I hereby claim:
- I am klprint on github.
- I am subfish (https://keybase.io/subfish) on keybase.
- I have a public key ASB7mGynrtArFJP7l3XxhFVDHk4Yxr5JqkMl_9mFEjPVMwo
To claim this, I am signing this object:
library(shiny) | |
library(tidyverse) | |
if(!require(plotly)){ | |
install.packages("plotly") | |
} | |
if(!require(viridis)){ | |
install.packages("viridis") | |
} |
<!DOCTYPE html> | |
<html> | |
<head> | |
<meta charset="utf-8" /> | |
<style>body{background-color:white;}</style> | |
<script>(function() { | |
// If window.HTMLWidgets is already defined, then use it; otherwise create a | |
// new object. This allows preceding code to set options that affect the | |
// initialization process (though none currently exist). | |
window.HTMLWidgets = window.HTMLWidgets || {}; |
library(hdf5r) | |
library(Matrix) | |
source("https://gist.githubusercontent.com/klprint/1ab4468eb3c54abcf0422dec6223b8fc/raw/b4cc33f5b4da25bcc2e678cf46b692fe67605460/single_cell_functions.R") | |
library(SingleCellExperiment) | |
library(tidyverse) | |
library(liger) | |
sce.raw.pca <- function(sce, k = 100){ | |
umi <- assay(sce, "umi") | |
library(hdf5r) | |
library(Matrix) | |
source("https://gist.githubusercontent.com/klprint/1ab4468eb3c54abcf0422dec6223b8fc/raw/b4cc33f5b4da25bcc2e678cf46b692fe67605460/single_cell_functions.R") | |
library(SingleCellExperiment) | |
library(tidyverse) | |
sce.raw.pca <- function(sce, k = 100){ | |
umi <- assay(sce, "umi") | |
cat("Getting informative genes\n") |
I hereby claim:
To claim this, I am signing this object:
# Taken from Simon | |
# compute variances across column or rows for column-sparse matrices | |
library(Matrix) | |
colVars_spm <- function( spm ) { | |
stopifnot( is( spm, "dgCMatrix" ) ) | |
ans <- sapply( seq.int(spm@Dim[2]), function(j) { | |
mean <- sum( spm@x[ (spm@p[j]+1):spm@p[j+1] ] ) / spm@Dim[1] | |
sum( ( spm@x[ (spm@p[j]+1):spm@p[j+1] ] - mean )^2 ) + | |
mean^2 * ( spm@Dim[1] - ( spm@p[j+1] - spm@p[j] ) ) } ) / ( spm@Dim[1] - 1 ) | |
names(ans) <- spm@Dimnames[[2]] |
library(rlc) | |
library(matrixStats) | |
library(biomaRt) | |
library(Matrix) | |
library(umap) | |
#sobj <- readRDS("make_analysis_out/SN010_E115/SN010_E115_normalized.rds") | |
makeENSMEBLlink <- function(geneID){ | |
sprintf( | |
"<a href='http://www.ensembl.org/Mus_musculus/Gene/Summary?db=core;g=%s' target='_blank'>%s</a>", |
#!/bin/bash | |
# The following script parses the 10x chromoium sparse matrix. | |
# It replaces the First column with the ENSEMBL gene ID and the second, | |
# if needed, with the cell barcode (just uncomment the second awk script). | |
# It needs the three 10x chromium outputs as follows: | |
# 1. genes.tsv | |
# 2. matrix.mtx | |
# 3. barcodes.tsv |
# Sets chmod 755 for folder and all subfolders | |
find /opt/lampp/htdocs -type d -exec chmod 755 {} \; | |
# Sets chmod 655 for all files in this folder & subfolder | |
find /opt/lampp/htdocs -type f -exec chmod 644 {} \; |
# Analyse data using a sliding window | |
slideFunct <- function(data, window, step){ | |
total <- length(data) | |
spots <- seq(from=1, to=(total-window), by=step) | |
result <- vector(length = length(spots)) | |
for(i in 1:length(spots)){ | |
result[i] <- median(data[spots[i]:(spots[i]+window)]) | |
} | |
return(result) | |
} |