v1.0.0

fchen365 · Mar 23, 2021 · 9f3b1f5 · 9f3b1f5
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diff --git a/.gitignore b/.gitignore
@@ -26,6 +26,8 @@
 # vignettes data
 vignettes/data/*
 vignettes/results/*
+vignettes/figures/*
+vignettes/*.gff2
 
 # OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
 .httr-oauth

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: surf
 Type: Package
 Title: Statistical Utility for RBP (RNA binding protein) Functions
-Version: 0.0.0.9000
-Date: 2020-12-12
+Version: 1.0.0
+Date: 2021-03-22
 Authors@R: 
     person(given = "Fan",
            family = "Chen",

diff --git a/NEWS.md b/NEWS.md
@@ -1,4 +1,7 @@
-# News: `surf` 0.0.0.9000
+# News: `surf` 1.0.0
+
+## Mar 22, 2021 
+* Ready for Bioconductor submission.
 
 ## Sep 7, 2020
 * Added a `NEWS.md` file to track changes to the package.

diff --git a/inst/CITATION b/inst/CITATION
@@ -0,0 +1,22 @@
+citHeader("To cite surf in publications use:")
+
+citEntry(
+  entry        = "Article",
+  title        = "SURF: integrative analysis of a compendium of RNA-seq and CLIP-seq datasets highlights complex governing of alternative transcriptional regulation by RNA-binding proteins.",
+  author       = personList(as.person("Fan Chen"),
+                   as.person("Sunduz Keles")),
+  journal      = "Genome Biology",
+  year         = "2020",
+  volume       = "21",
+  number       = "139",
+  pages        = "1--23",
+  url          = "https://doi.org/10.1186/s13059-020-02039-7",
+
+  textVersion  =
+  paste("Chen, F., Keles, S.",
+        "SURF: integrative analysis of a compendium of RNA-seq and",
+        "CLIP-seq datasets highlights complex governing of",
+        "alternative transcriptional regulation by RNA-binding proteins.",
+        "Genome Biol 21, 139 (2020).",
+        "URL https://doi.org/10.1186/s13059-020-02039-7.")
+)
diff --git a/vignettes/surf.Rmd b/vignettes/surf.Rmd
@@ -94,7 +94,7 @@ knitr::include_graphics("figures/0_pipeline.jpg")
 ```
 
 # Preparations
-To reproduce the results in this vignette, download the demo data from XXX and put them into a "data" folder under the working directory. 
+To reproduce the results in this vignette, download the demo data from [Zenodo](http://doi.org/10.5281/zenodo.4628573) and put them into a "data" folder under the working directory. 
 
 # Quick start
 

diff --git a/vignettes/surf.html b/vignettes/surf.html