View CB2bam.sh
BAM=$1 | |
SAM=${BAM%.bam}.sam | |
BAMCB=${BAM%.bam}.CB.bam | |
BAMCBSORT=${BAM%.bam}.CB.sorted.bam | |
BAMNFR=${BAM%%.bam}.CB.NFR.bam | |
BAMNFRSORT=${BAM%%.bam}.CB.NFR.sorted.bam | |
FRAGMENTS=${BAMNFRSORT%.bam}.fragments | |
NCORES=$2 | |
echo "Adding CB tag to" $BAM |
View comparison_app.R
# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # | |
# GLOBAL # | |
# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # | |
if (!require(shiny)) install.packages("shiny") | |
if (!require(shinydashboard)) install.packages("shinydashboard") | |
require(shiny) | |
require(shinydashboard) | |
require(stringr) | |
require(data.table) |
View lastexport.py
#!/usr/bin/env python | |
#-*- coding: utf-8 -*- | |
# This program is free software: you can redistribute it and/or modify | |
# it under the terms of the GNU General Public License as published by | |
# the Free Software Foundation, either version 3 of the License, or | |
# (at your option) any later version. | |
# | |
# This program is distributed in the hope that it will be useful, | |
# but WITHOUT ANY WARRANTY; without even the implied warranty of |
View eutilPMIDcitations.sh
#!/bin/bash | |
# find interesting articles PMIDs | |
db='pubmed' | |
query='Metagenome[mesh]+AND+Gastrointestinal+Microbiome[mesh]+AND+2008:2018[pdat]+AND+Journal+Article[ptyp]' | |
base='https://eutils.ncbi.nlm.nih.gov/entrez/eutils/' | |
url=$base"esearch.fcgi?db=$db&term=$query&retmax=100000" | |
curl $url -g -o esearch_pmid.xml | |
# save list of PMIDs to a text file |
View data.R
require(shiny) | |
require(shinydashboard) | |
require(data.table) | |
require(ggplot2) | |
require(ggpubr) | |
require(stringr) | |
require(DT) | |
require(kableExtra) | |
require(knitr) | |
require(plotly) |