Kamil Slowikowski slowkow

🐄

moooooo

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

slowkow / NeedlemanWunsch.png

Last active July 26, 2024 03:22

Plot the score matrix from a Needleman-Wunsch pairwise sequence alignment

slowkow / bioijobs.html

Last active March 7, 2023 01:12

View bioinformatics.org job listings on a Google map

	<!-- saved from url=(0093)http://www.bioinformatics.org/jobs/index.php?group_id=101&show=archives&offset=1680&length=24 -->
	<html style="zoom: 100%; "><style>#bitly_expanded_container {
	position:absolute;

	/* round the corners */
	bottom:1px;
	z-index:5000;
	/* width:100%;*/
	left:0px;
	display:none;

slowkow / query_ncbi.pl

Created March 24, 2011 06:27

Query any NCBI database (nucleotide, protein, nucgss, etc.) and retrieve resulting records.

	#!/usr/bin/perl
	# Author : Kamil Slowikowski <[email protected]>
	# Date : March 23, 2011
	# Version : 0.1
	# Description : Modified code from
	# http://www.bioperl.org/wiki/HOWTO:EUtilities_Cookbook

	use strict;
	use warnings;

slowkow / merge_intervals.py

Last active December 13, 2015 19:39

Python snippet: mimic the command `bedtools merge`

	#!/usr/bin/env python

	"""merge_intervals.py

	Merge tab-delimited intervals:

	cat tissue1.txt
	chr1,1-2
	chr1,3-4
	chr1,5-6

slowkow / ncbi_fetch.py

Created February 21, 2013 19:58

Query any NCBI database and retrieve batches of records as gzip archives

	#!/usr/bin/env python

	"""ncbi_fetch.py

	Query NCBI and fetch the results into gzipped files. Files will be saved in
	the current directory as: 001-050.gz, 051-100.gz, etc.

	You can then do:

	zcat 001-050.gz \| head

slowkow / barplot_heatmap.png

Last active April 15, 2023 19:24

Plot a horizontal bar plot and the lower triangle of a heatmap aligned at the base of the bars

slowkow / genomic_intervals.py

Last active December 20, 2015 18:59

Genomic intervals: 0-based, 1-based, overlaps, and distance

	"""
	genomic_intervals.py
	Kamil Slowikowski
	February 27, 2014

	Genomic intervals: 0-based, 1-based, overlaps, and distance
	===========================================================

	This document describes genomic intervals and includes source code for testing
	overlap and calculating distance between intervals.

slowkow / VCF.py

Last active May 29, 2024 13:57

VCF.py is a simple module for reading VCF files

	"""
	VCF.py
	Kamil Slowikowski
	October 30, 2013

	Read VCF files. Works with gzip compressed files and pandas.

	Note: This module ignores the genotype columns because
	I didn't need them at the time of writing.

slowkow / chromtree.py

Last active December 26, 2015 22:08

Python snippet: one interval tree for each chromosome

	"""
	chromtree.py
	Kamil Slowikowski
	October 30, 2013

	This module is a simple extension of

	bx.intervals.intersection.IntervalTree

	to neatly handle a dictionary of interval trees.

slowkow / GTF.py

Last active March 6, 2024 02:05

GTF.py is a simple module for reading GTF and GFF files

	#!/usr/bin/env python
	"""
	GTF.py
	Kamil Slowikowski
	December 24, 2013

	Read GFF/GTF files. Works with gzip compressed files and pandas.

	http://useast.ensembl.org/info/website/upload/gff.html