kviljoen

library(phyloseq)
library(pheatmap)
library(vegan)
library(ggplot2)
library(corrplot)#for cor.mtest
library(psych)#corr.test
library(matrixStats)#rowSds
library(metagenomeSeq)#differential abundance testing
library(randomForest)
library(dplyr)

shyuep

#!/usr/bin/env python

"""
Script for generating collaborators in a csv file from a bibtex, for easy
insertion into the new NSF format.
"""

from __future__ import division

import datetime

awwaiid

$ ./universal-greetings.p6
Hello from the Perl Universe!!!

sujaikumar

NCBI blastp seems to have a bug where it reports different top hits when -max_target_seqs is changed. This is a serious problem because the first 20 hits (for example) should be the same whether -max_target_seqs 100 or -max_target_seqs 500 is used.

The bug is reproducible on the command line when searching NCBI's nr blast database (dated 25-Nov-2015) using NCBI 2.2.28+, 2.2.30+ and 2.2.31+.

At first I thought it was something to do with my local exe/blastdb, but the same problem is also apparent on the NCBI blastp web interface (as of 30-Nov-2015)

r-brown

# install Homebrew
$ su ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"

# show brew commands
$ brew help

# check current user
$ echo $(whoami)

# grant access to the folders

dfjenkins3

IGV Batch Screenshots

IGV provides functionality that allows a user to create a script to take screenshots of regions of interest.

Table of Contents

1. Requirements
2. Workflow
3. Create BED File

lindenb

REF=/path/to/ref.fasta
.PHONY:all

all: align/variants.vcf

align/variants.vcf:  align/Sample1_sorted.bam  align/Sample2_sorted.bam  align/Sample3_sorted.bam 
	/path/to/samtools mpileup -uf ${REF}  $^  |\
	/path/to/bcftools view -vcg - >$@

markstos

#!/usr/bin/env perl
use v5.10;
use strict;
use warnings;
use Carp;
use IO::Prompt::Tiny 'prompt';
use Net::GitHub;
use Path::Tiny;
use RT::Client::REST::Ticket;
use RT::Client::REST;

jeffreykegler

#!perl
# Copyright 2012 Jeffrey Kegler
# This file is part of Marpa::R2.  Marpa::R2 is free software: you can
# redistribute it and/or modify it under the terms of the GNU Lesser
# General Public License as published by the Free Software Foundation,
# either version 3 of the License, or (at your option) any later version.
#
# Marpa::R2 is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU

chapmanb

#!/bin/bash

#--- config

SERVICE_NAME=galaxy
RUN_AS=galaxy
RUN_IN=/your/galaxy/directory

#--- main actions