knit to html instead since github actions complains about pdflatex

JEFworks · Jan 24, 2021 · 0396319 · 0396319
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diff --git a/README.md b/README.md
@@ -1,5 +1,6 @@
 # Lightweight Iterative Gene set Enrichment in R (LIGER)
 
+![R-CMD-check](https://github.com/JEFworks/liger/workflows/R-CMD-check/badge.svg)
 [![CRAN](https://www.r-pkg.org/badges/version/liger)](https://CRAN.R-project.org/package=liger)
 [![DOI](https://zenodo.org/badge/43224920.svg)](https://zenodo.org/badge/latestdoi/43224920)
 
@@ -10,10 +11,10 @@ Gene Set Enrichment Analysis (GSEA) is a computational method that determines wh
 The `liger` package provides a lightweight R implementation of this enrichment test on a list of values. Given a list of values, such as p-values or log-fold changes derived from differential expression analysis or other analyses comparing biological states, this package enables you to test a priori defined set of genes for enrichment to enable interpretability of highly significant or high fold-change genes.
 
 # Tutorials
-- **[Gene Set Enrichment Analysis with LIGER](vignettes/gsea.pdf)** 
-- **[Highlighting the power of gene set enrichment analysis using simulation](vignettes/simulation.pdf)** 
-- **[Interpreting Enrichment Scores and Edge Values](vignettes/interpreting.pdf)** 
-- **[Comparison with alternative gene set enrichment analysis approaches](vignettes/comparison.pdf)** 
+- **[Gene Set Enrichment Analysis with LIGER](vignettes/gsea.html)** 
+- **[Highlighting the power of gene set enrichment analysis using simulation](vignettes/simulation.html)** 
+- **[Interpreting Enrichment Scores and Edge Values](vignettes/interpreting.html)** 
+- **[Comparison with alternative gene set enrichment analysis approaches](vignettes/comparison.html)** 
 
 # Sample plots
 

diff --git a/vignettes/comparison.Rmd b/vignettes/comparison.Rmd
@@ -2,7 +2,7 @@
 title: "Comparison of `liger` with `fgsea`"
 author: "Jean Fan"
 date: "June 26, 2018"
-output: rmarkdown::pdf_document
+output: rmarkdown::html_document
 vignette: >
  %\VignetteIndexEntry{Comparison of liger with fgsea}
  %\VignetteEngine{knitr::rmarkdown}

diff --git a/vignettes/gsea.Rmd b/vignettes/gsea.Rmd
@@ -2,7 +2,7 @@
 title: "Gene Set Enrichment Analysis with LIGER"
 author: "Jean Fan"
 date: "September 27, 2015"
-output: rmarkdown::pdf_document
+output: rmarkdown::html_document
 vignette: >
  %\VignetteIndexEntry{Gene Set Enrichment Analysis with LIGER}
  %\VignetteEngine{knitr::rmarkdown}

diff --git a/vignettes/interpreting.Rmd b/vignettes/interpreting.Rmd
@@ -2,7 +2,7 @@
 title: "Interpreting `liger` results"
 author: "Jean Fan"
 date: "8/23/2018"
-output: rmarkdown::pdf_document
+output: rmarkdown::html_document
 vignette: >
  %\VignetteIndexEntry{Interpreting liger results}
  %\VignetteEngine{knitr::rmarkdown}

diff --git a/vignettes/permpvals.Rmd b/vignettes/permpvals.Rmd
@@ -2,7 +2,7 @@
 title: "Exploring Permutation P-values"
 author: "Jean Fan"
 date: "7/15/2020"
-output: rmarkdown::pdf_document
+output: rmarkdown::html_document
 vignette: >
  %\VignetteIndexEntry{Exploring Permutation P-values}
  %\VignetteEngine{knitr::rmarkdown}

diff --git a/vignettes/simulation.Rmd b/vignettes/simulation.Rmd
@@ -2,7 +2,7 @@
 title: "Highlighting the Power of Gene Set Enrichment Analysis using Simulation"
 author: "Jean Fan"
 date: "December 23, 2015"
-output: rmarkdown::pdf_document
+output: rmarkdown::html_document
 vignette: >
  %\VignetteIndexEntry{Highlighting the Power of Gene Set Enrichment Analysis using Simulation}
  %\VignetteEngine{knitr::rmarkdown}