Merge pull request #125 from kharchenkolab/devel

Version 1.0.5

Author: evanbiederstedt

CHANGELOG.md

@@ -1,5 +1,11 @@
 ## Upcoming
 
+## [1.0.5] - 2020-08-11
+
+### Changed
+
+- Removed the vignettes and dependency on the drat repository at https://github.com/kharchenkolab/p2data
+
 ## [1.0.4] - 2020-06-28
 
 ### Changed

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: pagoda2
 Title: Single Cell Analysis and Differential Expression
-Version: 1.0.4
+Version: 1.0.5
 Authors@R: c(person("Nikolas","Barkas", email="nikolas_barkas@hms.harvard.edu", role="aut"), person("Viktor", "Petukhov", email="viktor.s.petuhov@ya.ru", role="aut"), person("Peter", "Kharchenko", email = "peter_kharchenko@hms.harvard.edu", role = "aut"), person("Simon", "Steiger", email = "simon.steiger@gmail.com", role = "ctb"), person("Evan", "Biederstedt", email="evan.biederstedt@gmail.com", role=c("cre", "aut")))
 Description: Analyzing and interactively exploring large-scale single-cell RNA-seq datasets. 'pagoda2' primarily performs normalization and differential gene expression analysis, with an interactive application for exploring single-cell RNA-seq datasets. It performs basic tasks such as cell size normalization, gene variance normalization, and can be used to identify subpopulations and run differential expression within individual samples. 'pagoda2' was written to rapidly process modern large-scale scRNAseq datasets of approximately 1e6 cells. The companion web application allows users to explore which gene expression patterns form the different subpopulations within your data. The package also serves as the primary method for preprocessing data for conos, <https://github.com/kharchenkolab/conos>. This package interacts with data available through the 'p2data' package, which is available in a 'drat' repository. To access this data package, see the instructions at <https://github.com/kharchenkolab/pagoda2>. The size of the 'p2data' package is approximately 6 MB.
 License: GPL-3 
@@ -53,7 +53,6 @@ Suggests:
     org.Dr.eg.db,
     org.Hs.eg.db,
     org.Mm.eg.db,
-    p2data,
     pcaMethods, 
     pheatmap, 
     rgl, 
@@ -62,8 +61,6 @@ Suggests:
     scde,
     testthat,
     uwot
-VignetteBuilder: knitr
-Additional_repositories: https://kharchenkolab.github.io/drat/
 URL: https://github.com/kharchenkolab/pagoda2
 BugReports: https://github.com/kharchenkolab/pagoda2/issues
 NeedsCompilation: yes

README.md

@@ -11,7 +11,7 @@
 - [Installation](#installation)
   * [Installing Linux Dependencies](#installing-linux-dependencies)
   * [Installing with Mac OS](#installing-with-mac-os)
-  * [Pagoda2 via Docker](#pagoda2-via-docker)
+  * [pagoda2 via Docker](#pagoda2-via-docker)
 
 ## pagoda2: Rapid Processing and Interactive Analysis of Large Datasets
 
@@ -26,7 +26,7 @@ Several methods within this package were developed based on the originals implem
 
 **Basic Walkthrough**
 * [HTML version](https://htmlpreview.github.io/?https://raw.githubusercontent.com/kharchenkolab/pagoda2/master/doc/pagoda2.walkthrough.html) 
-* [Markdown version](https://github.com/kharchenkolab/pagoda2/blob/master/vignettes/pagoda2.walkthrough.md)
+* [Markdown version](https://github.com/kharchenkolab/pagoda2/blob/master/doc/pagoda2.walkthrough.md)
 
 [PCA-based Basic Walkthrough](http://pklab.med.harvard.edu/peterk/p2/walkthrough.nb.html)
 
@@ -50,7 +50,7 @@ To install the latest version of `pagoda2`, use:
 
 ```r
 install.packages('devtools')
-devtools::install_github('kharchenkolab/pagoda2', build_vignettes = TRUE)
+devtools::install_github('kharchenkolab/pagoda2')
 ```
 
 
@@ -101,5 +101,5 @@ If you find `pagoda2` useful for your publication, please cite:
 ```
 Nikolas Barkas, Viktor Petukhov, Peter Kharchenko and Evan
 Biederstedt (2021). pagoda2: Single Cell Analysis and Differential
-Expression. R package version 1.0.4.
+Expression. R package version 1.0.5.
 ```