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Michael Dondrup mdondrup

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  • University of Bergen
  • Bergen, Norway
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@mdondrup
mdondrup / RangeTree.pm
Created June 3, 2014 12:15
package RangeTree;
use strict;
use warnings;
use Set::IntervalTree;
sub new {
my $class = shift;
my $self = {}; # container is a hash with seqnames as keys
@mdondrup
mdondrup / mirdeep2-bowtie.html
Last active October 17, 2016 15:11
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN"
"http://www.w3.org/TR/html4/strict.dtd">
<html>
<head>
<title>miRDeep2</title>
<!-- CSS code -->
<style type="text/css">
body{
font: .75em Arial,sans-serif;
background: #FFFFFF;
@mdondrup
mdondrup / mirdeep2-bwa.html
Created October 17, 2016 15:12
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN"
"http://www.w3.org/TR/html4/strict.dtd">
<html>
<head>
<title>miRDeep2</title>
<!-- CSS code -->
<style type="text/css">
body{
font: .75em Arial,sans-serif;
background: #FFFFFF;
@mdondrup
mdondrup / gist:4adaac1ab045e9008caa1e54cc2fc940
Created March 31, 2017 09:33
Hello World!
@mdondrup
mdondrup / featureCounts.log
Last active June 12, 2017 08:27
Run in single end mode:
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.5.2
//========================== featureCounts setting ===========================\\
@mdondrup
mdondrup / install_UBUNTU_binary_only.sh
Created December 2, 2018 16:01
CURDIR=`pwd`
LOGFILE=$CURDIR/macsysfinder-install.log # give the logfile a proper name
# if [ -e $LOGFILE ]; then rm $LOGFILE ; fi # no need to delete the file each time
mkdir -p bin
mkdir -p src
#install vmatch
echo " downloading and compiling of Vmatch" >> $LOGFILE
echo "change directory to $CURDIR/src" >> $LOGFILE
cd src
@mdondrup
mdondrup / install_UBUNTU_safe.sh
Last active December 3, 2018 09:08
#!/bin/sh
set -eu
# WARNING: you need to adapt the dependency list first
#
# shell script allowing to install all CRISPRCasFinder.pl-v4.2's dependencies
#
# same version than CRISPRCasFinder.pl, here 4.2.17
# authors: David Couvin, Fabrice Leclerc, Claire Toffano-Nioche
# adapted to non sudo install by M. Dondrup
@mdondrup
mdondrup / gffdiff.pl
Created April 16, 2021 10:17
#!/usr/bin/env perl
use strict;
use warnings;
use Bio::Tools::GFF;
use Bio::SeqFeatureI;
my %fstore1 = ();
my %fstore2 = ();
my %conflicts = ();
@mdondrup
mdondrup / rmsd-helper.R
Created May 27, 2021 11:26
library(Rpdb)
library(pdist)
#mypdb <- read.pdb("SCARB_S361384_results_itasser/1dve-rmsd.pdb", HETATM = T, ATOM = T, MODEL = 1:2)
my.pdist <- function(x,y) {
ret <- as.matrix(pdist(x,y), nrow = nrow(x), ncol=nrow(y))
dimnames(ret) <- list(row.names(x), row.names(y))
return(list(ret))
@mdondrup
mdondrup / 1DVE-rmsd-example.pdb
Created May 27, 2021 12:04
MODEL 1
ATOM 1 C1 UNK 1 46.878 21.312-121.026 1.00 0.00 C
ATOM 2 C2 UNK 1 46.008 21.716-122.189 1.00 0.00 C
ATOM 3 C3 UNK 1 46.381 22.574-123.243 1.00 0.00 C
ATOM 4 C4 UNK 1 47.629 23.170-123.351 1.00 0.00 C
ATOM 5 C5 UNK 1 47.990 24.006-124.415 1.00 0.00 C
ATOM 6 N1 UNK 1 47.231 24.376-125.447 1.00 0.00 N
ATOM 7 C6 UNK 1 47.918 25.174-126.264 1.00 0.00 C
ATOM 8 C7 UNK 1 47.497 25.776-127.450 1.00 0.00 C
ATOM 9 C8 UNK 1 46.216 25.625-127.970 1.00 0.00 C