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


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

wckdouglas

#!/bin/env Rscript

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

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

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

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

#!/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

{
"mapQuality": ">10",
"isMapped" : "true",
"isMateMapped": "true",
"isPrimaryAlignment": "true",
"isProperPair": "true"
}

wckdouglas

#!/bin/bash

# Script for installing tmux on systems where you don't have root access.
# tmux will be installed in $INSTALLPATH/local/bin.
# It's assumed that wget and a C/C++ compiler are installed.

# exit on error
set -e

INSTALLPATH=$(pwd)

wckdouglas

#/usr/bin/env python

from Bio import SeqIO
import sys

def guessFileType(filename):
    if filename.endswith('fasta') or filename.endswith('fa'):
        fileType = 'fasta'
    elif filename.endswith('fastq') or filename.endswith('fq'):
        fileType = 'fastq'