anamariaelek

#!/usr/bin/env Rscript

library(data.table)
library(stringr)

# run example:
# Rscript --vanilla hr.R 99,119,139,158,178,198 ACTIVITY.csv

# params:

anamariaelek

require(data.table)
require(stringr)

# GTF TO BED
gtf_to_bed <- function(gtf, feature="transcript", bed_file=NULL) {
  if ("character" %in% class(gtf)) {
    gtf <- fread(gtf)
  } else if ("data.frame" %in% class(gtf)) {
    setDT(gtf)
  }

anamariaelek

#!/bin/bash
#$ -N dg2bw
#$ -cwd
#$ -q long-sl7,mem_512_12h,mem_512
#$ -l virtual_free=50G,h_rt=12:00:00,disk=50G
#$ -o bdg2bw.out
#$ -pe smp 8
#$ -j y

bdg2bw () {

anamariaelek

#!/bin/bash
#$ -N sinto
#$ -cwd
#$ -q long-sl7,mem_512_12h,mem_512
#$ -l virtual_free=50G,h_rt=12:00:00,disk=50G
#$ -M anamaria.elek@crg.eu
#$ -o sinto.out
#$ -pe smp 16
#$ -j y

anamariaelek

#!/bin/bash
#$ -N samtools.count
#$ -cwd
#$ -q long-sl7,mem_512_12h,mem_512
#$ -l virtual_free=50G,h_rt=12:00:00,disk=50G
#$ -M anamaria.elek@crg.eu
#$ -o samtools.count.out
#$ -pe smp 16
#$ -j y

anamariaelek

#!/bin/bash
#$ -N cb
#$ -cwd
#$ -q long-sl7,mem_512_12h,mem_512
#$ -l virtual_free=50G,h_rt=12:00:00,disk=50G
#$ -M anamaria.elek@crg.eu
#$ -o cb.out
#$ -pe smp 16
#$ -j y

anamariaelek

# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
#                           GLOBAL                          # 
# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #  

if (!require(shiny)) install.packages("shiny")
if (!require(shinydashboard)) install.packages("shinydashboard")
require(shiny)
require(shinydashboard)
require(stringr)
require(data.table)

anamariaelek

#!/usr/bin/env python
#-*- coding: utf-8 -*-

# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of

anamariaelek

#!/bin/bash

# find interesting articles PMIDs
db='pubmed'
query='Metagenome[mesh]+AND+Gastrointestinal+Microbiome[mesh]+AND+2008:2018[pdat]+AND+Journal+Article[ptyp]'
base='https://eutils.ncbi.nlm.nih.gov/entrez/eutils/'
url=$base"esearch.fcgi?db=$db&term=$query&retmax=100000"
curl $url -g -o esearch_pmid.xml

# save list of PMIDs to a text file

anamariaelek

require(shiny)
require(shinydashboard)
require(data.table)
require(ggplot2)
require(ggpubr)
require(stringr)
require(DT)
require(kableExtra)
require(knitr)
require(plotly)