Skip to content

Instantly share code, notes, and snippets.

View jdblischak's full-sized avatar

John Blischak jdblischak

View GitHub Profile
@brenopolanski
brenopolanski / merge-pdf-ghostscript.md
Last active April 25, 2025 03:15
Merge multiple PDFs using Ghostscript

A simple Ghostscript command to merge two PDFs in a single file is shown below:

gs -dNOPAUSE -sDEVICE=pdfwrite -sOUTPUTFILE=combine.pdf -dBATCH 1.pdf 2.pdf

Install Ghostscript:

Type the command sudo apt-get install ghostscript to download and install the ghostscript package and all of the packages it depends on.

@MonkmanMH
MonkmanMH / gist:3c0da6afd58eb61e2c51
Last active August 29, 2015 14:04
dplyr testing and goofing
#
# setwd("D:/R_the software/datatrials/Lahman")
#
require(Lahman)
require(dplyr)
#
# throwing by position
# version 1 - "merge"
MasterFielding <- data.frame(merge(Master, Fielding, by="playerID"))
MasterFielding <- merge(Master, Fielding, by="playerID")
@derhuerst
derhuerst / intro.md
Last active May 15, 2025 23:57
Installing Git on Linux, Mac OS X and Windows

Guidelines for contribution

This document described guidelines for contributions for projects led by members of the [Poisot lab of computational ecology][pl], Université de Montréal. It should be followed by lab members (at all times), as well as people with suggested added features, or willing to contribute enhancement or bug fixes.

Authorship

Any contribution to the code of a software grants authorship on the next paper

Starting at the beginning:

Let's just assume you're using an Ubuntu-ish distro of Linux. In some ways that makes this a little more complicated, but on the other hand, it lets me assume you have experience with other package managers. So the big thing here is that conda is it's own little scientific apt-get (python packages, GIS tools, R + R packages, gcc, etc) that goes off and builds sandboxes contained in individual rooms. Then there's pip. Pip is specifically for python packages only and in my opinion, should only be used when the conda package isn't available.

Back to conda: conda is a package manager that depends on python, but is not per se an installation of python. So:

@BCasal
BCasal / Colaborar Proyecto GitHub.markdown
Last active April 7, 2025 11:45
Pasos a seguir para colaborar en un proyecto de GitHub

Cómo colaborar en un proyecto en GitHub

  • Fork del repositorio
  • Clonar el repositorio
  • Actualizar la rama master
  • Crear una rama
  • Hacer los cambios
  • Hacer un Pull Request

Fork del repositorio

@maxim
maxim / gh-dl-release
Last active May 13, 2025 00:14
Download assets from private Github releases
#!/usr/bin/env bash
#
# gh-dl-release! It works!
#
# This script downloads an asset from latest or specific Github release of a
# private repo. Feel free to extract more of the variables into command line
# parameters.
#
# PREREQUISITES
#
@joepie91
joepie91 / vpn.md
Last active May 20, 2025 14:11
Don't use VPN services.

Don't use VPN services.

No, seriously, don't. You're probably reading this because you've asked what VPN service to use, and this is the answer.

Note: The content in this post does not apply to using VPN for their intended purpose; that is, as a virtual private (internal) network. It only applies to using it as a glorified proxy, which is what every third-party "VPN provider" does.

  • A Russian translation of this article can be found here, contributed by Timur Demin.
  • A Turkish translation can be found here, contributed by agyild.
  • There's also this article about VPN services, which is honestly better written (and has more cat pictures!) than my article.
@slowkow
slowkow / counts_to_tpm.R
Last active March 30, 2025 15:36
Convert read counts to transcripts per million (TPM).
#' 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.
@briandk
briandk / rmarkdown.yml
Created March 21, 2016 01:31
Default YAML block for RMarkdown Manuscripts
title: "[Title Goes Here]"
author: "[Blinded for Review]"
documentclass: "article"
output:
pdf_document:
keep_tex: true
number_sections: true
highlight: "tango"
toc: true
md_extensions: +implicit_figures +grid_tables +fenced_code_blocks +fenced_code_attributes