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@anamariaelek
anamariaelek / data.R
Last active Jan 16, 2020
Nanopore sequencing summary
View data.R
require(shiny)
require(shinydashboard)
require(data.table)
require(ggplot2)
require(ggpubr)
require(stringr)
require(DT)
require(kableExtra)
require(knitr)
require(plotly)
@anamariaelek
anamariaelek / eutilPMIDcitations.sh
Created Dec 3, 2018
E-utilities pipeline for exploration and retrieval of PubMed citations
View eutilPMIDcitations.sh
#!/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
anamariaelek / lastexport.py
Created Feb 1, 2019 — forked from bitmorse/lastexport.py
lastfm scrobble exporter (from https://gitorious.org/fmthings/lasttolibre/blobs/master/lastexport.py // changed the script to try more often on failure )
View lastexport.py
#!/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
anamariaelek / comparison_app.R
Last active Apr 16, 2019
comparisons for GSEA
View comparison_app.R
# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
# GLOBAL #
# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
if (!require(shiny)) install.packages("shiny")
if (!require(shinydashboard)) install.packages("shinydashboard")
require(shiny)
require(shinydashboard)
require(stringr)
require(data.table)
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