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@paulklemm
paulklemm / maldi_theodora_normalisation.py
Created January 16, 2024 14:42
Revise Theodora's Data Normalisation
import uMAIA
import numpy as np
import matplotlib.pyplot as plt
import pandas as pd
import warnings
import os
# Define the path to save the data
workdir = '/beegfs/scratch/bruening_scratch/pklemm/2024-01-theodora/uMAIA/data_maldi'
@paulklemm
paulklemm / install.R
Last active May 3, 2024 09:16
Install these packages after creating a new R installation
renv::install("BiocManager", prompt = FALSE)
renv::install("languageserver", prompt = FALSE)
renv::install("tidyverse", prompt = FALSE)
renv::install("xaringan", prompt = FALSE)
renv::install("targets", prompt = FALSE)
renv::install("visNetwork", prompt = FALSE)
renv::install("httpgd", prompt = FALSE)
renv::install("patchwork", prompt = FALSE)
renv::install("devtools", prompt = FALSE)
renv::install("roxygen2", prompt = FALSE)
@paulklemm
paulklemm / .Rprofile
Created August 29, 2018 06:12
My default .Rprofile settings
# 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 April 27, 2017 18:50
Hyper.js settings
// 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 December 13, 2016 11:03
Install Flexbar Error
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 November 14, 2016 13:17
DEXSeq prepare annotation throws error for RNACentral GTF file
# 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 October 28, 2016 07:46
RNACentral Transcripts throwing warnings in Cuffdiff
AC020968.3
AC021630.11
AC021667.21
AC024069.29
AC024608.4
AC024913.33
AC025622.3
AC025669.19
AC025794.9
AC025913.11

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I hereby claim:

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To claim this, I am signing this object:

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 August 29, 2015 14:17
Here are some things you can do with Gists in GistBox.
// Use Gists to store code you would like to remember later on
console.log(window); // log the "window" object to the console