slowkow

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',

slowkow

#!/usr/bin/bash
#$ -N MY_JOB_NAME
#$ -o /path/on/broad/server/
#$ -e /path/on/broad/server/
#$ -cwd
#$ -j y
#$ -l h_rt=12:00:00
#$ -pe smp 8 -R y -binding linear:8
#$ -l h_vmem=2G
#

slowkow

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:

slowkow

#!/usr/bin/env python3
# pay-water-bill.py
# 2021-05-02

"""
Pay your water bill in Baltimore City
=====================================

Steps:

slowkow

#!/usr/bin/env python
"""
montage.py
2020-12-23
Kamil Slowikowski

Usage
-----

Write montage.png from a list of PDF files, each panel 500px wide:

slowkow

#!/usr/bin/env Rscript
# rsa-example.R
#
# Inspired by Alex Van de Sande
# https://twitter.com/avsa/status/1318672796415819776

last_digit <- function(x) {
  x_char <- as.character(x)
  as.numeric(substr(x_char, nchar(x_char), nchar(x_char)))
}

slowkow

slowkow

#' @param x A sparse matrix from the Matrix package.
#' @param file A filename that ends in ".gz".
writeMMgz <- function(x, file) {
  mtype <- "real"
  if (is(x, "ngCMatrix")) {
    mtype <- "integer"
  }
  writeLines(
    c(
      sprintf("%%%%MatrixMarket matrix coordinate %s general", mtype),

slowkow

#!/usr/bin/env python
"""
The Needleman-Wunsch Algorithm
==============================

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

Example
-------

slowkow

# 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"
)