Felix Grünberger

Felix Grünberger

Postdoctoral researcher at the University of Regensburg

Posts by Tags

KAGGLE

The joy of spreadsheets

9 minute read

Published:

To get straight to the point: This post is about data manipulation and visualization in R.
Obviously, that is something completely different from my first post and with more content coming up, I have to think about giving the blog a clearer structure 🤔
But for now, it should be fine. As you will definitely see some code during your read, please do not be intimidated! You will not miss the final statement, even if you are not familiar with programming. As some kind of a reminiscence to the previous topic, this post again deals with movies and the development of their duration over the years.

RMarkdown

How I start a bioinformatics project

2 minute read

Published:

I started analyzing sequencing data just over one year ago. In the beginning it was so exciting to finally receive the first reads, do some quality checks and start further analysis, that I didn´t think about reproducibility. I ended up with multiple distinct versions of mapped reads, adapter/quality trimmed reads from scripts using different parameters. It was bad…
So I had to force myself to rethink my workflow, which I will show you (in a simplifed way) in the following.

RPackage

Write your first R package

6 minute read

Published:

In my opinion packages are one of the main reasons why R is so successfull. They add a whole new level of functionality and reproducibility and also increase the productivity of every user by reusable R functions, their documentation and sample data.

RStudio

Write your first R package

6 minute read

Published:

In my opinion packages are one of the main reasons why R is so successfull. They add a whole new level of functionality and reproducibility and also increase the productivity of every user by reusable R functions, their documentation and sample data.

data-visualization

The joy of spreadsheets

9 minute read

Published:

To get straight to the point: This post is about data manipulation and visualization in R.
Obviously, that is something completely different from my first post and with more content coming up, I have to think about giving the blog a clearer structure 🤔
But for now, it should be fine. As you will definitely see some code during your read, please do not be intimidated! You will not miss the final statement, even if you are not familiar with programming. As some kind of a reminiscence to the previous topic, this post again deals with movies and the development of their duration over the years.

devtools

Write your first R package

6 minute read

Published:

In my opinion packages are one of the main reasons why R is so successfull. They add a whole new level of functionality and reproducibility and also increase the productivity of every user by reusable R functions, their documentation and sample data.

gg_joy

The joy of spreadsheets

9 minute read

Published:

To get straight to the point: This post is about data manipulation and visualization in R.
Obviously, that is something completely different from my first post and with more content coming up, I have to think about giving the blog a clearer structure 🤔
But for now, it should be fine. As you will definitely see some code during your read, please do not be intimidated! You will not miss the final statement, even if you are not familiar with programming. As some kind of a reminiscence to the previous topic, this post again deals with movies and the development of their duration over the years.

gganimate

Animated bar graphs in R

2 minute read

Published:

Last week I saw this post on Twitter where Adam Spannbauer visualized an animated ‘growing’ bar graph in R. Pretty impressive!


ASpannbauer_growing_barchart


Is an animated graph contributing to a better understanding?

From the comments and a related second post it became clear, that this animation was visually appealing, but in no way contributing to a better understanding of the data behind the graph. So I sat down and thought about requirements for an animated bar chart that can be embedded in a presentation and contribute (maybe) to a better understanding:

ggplot2

The power of interactive plots

5 minute read

Published:

At the beginning of the year, I remember myself staring at the screen, sitting on a bunch of genomic data and thinking:
“Man, it would be really helpful to hover over my data points and check what properties they have…”
As this may seem a bit nerdy, nowadays dynamic content has become quite natural and offers a whole new range of possibilities especially when dealing with large, complex data sets.

Animated bar graphs in R

2 minute read

Published:

Last week I saw this post on Twitter where Adam Spannbauer visualized an animated ‘growing’ bar graph in R. Pretty impressive!


ASpannbauer_growing_barchart


Is an animated graph contributing to a better understanding?

From the comments and a related second post it became clear, that this animation was visually appealing, but in no way contributing to a better understanding of the data behind the graph. So I sat down and thought about requirements for an animated bar chart that can be embedded in a presentation and contribute (maybe) to a better understanding:

organization

How I start a bioinformatics project

2 minute read

Published:

I started analyzing sequencing data just over one year ago. In the beginning it was so exciting to finally receive the first reads, do some quality checks and start further analysis, that I didn´t think about reproducibility. I ended up with multiple distinct versions of mapped reads, adapter/quality trimmed reads from scripts using different parameters. It was bad…
So I had to force myself to rethink my workflow, which I will show you (in a simplifed way) in the following.

plotly

The power of interactive plots

5 minute read

Published:

At the beginning of the year, I remember myself staring at the screen, sitting on a bunch of genomic data and thinking:
“Man, it would be really helpful to hover over my data points and check what properties they have…”
As this may seem a bit nerdy, nowadays dynamic content has become quite natural and offers a whole new range of possibilities especially when dealing with large, complex data sets.

projectTemplate

How I start a bioinformatics project

2 minute read

Published:

I started analyzing sequencing data just over one year ago. In the beginning it was so exciting to finally receive the first reads, do some quality checks and start further analysis, that I didn´t think about reproducibility. I ended up with multiple distinct versions of mapped reads, adapter/quality trimmed reads from scripts using different parameters. It was bad…
So I had to force myself to rethink my workflow, which I will show you (in a simplifed way) in the following.

roxygen2

Write your first R package

6 minute read

Published:

In my opinion packages are one of the main reasons why R is so successfull. They add a whole new level of functionality and reproducibility and also increase the productivity of every user by reusable R functions, their documentation and sample data.

sequencing

How I start a bioinformatics project

2 minute read

Published:

I started analyzing sequencing data just over one year ago. In the beginning it was so exciting to finally receive the first reads, do some quality checks and start further analysis, that I didn´t think about reproducibility. I ended up with multiple distinct versions of mapped reads, adapter/quality trimmed reads from scripts using different parameters. It was bad…
So I had to force myself to rethink my workflow, which I will show you (in a simplifed way) in the following.

KsgA

Nanopore

RNA modifications

RNA-binding

RNA-seq

archaea

heat-shock

proteomics

rRNA

transcription

transcriptomics