Kamil Slowikowski slowkow

## ssh-tutorial.md

      
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                slowkow
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                ssh to a server without typing your password
              
          
    How to ssh to a remote server without typing your password

Save yourself a few keystrokes. Follow the steps below:


Run this Bash script on your laptop:
#!/usr/bin/env bash


The hostname of your remote server.


## remove-emoji.py
#!/usr/bin/env python
"""
Remove emoji from a text file and print it to stdout.

Usage
-----

    python remove-emoji.py input.txt > output.txt

"""

## counts_to_tpm.R
#' Convert counts to transcripts per million (TPM).
#'
#' Convert a numeric matrix of features (rows) and conditions (columns) with
#' raw feature counts to transcripts per million.
#'
#'    Lior Pachter. Models for transcript quantification from RNA-Seq.
#'    arXiv:1104.3889v2
#'
#'    Wagner, et al. Measurement of mRNA abundance using RNA-seq data:
#'    RPKM measure is inconsistent among samples. Theory Biosci. 24 July 2012.

## needleman-wunsch.py
#!/usr/bin/env python
"""
The Needleman-Wunsch Algorithm
==============================

This is a dynamic programming algorithm for finding the optimal alignment of
two strings.

Example
-------

## GTF.py
#!/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

## take-screenshot.scpt
-- take-screenshot.scpt
-- Kamil Slowikowski
-- 2025-05-26

-- Get the title of the frontmost application window.
-- https://stackoverflow.com/questions/5292204
global frontApp, frontAppName, windowTitle
set windowTitle to ""
tell application "System Events"
    set frontApp to first application process whose frontmost is true

## coding_lengths.png

      
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                slowkow
                / coding_lengths.png
            
            
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              March 31, 2025 08:04
            
              
                Count the number of coding base pairs in each Gencode gene.
              
          
## barplot_heatmap.png

      
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                slowkow
                / barplot_heatmap.png
            
            
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              February 22, 2025 00:05
            
              
                Plot a horizontal bar plot and the lower triangle of a heatmap aligned at the base of the bars
              
          
## pubmed-publications.html
<!DOCTYPE html>
<body>

<!-- Copied directly from http://www.ephys.org/ by Damian J Williams -->

<input placeholder="Kamil Slowikowski" name="name"/>

<p id="demo"></p>

<script>

## index.html
<html>
  <body>
<a href="karabiner://karabiner/assets/complex_modifications/import?url=https%3A%2F%2Fgist.githubusercontent.com%2Fslowkow%2F275e53573e2aeb60c8304add1e54faf5%2Fraw%2Fc63540925dba76f46293834c24700ebf1578ed10%2Fmouse-buttons-back-forward.json">click here to import into Karabiner-Elements</a>
  </body>
</html>
	#' Convert counts to transcripts per million (TPM).
	#'
	#' Convert a numeric matrix of features (rows) and conditions (columns) with
	#' raw feature counts to transcripts per million.
	#'
	#' Lior Pachter. Models for transcript quantification from RNA-Seq.
	#' arXiv:1104.3889v2
	#'
	#' Wagner, et al. Measurement of mRNA abundance using RNA-seq data:
	#' RPKM measure is inconsistent among samples. Theory Biosci. 24 July 2012.
	#!/usr/bin/env python
	"""
	The Needleman-Wunsch Algorithm
	==============================

	This is a dynamic programming algorithm for finding the optimal alignment of
	two strings.

	Example
	-------
	#!/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
	-- take-screenshot.scpt
	-- Kamil Slowikowski
	-- 2025-05-26

	-- Get the title of the frontmost application window.
	-- https://stackoverflow.com/questions/5292204
	global frontApp, frontAppName, windowTitle
	set windowTitle to ""
	tell application "System Events"
	set frontApp to first application process whose frontmost is true
	<!DOCTYPE html>
	<body>

	<!-- Copied directly from http://www.ephys.org/ by Damian J Williams -->

	<input placeholder="Kamil Slowikowski" name="name"/>

	<p id="demo"></p>

	<script>
	<html>
	<body>
	<a href="karabiner://karabiner/assets/complex_modifications/import?url=https%3A%2F%2Fgist.githubusercontent.com%2Fslowkow%2F275e53573e2aeb60c8304add1e54faf5%2Fraw%2Fc63540925dba76f46293834c24700ebf1578ed10%2Fmouse-buttons-back-forward.json">click here to import into Karabiner-Elements</a>
	</body>
	</html>