wckdouglas

#!/usr/bin/env Rscript

args = commandArgs(trailingOnly=TRUE)
if (length(args)<1) {
      stop("A Rmarkdown file has to be specified\n", call.=FALSE)
} else if (length(args)>0) {
      # default output file
      markdownFile = args[1]
    for (markdownFile in args){
        rmarkdown::render(markdownFile)

wckdouglas

#!/bin/env python

import bibtexparser
import argparse
import sys
import re
from bibtexparser.bibdatabase import BibDatabase
from bibtexparser.bwriter import BibTexWriter

def modifiedTitle(title):

wckdouglas

#!/bin/env Rscript

library(RMySQL)
library(dplyr)
library(stringr)
library(readr)

conn <- dbConnect(MySQL(),
                user='genome',
                dbname='hg38',

wckdouglas

#!/bin/bash

BAMPATH=.
RESULTPATH=.
GENESFILE=allRegions.SAF
STRANDENESS=1
THREADS=20

featureCounts -a $GENESFILE -F SAF  \
            -o /dev/stdout -O -s $STRANDENESS -Q 5 \

wckdouglas

#!/bin/env Rscript

library(readr)
library(DESeq2)
library(BiocParallel)
library(dplyr)
library(stringr)
library(tidyr)
library(cowplot)
library(ggrepel)

wckdouglas

#!/bin/bash


if ! [ -x $(command -v conda) ] 
then 
  echo Conda not installed in PATH 
  exit
else
  if ! [ -x $(command -v pip) ]
  then 

wckdouglas

set guioptions=T 
colorscheme onedark

let g:airline#extensions#tabline#enabled = 1
let g:airline_theme='onedark'
set laststatus=2


"tab 
noremap <D-1> :tabn 1<CR>

wckdouglas

#!/bin/bash

#install pathogen
mkdir -p ~/.vim/autoload ~/.vim/bundle && \
	curl -LSso ~/.vim/autoload/pathogen.vim https://tpo.pe/pathogen.vim

echo '
execute pathogen#infect()
syntax on
filetype plugin indent on

wckdouglas

# This file may be used to create an environment using:
# $ conda create --name <env> --file <this file>
# platform: linux-64
backports=1.0=py27_0
backports_abc=0.4=py27_0
bamtools=2.4.0=3
bcftools=1.3=0
bedops=2.4.19=0
bedtools=2.25.0=1
bioconductor-annotationdbi=1.32.3=0

wckdouglas

{
	"filters":[
		{ "id":"firstPairForward",
			"alignmentFlag" : "99" },
		{"id":"firstPairReverse",
			"alignmentFlag" : "83"},
		{"id":"secondPairForward",
			"alignmentFlag" : "163"},
		{"id":"secondPairReverse",
			"alignmentFlag" : "147"}