kevinrue

p.caption {
  color: #777;
  margin-top: 10px;
}
p code {
  white-space: inherit;
}
pre {
  word-break: normal;
  word-wrap: normal;

kevinrue

* Restoring project ... 
The following package(s) will be updated:

# Bioconductor =======================
- Biobase                [* -> 2.48.0]
- BiocGenerics           [* -> 0.34.0]
- BiocParallel           [* -> 1.22.0]
- BiocVersion            [* -> 3.11.1]
- Biostrings             [* -> 2.56.0]
- DelayedArray           [* -> 0.14.0]

kevinrue

on:
  push:
    branches:
      - master
  pull_request:
    branches:
      - master
jobs:
  build_check_deploy:
    runs-on: ubuntu-latest

kevinrue

############# The usual ################
library(scRNAseq)

# Example data ----
sce <- ReprocessedAllenData(assays="tophat_counts")
class(sce)

library(scater)
sce <- logNormCounts(sce, exprs_values="tophat_counts")

kevinrue

setClass("RedDimHexbinPlot", contains="RedDimPlot")

#' The reduced dimension hexbin plot panel
#'
#' Plots reduced dimensions summarizing points into hexagon bins.
#'
#' @section Constructor:
#' \code{RedDimHexbinPlot()} creates an instance of a RedDimHexbinPlot class.
#'
#' @author Kevin Rue

kevinrue

cloneRepo <- function(from, to) {
    repoFiles <- list.files(cloneSourceFolder, all.files = TRUE, include.dirs = TRUE)
    repoFiles <- setdiff(repoFiles, c(".", "..", ".git"))
    dir.create(to, recursive = TRUE)
    for (rootFile in repoFiles) {
        message(rootFile)
        file.copy(
            from = file.path(from, rootFile),
            to = file.path(to),
            recursive = TRUE, overwrite = TRUE)

kevinrue

#!/bin/bash

original_path=$(pwd)

source_path="/Users/kevin/git/kevinrue.github.io-academic"
site_path="/Users/kevin/git/kevinrue.github.io"

echo_eval () {
  echo "> $1"
  eval "$1"

kevinrue

library(scRNAseq)
data(allen)
class(allen)

# Example data ----

library(scater)
sce <- as(allen, "SingleCellExperiment")
counts(sce) <- assay(sce, "tophat_counts")
sce <- normalize(sce)

kevinrue

clonePackageSource <- function(from, to, ignore=c(".git")) {
    unisetRootFiles <- list.files(cloneSourceFolder, all.files = TRUE, include.dirs = TRUE)
    unisetRootFiles <- setdiff(unisetRootFiles, c(".", "..", ".git"))
    dir.create(cloneDestinationFolder, recursive = TRUE)
    for (rootFile in unisetRootFiles) {
        message(rootFile)
        file.copy(
            from = file.path(cloneSourceFolder, rootFile),
            to = file.path(cloneDestinationFolder),
            recursive = TRUE, overwrite = TRUE)

kevinrue

---
title: "Proportion of cells matching signatures"
author: "Kevin Rue-Albrecht"
date: "24/11/2018"
output: html_document
editor_options: 
  chunk_output_type: console
---

```{r setup, include=FALSE}