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Kevin klprint

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View hum3d.html
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<!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).
View sce_helper.R
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")
View sce_functions.R
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")
View keybase.md

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
klprint / single_cell_functions.R
Last active Jan 30, 2020
Widely used single cell functions in R
View single_cell_functions.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]]
View explore_seurat.R
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
klprint / parse_10x_output.sh
Created Jun 4, 2018
Parse a 10x chromium sparse matrix output into a single file, inserting the ENSEMBL gene ID and the cell barcode
View parse_10x_output.sh
#!/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
klprint / TMHMM_parser.py
Last active Dec 14, 2016
This script parses TMHMM short output to a full-length topology output.
View TMHMM_parser.py
#################################################################
######################## 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
klprint / check_file.py
Created Sep 30, 2016
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.
View check_file.py
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
klprint / FastGrep.py
Created Aug 9, 2016
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.
View FastGrep.py
import subprocess
import glob
# Functions
def read_multifasta(file_path):
is_entry = False
fasta_dict = {}
sequence = []
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