v0.1.1 Added readme and documentation

Author: innesbre

AgingMouseBrainCCInx.Rproj

@@ -18,3 +18,4 @@ StripTrailingWhitespace: Yes
 BuildType: Package
 PackageUseDevtools: Yes
 PackageInstallArgs: --no-multiarch --with-keep.source
+PackageRoxygenize: rd,collate,namespace,vignette

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: AgingMouseBrainCCInx
 Type: Package
 Title: Cell-cell interaction prediction from single-cell transcriptomic profiling of the aging mouse brain
-Version: 0.1.0
+Version: 0.1.1
 Author: Methodios Ximerakis, 
   Scott L. Lipnick,
   Brendan T. Innes,
@@ -22,7 +22,7 @@ Author: Methodios Ximerakis,
   Lee L. Rubin
 Maintainer: Brendan T. Innes <brendan.innes@mail.utoronto.ca>
 Description: Data package for the cell-cell interaction predictions from the 
-    paper "single-cell transcriptomic profiling of the aging mouse brain". The 
+    paper "Single-cell transcriptomic profiling of the aging mouse brain". The 
     package contains an RData list object with both the edge list and node 
     metadata of predicted cell-cell interactions between cell types in the mouse
     brain, and their changes with aging.  The predictions were generated using 
@@ -33,3 +33,4 @@ Encoding: UTF-8
 LazyData: true
 Depends: CCInx (>= 0.3.0)
 Remotes: Baderlab/CCInx
+RoxygenNote: 6.1.1

NAMESPACE

@@ -1 +1,3 @@
-exportPattern("^[[:alpha:]]+")
+# Generated by roxygen2: do not edit by hand
+
+export(ViewAgingMouseBrainCCInx)

R/ViewAgingMouseBrainCCInx.R

@@ -15,10 +15,7 @@
 #' @export
 
 ViewAgingMouseBrainCCInx <- function() {
-  if (exists("OxYxCCInx")) {
-    ViewCCInx(OxYxCCInx)
-  } else {
-    load(system.file("data/OX_YX_CCInx_forPub.RData",package="AgingMouseBrainCCInx"))
-    ViewCCInx(OxYxCCInx)
-  }
+  temp <- load(system.file("data/OX_YX_CCInx_forPub.RData",
+                           package="AgingMouseBrainCCInx"))
+  CCInx::ViewCCInx(get(temp))
 }

README.md

@@ -1,9 +1,28 @@
 # AgingMouseBrainCCInx
+# Single-cell transcriptomic profiling of the aging mouse brain
+Methodios Ximerakis, Scott L. Lipnick, Brendan T. Innes, Sean K. Simmons, Xian
+Adiconis, Danielle Dionne, Brittany A. Mayweather, Lan Nguyen, Zachary Niziolek,
+Ceren Ozek, Vincent L. Butty, Ruth Isserlin, Sean M. Buchanan, Stuart S. Levine, 
+Aviv Regev, Gary D. Bader, Joshua Z. Levin, and Lee L. Rubin.
+  
+## Abstract
+The mammalian brain is complex, with multiple cell types performing a variety of diverse
+functions, but exactly how the brain is affected with aging remains largely unknown. Here
+we performed a single-cell transcriptomic analysis of young and old mouse brains. We
+provide a comprehensive dataset of aging-related genes, pathways and ligand-receptor
+interactions in nearly all brain cell types. Our analysis identified gene signatures that vary
+in a coordinated manner across cell types and gene sets that are regulated in a cell type
+specific manner, even at times in opposite directions. Thus, our data reveal that aging,
+rather than inducing a universal program, drives a distinct transcriptional course in each
+cell population. These data provide an important resource for the aging community and
+highlight key molecular processes, including ribosome biogenesis, underlying aging. We
+believe that this large-scale dataset, which is publicly accessible online ([aging-mouse-brain](https://portals.broadinstitute.org/single_cell/study/aging-mouse-brain)), 
+will facilitate additional discoveries directed towards understanding and modifying
+the aging process.
 
 ## Usage
 This is an R package used to explore the cell-cell interaction predictions from the 
-paper "Single-cell transcriptomic profiling of the aging mouse brain". The
-package contains an RData list object with both the edge list and node 
+paper. The package contains an RData list object with both the edge list and node 
 metadata of predicted cell-cell interactions between cell types in the mouse
 brain, and their changes with aging.  The predictions were generated using 
 CCInx (baderlab.github.io/CCInx). You can install this package in R by running: