mikelove

#!/bin/bash
for p in DESeq2 apeglm tximport; do
    echo "----- syncing $p -----";
    cd $p/github/$p
    git pull
    git fetch --all
    git merge upstream/master
    git push
    cd ../../..
done;

mikelove

library(shiny)
ui <- fluidPage(mainPanel(
  plotOutput("plot1", click="plot_click"),
  plotOutput("plot2")
))
server <- function(input, output) {
  output$plot1 <- renderPlot({
    plot(x,y)
  })
  output$plot2 <- renderPlot({

mikelove

library(shiny)
library(ggplot2)
ui <- fluidPage(mainPanel(
  plotOutput("plot1", click="plot_click")
))
server <- function(input, output) {
  selected <- reactive({
    near <- nearPoints(dat,input$plot_click,maxpoints=1,"x","y",threshold=20)
    if (nrow(near) > 0) {
      selected_points <<- near

mikelove

suppressPackageStartupMessages(library(plyranges))
suppressPackageStartupMessages(library(AnnotationHub))
suppressPackageStartupMessages(library(TxDb.Hsapiens.UCSC.hg19.knownGene))

ah <- AnnotationHub()
query(ah, c("K562","CTCF","unipk"))
peaks <- ah[["AH22543"]]
peaks <- peaks %>% keepStandardChromosomes(pruning.mode="coarse")

txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene

mikelove

library(hexSticker)
library(rafalib)
e <- expression({
  nullplot(bty="n",xaxt="n",yaxt="n")
  text(.5,.5,"⇲",cex=15,col="white")
})
set.seed(1)
sticker(e, p_size=24,
        s_x=.8, s_y=.6, s_width=.2, s_height=.2,
        url="www.bioconductor.org", u_color="white", u_size=4.5,

mikelove

sudo apt install sra-toolkit
fastq-dump -X 1000000 --split-files SRR1039508

mikelove

library(DEXSeq)
alpha1 <- .1
alpha2 <- .01
ngene <- 5000
sig.ratio <- .1
niso <- 5
set.seed(1)
fdr <- replicate(100, {
  gene <- factor(rep(1:ngene,each=niso))
  pval <- runif(ngene*niso)

mikelove

dir <- system.file("extdata/salmon", package="tximportData")
ids <- list.files(dir)

# here gzipped, normally these are not
files <- file.path(dir, ids, "quant.sf.gz") 
file.exists(files)

coldata <- data.frame(files, names=ids, population="TSI", stringsAsFactors=FALSE)

library(tximeta)

mikelove

# this is using SummarizedExperiment v1.11.5
suppressPackageStartupMessages(library(SummarizedExperiment))
m <- matrix(1:20, nrow=5, ncol=4, dimnames=list(letters[1:5], LETTERS[1:4]))

# this gives an error, good.
rowdata <- data.frame(x=1:5, row.names=letters[5:1])
se <- SummarizedExperiment(m, rowData=rowdata)

# build the right way
rowdata <- data.frame(x=1:5, row.names=letters[1:5])

mikelove

# load the SummarizedExperiment object but don't load SummarizedExperiment
rowdata <- attr(se,"rowData")
save(rowdata, file="rowdata.rda")
#coldata <- attr(se,"colData")
#save(coldata, file="coldata.rda")
counts <- get("data",attr(attr(se,"assays"),".xData"))$counts
save(counts, file="counts.rda")

# restart R
load("rowdata.rda")