lint

Author: scottgigante

.github/ISSUE_TEMPLATE/question.md

@@ -6,5 +6,3 @@ labels: question
 assignees: ''
 
 ---
-
-

.github/workflows/deploy.yml

@@ -23,7 +23,7 @@ jobs:
 
     - name: Install pypa/build
       run: >-
-        cd python && 
+        cd python &&
         python -m
         pip install
         build

LICENSE

@@ -337,4 +337,3 @@ proprietary programs.  If your program is a subroutine library, you may
 consider it more useful to permit linking proprietary applications with the
 library.  If this is what you want to do, use the GNU Lesser General
 Public License instead of this License.
-

README.md

@@ -17,13 +17,13 @@ To see how MAGIC can be applied to single-cell RNA-seq, elucidating the epitheli
 
 MAGIC has been implemented in Python, Matlab, and R.
 
-#### To get started immediately, check out our tutorials:  
-##### Python  
-* [Epithelial-to-Mesenchymal Transition Tutorial](http://nbviewer.jupyter.org/github/KrishnaswamyLab/MAGIC/blob/master/python/tutorial_notebooks/emt_tutorial.ipynb)  
-* [Bone Marrow Tutorial](http://nbviewer.jupyter.org/github/KrishnaswamyLab/MAGIC/blob/master/python/tutorial_notebooks/bonemarrow_tutorial.ipynb)  
-##### R  
-* [Epithelial-to-Mesenchymal Transition Tutorial](http://htmlpreview.github.io/?https://github.com/KrishnaswamyLab/MAGIC/blob/master/Rmagic/inst/examples/emt_tutorial.html)  
-* [Bone Marrow Tutorial](http://htmlpreview.github.io/?https://github.com/KrishnaswamyLab/MAGIC/blob/master/Rmagic/inst/examples/bonemarrow_tutorial.html)  
+#### To get started immediately, check out our tutorials:
+##### Python
+* [Epithelial-to-Mesenchymal Transition Tutorial](http://nbviewer.jupyter.org/github/KrishnaswamyLab/MAGIC/blob/master/python/tutorial_notebooks/emt_tutorial.ipynb)
+* [Bone Marrow Tutorial](http://nbviewer.jupyter.org/github/KrishnaswamyLab/MAGIC/blob/master/python/tutorial_notebooks/bonemarrow_tutorial.ipynb)
+##### R
+* [Epithelial-to-Mesenchymal Transition Tutorial](http://htmlpreview.github.io/?https://github.com/KrishnaswamyLab/MAGIC/blob/master/Rmagic/inst/examples/emt_tutorial.html)
+* [Bone Marrow Tutorial](http://htmlpreview.github.io/?https://github.com/KrishnaswamyLab/MAGIC/blob/master/Rmagic/inst/examples/bonemarrow_tutorial.html)
 
 
 <p align="center">

Rmagic/DESCRIPTION

@@ -3,7 +3,7 @@ Type: Package
 Title: MAGIC - Markov Affinity-Based Graph Imputation of Cells
 Version: 2.0.3.999
 Authors@R: c(person(given = "David", family = "van Dijk", email = "[email protected]", role = c("aut")),
-		         person(given = 'Scott', family = 'Gigante', email = '[email protected]', role = 'cre', 
+		         person(given = 'Scott', family = 'Gigante', email = '[email protected]', role = 'cre',
 		                comment = c(ORCID = '0000-0002-4544-2764')))
 Maintainer: Scott Gigante <[email protected]>
 Description: MAGIC (Markov affinity-based graph imputation of cells) is a method for addressing technical noise in single-cell data, including under-sampling of mRNA molecules, often termed "dropout" which can severely obscure important gene-gene relationships. MAGIC shares information across similar cells, via data diffusion, to denoise the cell count matrix and fill in missing transcripts. Read more: van Dijk et al. (2018) <DOI:10.1016/j.cell.2018.05.061>.

Rmagic/LICENSE

@@ -337,4 +337,3 @@ proprietary programs.  If your program is a subroutine library, you may
 consider it more useful to permit linking proprietary applications with the
 library.  If this is what you want to do, use the GNU Lesser General
 Public License instead of this License.
-

Rmagic/R/magic_testdata.R

@@ -5,4 +5,4 @@
 #' @format A matrix with 500 rows and 197 variables
 #'
 #' @source The authors
-"magic_testdata"
+"magic_testdata"

Rmagic/R/utils.R

@@ -66,11 +66,11 @@ load_pymagic <- function() {
 }
 
 #' Check whether MAGIC Python package is available and can be loaded
-#' 
+#'
 #' This is used primarily to avoid running tests on CRAN
 #' and elsewhere where the Python package should not be
 #' installed.
-#' 
+#'
 #' @export
 pymagic_is_available <- function() {
   tryCatch({

Rmagic/README.md

@@ -138,10 +138,10 @@ library(ggplot2)
 library(viridis)
 #> Loading required package: viridisLite
 library(phateR)
-#> 
+#>
 #> Attaching package: 'phateR'
 #> The following object is masked from 'package:Rmagic':
-#> 
+#>
 #>     library.size.normalize
 ```
 

Rmagic/inst/CITATION

@@ -2,20 +2,20 @@ bibentry(
 	bibtype="Article",
 	title="Recovering Gene Interactions from Single-Cell Data Using Data Diffusion",
 	author = c(
-		person("David", "van Dijk"), 
-		person("Roshan", "Sharma"), 
-		person("Juozas", "Nainys"), 
-		person("Kristina", "Yim"), 
-		person("Pooja", "Kathail"), 
-		person("Ambrose J.", "Carr"), 
-		person("Cassandra", "Burdziak"), 
-		person("Kevin R.", "Moon"), 
-		person("Christine L.", "Chaffer"), 
-		person("Diwakar", "Pattabiraman"), 
-		person("Brian", "Bierie"), 
-		person("Linas", "Mazutis"), 
-		person("Guy", "Wolf"), 
-		person("Smita", "Krishnaswamy"), 
+		person("David", "van Dijk"),
+		person("Roshan", "Sharma"),
+		person("Juozas", "Nainys"),
+		person("Kristina", "Yim"),
+		person("Pooja", "Kathail"),
+		person("Ambrose J.", "Carr"),
+		person("Cassandra", "Burdziak"),
+		person("Kevin R.", "Moon"),
+		person("Christine L.", "Chaffer"),
+		person("Diwakar", "Pattabiraman"),
+		person("Brian", "Bierie"),
+		person("Linas", "Mazutis"),
+		person("Guy", "Wolf"),
+		person("Smita", "Krishnaswamy"),
 		person("Dana", "Pe'er")),
 	year=2018,
 	url="https://www.cell.com/cell/abstract/S0092-8674(18)30724-4",