Gregor Sturm grst

Clinical Bioinformatics @Boehringer-Ingelheim. @scverse core dev. Formerly PhD student @icbi-lab. My private account.

grst / single_cell_analysis

Created September 16, 2019 15:02

grst / server.py

Created January 20, 2019 15:55

slow dropdown in dash

	import dash
	import dash_html_components as html
	import dash_core_components as dcc

	external_stylesheets = ['https://codepen.io/chriddyp/pen/bWLwgP.css']

	app = dash.Dash(__name__, external_stylesheets=external_stylesheets)
	app.layout = html.Div([
	dcc.Dropdown(
	id='dropdown-selector',

grst / rsession.sh

Created November 30, 2018 08:27

Use conda-env for rstudio-server

	#!/bin/bash
	USER=`whoami`
	source /etc/profile

	# Source global definitions
	if [ -f /etc/bashrc ]; then
	. /etc/bashrc
	fi

	source /storage/apps/dotfiles/bashrc.sh

grst / test.Rmd

Created November 17, 2018 16:56

reticulate logging

	---
	title: "test"
	output: html_document
	---


	```{python}
	import logging
	l = logging.getLogger('test')
	l.addHandler(logging.StreamHandler())

grst / UVM.rda

Last active April 23, 2018 14:31

UVM

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grst / pandas-vs-d.ipynb

Created February 14, 2018 21:08

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grst / perl_log.txt

Created January 29, 2018 08:27

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	== 2018-01-29 09:00:32,285 main.py:79 INFO This is EasyBuild 3.5.1 (framework: 3.5.1, easyblocks: 3.5.1) on host eldorado.
	== 2018-01-29 09:00:32,285 main.py:82 INFO Command line: --buildpath='/storage/apps/easybuild/build' --installpath='/storage/apps/easybuild' --packagepath='/storage/apps/easybuild/packages' --prefix='/storage/apps/easybuild' --repositorypath='/storage/apps/easybuild/ebfiles_repo' --robot='/storage/apps/easybuild/software/EasyBuild/3.5.1/lib/python2.7/site-packages/easybuild_easyconfigs-3.5.1-py2.7.egg/easybuild/easyconfigs' --software='Perl,5.26.0' --sourcepath='/storage/apps/easybuild/sources' --toolchain-name='GCCcore'
	== 2018-01-29 09:00:32,285 main.py:84 INFO Using /storage/home/sturm/tmp/eb-1FfxLn as temporary directory
	== 2018-01-29 09:00:32,285 robot.py:56 INFO Using robot path(s): ['/storage/apps/easybuild/software/EasyBuild/3.5.1/lib/python2.7/site-packages/easybuild_easyconfigs-3.5.1-py2.7.egg/easybuild/easyconfigs']
	== 2018-01-29 09:00:32,285 options.py:1199 INFO Using default

grst / eb_log.txt

Created January 26, 2018 10:17

EasyBuild binutils

	== 2018-01-26 11:11:43,530 easyblock.py:264 INFO This is EasyBuild 3.5.1 (framework: 3.5.1, easyblocks: 3.5.1) on host eldorado.
	== 2018-01-26 11:11:43,530 easyblock.py:270 INFO This is easyblock EB_binutils from module easybuild.easyblocks.binutils (/storage/apps/easybuild/software/EasyBuild/3.5.1/lib/python2.7/site-packages/easybuild_easyblocks-3.5.1-py2.7.egg/easybuild/easyblocks/b/binutils.pyo)
	== 2018-01-26 11:11:43,531 easyblock.py:815 INFO Build dir set to /storage/apps/easybuild/build/binutils/2.29/GCCcore-system
	== 2018-01-26 11:11:43,531 easyblock.py:856 INFO Software install dir set to /storage/apps/easybuild/software/binutils/2.29-GCCcore-system
	== 2018-01-26 11:11:43,532 easyblock.py:861 INFO Module install dir set to /storage/apps/easybuild/modules/all
	== 2018-01-26 11:11:43,532 easyblock.py:249 INFO Init completed for application name binutils version 2.29
	== 2018-01-26 11:11:43,532 easyblock.py:2659 INFO Obtained application instance of for binutils (easyblock: None)
	== 2018-01-26 11:11:43,533

grst / bibliography.bib

Created June 26, 2017 20:26

RMarkdown test multicite

	@Article{Bartel2004,
	Author="Bartel, D. P. ",
	Title="{{M}icro{R}{N}{A}s: genomics, biogenesis, mechanism, and function}",
	Journal="Cell",
	Year="2004",
	Volume="116",
	Number="2",
	Pages="281--297",
	Month="Jan",
	doi = {10.1016/s0092-8674(04)00045-5},

grst / data_vector.tsv

Created May 17, 2017 17:24

ggplot + geom_histogram() vs. hist() on p-value distributions.

We can make this file beautiful and searchable if this error is corrected: No tabs found in this TSV file in line 0.