klprint’s gists

klprint / app.R

Last active October 6, 2021 20:19

Bundestagswahl 2021 Wahlkreise: Ergebnisse und Strukturdaten

	library(shiny)
	library(tidyverse)

	if(!require(plotly)){
	install.packages("plotly")
	}
	if(!require(viridis)){
	install.packages("viridis")
	}

klprint / hum3d.html

Last active November 11, 2020 07:32

3dembs

This file has been truncated, but you can view the full file.

	<!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 \|\| {};

klprint / sce_helper.R

Created September 28, 2020 13:21

	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")

klprint / sce_functions.R

Created March 6, 2020 13:20

	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")

klprint / keybase.md

Created January 31, 2020 09:41

Keybase proof

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:

klprint / single_cell_functions.R

Last active January 30, 2020 12:45

Widely used single cell functions in R

	# 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]]

klprint / explore_seurat.R

Last active November 28, 2018 09:31

	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>",

klprint / parse_10x_output.sh

Created June 4, 2018 11:53

Parse a 10x chromium sparse matrix output into a single file, inserting the ENSEMBL gene ID and the cell barcode

	#!/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

klprint / TMHMM_parser.py

Last active December 14, 2016 12:20

This script parses TMHMM short output to a full-length topology output.

	#################################################################
	######################## TMHMM Parser ###########################
	#################################################################

	# Created by: Kevin Leiss
	# Last Updated: 14.12.2016
	#
	# License: Feel free to use the script, but please refer to me if
	# you used it for publication.
	#

klprint / check_file.py

Created September 30, 2016 08:59

This python function checks whether a file exists. If not, the function waits for a user specified time and checks again. As soon as the file appears, a reaction can be specified. A log is written while the function runs to inform the user about the current status.

	def check_output(file, interval_time, logfile_path):
	import os
	import time

	status = os.path.isfile(file)


	while status is not True:
	f_log = open(logfile_path, 'a')
	f_log.write(time.asctime() + '\t' + 'Still running\n')

Kevin klprint

Keybase proof