber.html), we select tumor sample, and get bin counts with `cn.mops::getReadCountsFromBAM` with `WL` 1000.
+The DNA-seq data used here are from [Copy number work flow](https://bioconductor.org/help/course-materials/2014/SeattleOct2014/B02.2.3_CopyNumber.html), we select tumor sample, and get bin counts with `cn.mops::getReadCountsFromBAM` with `WL` 1000.
 
 ```{r load_bin_counts}
 # prepare metafile
@@ -755,7 +755,7 @@ basic_coverage +
 
 ### Load coverage
 
-The exported coverage from [Proteome Discoverer](https://www.thermofisher.cn/cn/zh/home/industrial/mass-spectrometry/liquid-chromatography-mass-spectrometry-lc-ms/lc-ms-software/multi-omics-data-analysis/proteome-discoverer-software.html?adobe_mc=MCMID%7C90228073352279367993013412919222863692%7CMCAID%3D3208C32C269355DE-4000028116B65FEB%7CMCORGID%3D5B135A0C5370E6B40A490D44%40AdobeOrg%7CTS=1614293705):
+The exported coverage from [Proteome Discoverer](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8006021/):
 
 ```{r ms_coverage_data}
 library(openxlsx)

README.md

@@ -332,7 +332,7 @@ basic_coverage +
 ##### Load the data
 
 The DNA-seq data used here are from [Copy number work
-flow](http://bioconductor.org/help/course-materials/2014/SeattleOct2014/B02.2.3_CopyNumber.html),
+flow](https://bioconductor.org/help/course-materials/2014/SeattleOct2014/B02.2.3_CopyNumber.html),
 we select tumor sample, and get bin counts with
 `cn.mops::getReadCountsFromBAM` with `WL` 1000.
 
@@ -948,8 +948,7 @@ experiment.
 
 ### Load coverage
 
-The exported coverage from [Proteome
-Discoverer](https://www.thermofisher.cn/cn/zh/home/industrial/mass-spectrometry/liquid-chromatography-mass-spectrometry-lc-ms/lc-ms-software/multi-omics-data-analysis/proteome-discoverer-software.html?adobe_mc=MCMID%7C90228073352279367993013412919222863692%7CMCAID%3D3208C32C269355DE-4000028116B65FEB%7CMCORGID%3D5B135A0C5370E6B40A490D44%40AdobeOrg%7CTS=1614293705):
+The exported coverage from [Proteome Discoverer](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8006021/):
 
 ``` r
 library(openxlsx)

vignettes/ggcoverage.Rmd

@@ -287,7 +287,7 @@ knitr::include_graphics("../man/figures/README-ideogram_coverage_2-1.png")
 
 ##### Load the data
 
-The DNA-seq data used here are from [Copy number work flow](http://bioconductor.org/help/course-materials/2014/SeattleOct2014/B02.2.3_CopyNumber.html), we select tumor sample, and get bin counts with `cn.mops::getReadCountsFromBAM` with `WL` 1000.
+The DNA-seq data used here are from [Copy number work flow](https://bioconductor.org/help/course-materials/2014/SeattleOct2014/B02.2.3_CopyNumber.html), we select tumor sample, and get bin counts with `cn.mops::getReadCountsFromBAM` with `WL` 1000.
 
 ```{r load_bin_counts}
 # prepare metafile
@@ -784,7 +784,7 @@ knitr::include_graphics("../man/figures/README-hic_coverage-1.png")
 
 ### Load coverage
 
-The exported coverage from [Proteome Discoverer](https://www.thermofisher.cn/cn/zh/home/industrial/mass-spectrometry/liquid-chromatography-mass-spectrometry-lc-ms/lc-ms-software/multi-omics-data-analysis/proteome-discoverer-software.html?adobe_mc=MCMID%7C90228073352279367993013412919222863692%7CMCAID%3D3208C32C269355DE-4000028116B65FEB%7CMCORGID%3D5B135A0C5370E6B40A490D44%40AdobeOrg%7CTS=1614293705):
+The exported coverage from [Proteome Discoverer](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8006021/):
 
 ```{r ms_coverage_data}
 library(openxlsx)