Skip to content

Instantly share code, notes, and snippets.

Avatar

Paul Klemm paulklemm

View GitHub Profile
@paulklemm
paulklemm / install.R
Last active Aug 27, 2020
Install these packages after creating a new R installation
View install.R
install.packages("renv")
library(renv)
renv::install("languageserver")
renv::install("tidyverse")
renv::install("devtools")
renv::install("roxygen2")
renv::install("ggrepel")
renv::install("usethis")
renv::install("WriteXLS")
renv::install("plotly")
@paulklemm
paulklemm / .Rprofile
Created Aug 29, 2018
My default .Rprofile settings
View .Rprofile
# See https://github.com/randy3k/rtichoke#settings
options(
# auto match brackets and quotes
rtichoke.auto_match = TRUE,
# when using history search (ctrl-r/ctrl-s in emacs mode), do not show duplicate results
rtichoke.history_search_no_duplicates = TRUE
)
@paulklemm
paulklemm / hyper.js
Created Apr 27, 2017
Hyper.js settings
View hyper.js
// Future versions of Hyper may add additional config options,
// which will not automatically be merged into this file.
// See https://hyper.is#cfg for all currently supported options.
module.exports = {
config: {
// default font size in pixels for all tabs
fontSize: 16,
// font family with optional fallbacks
@paulklemm
paulklemm / install_flexbar.sh
Last active Dec 13, 2016
Install Flexbar Error
View install_flexbar.sh
curl -sL https://github.com/seqan/flexbar/archive/v2.7.0.tar.gz | tar xz
# Download required libraries
curl -sL https://www.threadingbuildingblocks.org/sites/default/files/software_releases/linux/tbb2017_20161128oss_lin_0.tgz | tar xz
curl -sL https://github.com/seqan/seqan/releases/download/seqan-v2.1.1/seqan-library-2.1.1.tar.xz | tar xJ
mv tbb2017_20161128oss/include flexbar-2.7.0
mv seqan-library-2.1.1/include/* flexbar-2.7.0/include
cd flexbar-2.7.0
cmake .
make
@paulklemm
paulklemm / DEXSeq-RNACentral-Bug.sh
Created Nov 14, 2016
DEXSeq prepare annotation throws error for RNACentral GTF file
View DEXSeq-RNACentral-Bug.sh
# Convert GFF3 to GTF file
wget ftp://ftp.ebi.ac.uk/pub/databases/RNAcentral/releases/5.0/genome_coordinates/Mus_musculus.GRCm38.gff3.gz
gunzip --verbose Mus_musculus.GRCm38.gff3.gz
# Download gffread source and compile it
mkdir gffread_build
cd gffread_build
git clone https://github.com/gpertea/gclib
git clone https://github.com/gpertea/gffread
cd gffread
@paulklemm
paulklemm / RNAcentral_Transcripts_Cuffdiff_warnings.txt
Created Oct 28, 2016
RNACentral Transcripts throwing warnings in Cuffdiff
View RNAcentral_Transcripts_Cuffdiff_warnings.txt
AC020968.3
AC021630.11
AC021667.21
AC024069.29
AC024608.4
AC024913.33
AC025622.3
AC025669.19
AC025794.9
AC025913.11
View keybase.md

Keybase proof

I hereby claim:

  • I am paulklemm on github.
  • I am paulklemm (https://keybase.io/paulklemm) on keybase.
  • I have a public key ASA2miJvr-QmLL17BrLg8v_l3dv3rxDDw5BgO5H357er6wo

To claim this, I am signing this object:

View gist:72690458056e8ddb79c2
All criticized points were considered in the revision. I think the paper substantially improved. The distinction between `Kvik` and `Kvik Pathways` is made clear. A list of contributions makes it easier to follow the structure. I think you should consider putting the requirement analysis into a dedicated section.
I see nothing in the paper that gives me a reason to not approve it.
I have noticed two minor typos:
Abstract
Typo: Missing whitespace after sentence „Kvik Pathways follows the three-tier architecture in web applications using a powerful back-end for statistical analyses and retrieval of metadata.“
Implementation
Missing verb? „Kvik Pathways Cytoscape.js to create a pathway visualization from the list of nodes and edges and overlay the nodes on the pathway image.“
Apart from the paper, I have one comment on your response on my review w.r.t. the differences regarding the NIK paper. You stated that
@paulklemm
paulklemm / 0_reuse_code.js
Last active Aug 29, 2015
Here are some things you can do with Gists in GistBox.
View 0_reuse_code.js
// Use Gists to store code you would like to remember later on
console.log(window); // log the "window" object to the console
@paulklemm
paulklemm / Shader_Error
Last active Aug 29, 2015
WebGL Shader Fehler
View Shader_Error
THREE.WebGLShader: gl.getShaderInfoLog() ERROR: 0:55: '*' : wrong operand types no operation '*' exists that takes a left-hand operand of type 'highp float' and a right operand of type 'const int' (or there is no acceptable conversion)
three.min.js:581 1: precision highp float;
2: precision highp int;
3:
4:
5: #define MAX_DIR_LIGHTS 0
6: #define MAX_POINT_LIGHTS 0
7: #define MAX_SPOT_LIGHTS 0
8: #define MAX_HEMI_LIGHTS 0