Kamil Slowikowski slowkow

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moooooo

Computational biologist. Using transcriptomics to learn about inflammation and cancer.

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slowkow / hg19.rRNA.interval_list

Last active April 9, 2023 14:56

Make a ribosomal RNA interval_list for Picard Tools CollectRnaSeqMetrics

	@SQ SN:chrM LN:16571
	@SQ SN:chr1 LN:249250621
	@SQ SN:chr2 LN:243199373
	@SQ SN:chr3 LN:198022430
	@SQ SN:chr4 LN:191154276
	@SQ SN:chr5 LN:180915260
	@SQ SN:chr6 LN:171115067
	@SQ SN:chr7 LN:159138663
	@SQ SN:chr8 LN:146364022
	@SQ SN:chr9 LN:141213431

slowkow / bash-cheatsheet.md

Last active January 19, 2022 10:47

Bash cheatsheet

Regular expression matching:

a=foobar
[[ "$a" =~ "^foo" ]] && echo "matches ^foo"

Array from a glob:

slowkow / fix_alleles.py

Last active July 27, 2016 13:27

Join multiple PLINK dosage files into one file.

	#!/usr/bin/env python
	"""
	Kamil Slowikowski

	fix_alleles.py
	==============

	Change the alleles in a dosage file to match the alleles specified in
	a separate reference file. If a variant is not present in the reference file,
	then it will not be changed.

slowkow / mygene.html

Last active August 29, 2015 14:07

Autocomplete genes with mygene.info and typeahead.js http://slowkow.com/2014/10/05/geneinfo-typeahead/

	<!DOCTYPE HTML>
	<html>

	<head>

	<meta http-equiv="Content-Type" content="text/html; charset=utf-8">

	<script src="//ajax.googleapis.com/ajax/libs/jquery/1.11.1/jquery.min.js"></script>
	<script type="text/javascript" src="js/typeahead.bundle.min.js"></script>

slowkow / phred.md

Last active August 29, 2015 14:06

Illumina v1.8+ Phred base quality scores. https://plot.ly/~slowkow/2/

P is the probability of a base-call error.

Q	P	Symbol	ASCII
1	0.79433	"	34
2	0.63096	#	35
3	0.50119	$	36
4	0.39811	%	37
5	0.31623	&	38
6	0.25119	'	39

slowkow / rnaseq-notes.md

Last active August 29, 2015 14:06

RNA-seq notes

RNA-Seq Notes

This document summarizes some of the distinguishing features of tools used to analyze RNA-Seq data.

Aligners:

slowkow / connect-to-vpn.applescript

Last active March 11, 2022 16:24

Connect to VPN and type your password automatically

	on ButtonClick(theObjectID)
	tell application "System Events"
	repeat until exists theObjectID
	delay 0.5
	end repeat
	click theObjectID
	end tell
	end ButtonClick

	set targetApp to "Cisco AnyConnect Secure Mobility Client"

slowkow / notify-toggle.sh

Last active August 15, 2017 08:18

Toggle notify-osd notifications, optionally toggle sound

	#!/usr/bin/env bash
	# notify-toggle.sh
	# Kamil Slowikowski
	# May 31, 2014
	#
	# Toggle libnotify notification bubbles that appear in the top-right corner
	# of your screen.
	# You can uncomment some lines to mute and unmute sound, too.
	#
	# Works on:

slowkow / Binomial-Probability-Mass-Function_Speed-Comparison.ipynb

Last active January 4, 2021 21:41

Implementations of the Binomial PMF in sympy, scipy, numpy, python, GSL, and C http://nbviewer.ipython.org/11504548

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slowkow / mycd.sh

Last active September 8, 2015 15:55 — forked from leipzig/mycd.sh

Record folder-specific history in `.dir_bash_history`

	function cd_dir_history()
	{
	OLDPWD="$PWD"
	echo "# $(date) $USER -> $@" >> "$HISTFILE"

	command cd "$@"

	# If this directory is writable then write to directory-based history file
	# otherwise write history in the usual home-based history file.
	touch "$PWD/.dir_bash_history" 2>/dev/null \

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