Kamil Slowikowski slowkow

## 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>

## rotating-3d-mp4.R
library(data.table)
library(glue)
library(rgl)

# https://github.com/google/palette.js/blob/master/palette.js
mpn65 <- c(
  '#ff0029', '#377eb8', '#66a61e', '#984ea3', '#00d2d5', '#ff7f00', '#af8d00',
  '#7f80cd', '#b3e900', '#c42e60', '#a65628', '#f781bf', '#8dd3c7', '#bebada',
  '#fb8072', '#80b1d3', '#fdb462', '#fccde5', '#bc80bd', '#ffed6f', '#c4eaff',
  '#cf8c00', '#1b9e77', '#d95f02', '#e7298a', '#e6ab02', '#a6761d', '#0097ff',

## read_cellranger.R
# install.packages(c("Matrix", "rhdf5", "tidyverse"))
library(Matrix)
library(rhdf5)
library(tidyverse)
library(glue)

my_h5_files <- Sys.glob(
  "path/to/cellranger-per-channel/output/*/filtered_feature_bc_matrix.h5"
)

## 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.

## 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

"""

## install-units.md

      
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                slowkow
                / install-units.md
            
            
              Last active
              September 8, 2024 02:54
            
              
                Install the 'units' R package on Partners
              
          
    Summary

I had a difficult time installing the units R package on the Partners ERIS servers.
I hope this post helps you to figure out how to work around the errors.
Instructions


## rpkm_versus_tpm.R
# RPKM versus TPM
#
# RPKM and TPM are both normalized for library size and gene length.
#
# RPKM is not comparable across different samples.
#
# For more details, see: http://blog.nextgenetics.net/?e=51

rpkm <- function(counts, lengths) {
  rate <- counts / lengths

## plot-umap-experiment.R
library(uwot)
library(scattermore)
library(foreach)
library(doParallel)
library(data.table)
library(ggplot2)
library(scales)
library(glue)

# This code snippet assumes we have these objects:

## Apache www-data setup
sudo mkdir -m 0700  /var/www/.ssh
sudo chown -R www-data:www-data /var/www/.ssh
sudo -u www-data ssh-keygen (empty passphrase)

# On Github, paste public key into "Deploy keys"

sudo -u www-data bash
cd /path/to/repo
git clone ...

## zotero-pdf-program.md

      
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              3 comments
            
          
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                slowkow
                / zotero-pdf-program.md
            
            
              Last active
              August 1, 2024 09:21
            
              
                Open pdfs in Zotero with a different program than your other pdfs
              
          
    I want to open pdf files with program A unless it is stored in Zotero, in which case I want to open it program B.

Change the OS settings, so the default program for opening pdf files is the shell script shown below.
Set Zotero preferences to store files in "zotero-data".

Below, I use playonlinux to launch Foxit Reader for my Zotero pdf files because Foxit has nice highlighting and annotation features that I like to use on scientific articles. I use [evince][4] for all other pdf files (figures, books, documents, etc.)
	<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>
	library(data.table)
	library(glue)
	library(rgl)

	# https://github.com/google/palette.js/blob/master/palette.js
	mpn65 <- c(
	'#ff0029', '#377eb8', '#66a61e', '#984ea3', '#00d2d5', '#ff7f00', '#af8d00',
	'#7f80cd', '#b3e900', '#c42e60', '#a65628', '#f781bf', '#8dd3c7', '#bebada',
	'#fb8072', '#80b1d3', '#fdb462', '#fccde5', '#bc80bd', '#ffed6f', '#c4eaff',
	'#cf8c00', '#1b9e77', '#d95f02', '#e7298a', '#e6ab02', '#a6761d', '#0097ff',
	# install.packages(c("Matrix", "rhdf5", "tidyverse"))
	library(Matrix)
	library(rhdf5)
	library(tidyverse)
	library(glue)

	my_h5_files <- Sys.glob(
	"path/to/cellranger-per-channel/output/*/filtered_feature_bc_matrix.h5"
	)
	#' 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.
	# RPKM versus TPM
	#
	# RPKM and TPM are both normalized for library size and gene length.
	#
	# RPKM is not comparable across different samples.
	#
	# For more details, see: http://blog.nextgenetics.net/?e=51

	rpkm <- function(counts, lengths) {
	rate <- counts / lengths
	library(uwot)
	library(scattermore)
	library(foreach)
	library(doParallel)
	library(data.table)
	library(ggplot2)
	library(scales)
	library(glue)

	# This code snippet assumes we have these objects:
	sudo mkdir -m 0700 /var/www/.ssh
	sudo chown -R www-data:www-data /var/www/.ssh
	sudo -u www-data ssh-keygen (empty passphrase)

	# On Github, paste public key into "Deploy keys"

	sudo -u www-data bash
	cd /path/to/repo
	git clone ...