atomashevic

Run R code in ZED

Tested using Zed 0.144.4 on Ubuntu 22.04.4 LTS.

1. Download the Ark R kernel 0.1.117
2. Run the binary: ark --install
3. Run jupyter-kernelspec list and find the path to ARK kernel
4. Open ZED and install R Extension
5. Open ZED and edit settings and insert the following code (update the exact path to Ark)

krisleech

Renew GPG key

Given that your key has expired.

$ gpg --list-keys
$ gpg --edit-key KEYID

Use the expire command to set a new expire date:

rnwolf

spacemacs-keybindings

Ref: https://gist.github.com/rnwolf/e09ae9ad6d3ac759767d129d52cab1f1

Key Binding	Description
SPC	< space >
RET	< return >
C	< ctrl >
M	< alt >, M stands for Meta

slavailn

library("ChIPpeakAnno")
library("GenomicRanges")
library("org.At.tair.db")
library("TxDb.Athaliana.BioMart.plantsmart28")
library("biomaRt")

# Annotate genomic intervals in bed format using ChIPpeakAnno 
# This script was designed for Arabidopsis, but can be easily changed for
# any other organism available through biomaRt

soxofaan

pretty_csv/pretty_tsv

These are some simple bash functions and scripts for making CSV/TSV files prettier on the command line

see http://stefaanlippens.net/pretty-csv.html for more information.

andrewparkermorgan

# rnaseq.R
# plots related to RNAseq data

library(GenomicAlignments)
library(GenomicRanges)
library(ggplot2)
library(grid)
#library(gtable) # for combining plots vertically

#' Make a 'sashimi plot': coverage plus splice events

wizioo

How to have specific .gitignore for each git branch

Objective

My objective is to have some production files ignored on specific branches. Git doesn't allow to do it.

Solution

My solution is to make a general .gitignore file and add .gitignore.branch_name files for the branches I want to add specific file exclusion. I'll use post-checkout hook to copy those .gitignore.branch_name in place of .git/info/exclude each time I go to the branch with git checkout branch_name.

uupaa

Image source

https://gyazo.com/eb5c5741b6a9a16c692170a41a49c858.png

Try resize it!

• ![](https://gyazo.com/eb5c5741b6a9a16c692170a41a49c858.png | width=100)

hotoo

#!/usr/bin/env bash

for x
do
  filename=$(echo $x|sed -e "s/\.wiki$/.md/")
  sed -f ex $x > $filename
done

nathanhaigh

#!/bin/bash
# Usage: interleave_fastq.sh f.fastq r.fastq > interleaved.fastq
# 
# Interleaves the reads of two FASTQ files specified on the
# command line and outputs a single FASTQ file of STDOUT.
# 
# Can interleave 100 million paired reads (200 million total
# reads; a 2 x 22Gbyte files), in memory (/dev/shm), in 6m54s (414s)
# 
# Latest code: https://gist.github.com/4544979