From 784ae4f3ad4b2e3e548ee215279866b3462c35b2 Mon Sep 17 00:00:00 2001 From: jahn Date: Wed, 24 Apr 2024 16:32:29 +0200 Subject: [PATCH] fix: fixed unavailable URLS, related to #29 --- README.Rmd | 4 ++-- README.md | 5 ++--- vignettes/ggcoverage.Rmd | 4 ++-- 3 files changed, 6 insertions(+), 7 deletions(-) diff --git a/README.Rmd b/README.Rmd index bd0e5e2..9da7c4f 100644 --- a/README.Rmd +++ b/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) diff --git a/README.md b/README.md index 3888750..c5514e0 100644 --- a/README.md +++ b/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) diff --git a/vignettes/ggcoverage.Rmd b/vignettes/ggcoverage.Rmd index 6343072..7342b60 100644 --- a/vignettes/ggcoverage.Rmd +++ b/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)