jdblischak

# HGEN 473 - Genomics
# Spring 2017
# Tuesday, May 9 & Thursday, May 11
#
# RNA-seq analysis with R/Bioconductor
#
# John Blischak
#
# Last updated: 2020-04-08

rccordell

# This script builds on Aleszu Bajak's excellent 
# [tutorial on building a course website using R Markdown and Github pages](http://www.storybench.org/convert-google-doc-rmarkdown-publish-github-pages/). 
# I was excited about the concept but wanted to automate a few of the production steps: namely generating the HTML files 
# for the site from the RMD pages (which Aleszu describes doing one-by-one) and generating the site navigation menu, 
# which Aleszu handcodes in the `_site.yml` file. This script should automate both processes, though it may have some quirks 
# unique to my setup that you'd want to tweak to fit your own. It's likely more loquacious than necessary as well, so feel free 
# to condense as you can. Ideally, each time you make updates to your RMD files you can run this script to generate updated HTML 
# pages and a new `_site.yml`. Then commit changes to Github and you're up and running!

# Once you've got everything configured for your own site below, you should be able to run `source('rend

benmarwick

# Adapted from https://stackoverflow.com/a/7267364/1036500 by Andrie de Vries

# This is it: theme(axis.text.x = element_text(angle = 90, hjust = 1, vjust = 0.5))

library(ggplot2)

td <- expand.grid(
  hjust=c(0, 0.5, 1),
  vjust=c(0, 0.5, 1),
  angle=c(0, 45, 90),

dylanjm

library(tidyverse)
library(rio)
library(rvest)
library(janitor)


# Rcode to go and fetch country codes
country_codes <- read_html("http://web.stanford.edu/~chadj/countrycodes6.3") %>% 
  html_text() %>% 
  str_extract_all("[A-Z]{3}") %>% 

ColinFay

snippet module
	${1:name}UI <- function(id){
		ns <- NS(id)
		tagList(
		
		)
	}

	${1:name} <- function(input, output, session){
	

hiraksarkar

## requirement bed tools
BIN='/home/hirak/bedtools2/bin'
## Gencode 
## gencode.v29.chr_patch_hapl_scaff.annotation.gtf
GTF_FILE="gencode.v29.chr_patch_hapl_scaff.annotation.gtf"

# extract transcript boundaries 
cat $GTF_FILE | awk 'BEGIN{OFS="\t";} $3=="transcript" {print $1,$4-1,$5,$12}' | tr -d "\"" | tr -d ";" | $BIN/sortBed > gencode_transcript_intervals.bed

# merge exon boundaris 

toniher

#!/bin/bash

# Based on https://github.com/sylabs/singularity/issues/1537
# Usage: bash docker2singularity.sh mydockerimg mysingularity.simg

set -ueo pipefail

IMG=$1
FILEOUT=$2
PORT=${3:-5000}

hannes-brt

# Copyright 2019 Hannes Bretschneider
# 
# Permission is hereby granted, free of charge, to any person
# obtaining a copy of this software and associated documentation
# files (the "Software"), to deal in the Software without
# restriction, including without limitation the rights to use,
# copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the
# Software is furnished to do so, subject to the following
# conditions:

mikelove

RUNS, = glob_wildcards("fastq/{run}_1.fastq.gz")

SALMON = "/proj/milovelab/bin/salmon-1.4.0_linux_x86_64/bin/salmon"

ANNO = "/proj/milovelab/anno"

rule all:
    input: expand("quants/{run}/quant.sf", run=RUNS)

rule salmon_index:

upkarlidder

Deep Learning Hands-On Series with Eric Schles

05/22 - Deep Learning Hands-On Series - Data Exploration and API First Design 🎥

05/29 - Deep Learning Hands-On Series - Model Tuning 🎥

06/05 - Deep Learning Hands-On Series - Monitoring [cancelled]

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