klprint’s gists

klprint / R_Functions.R

Last active December 20, 2016 10:20

	# 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)
	}

klprint / gist:5b10ff18c91f26d890631a8780faffe1

Created August 1, 2016 07:12 — forked from fajrif/gist:1265203

git clone specific tag

	git clone <repo-address>

	git tag -l

	git checkout <tag-name>

	git branch -D master

	git checkout -b master

klprint / ChangeChmod.txt

Created August 1, 2016 08:18

Change chmod for folder & all subfolders

	# 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 {} \;

klprint / ChangeChmod.txt

Created August 1, 2016 08:18

Change chmod for folder & all subfolders

	# 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 {} \;

klprint / FastGrep.py

Created August 9, 2016 10:39

Searches in files with the same extension for sequences being provided by a fasta file. The script picks 15-16 base-pairs in the middle of each sequence in the fasta file and uses grep to find the number of occurrences.

	import subprocess
	import glob

	# Functions

	def read_multifasta(file_path):

	is_entry = False
	fasta_dict = {}
	sequence = []

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')

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 / 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 / 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 / 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]]

Kevin klprint