Posts by Tags

bioinformatics

Sequin Submission to Genbank Tutorial

5 minute read

Published:

As I came to the end of my M.Sc. and writing the corresponding journal article, one thing I was aware of was that all previous papers on woolly mammoth mitchondrial genomes to NCBI’s GenBank database. To continue with this established ‘tradition’, I decided to investigate how to do this. Worringly, most people I spoke to didn’t have very positive views on this procdure, saying that it was complicated, error prone and badly documented and that it wasn’t worth my time. In fact, with a bit of help from the authors of some of the previous papers and with NCBI itself, the overall task ended up being easier than expected (admittedly after a considerable bit of trial and error).

github

pvclust Node Values In ggtree

3 minute read

Published:

I recently was using the R package pvclust to test the ‘robusticity’ of clusters in a microbiome-related clustering analysis. While pvclust provides it’s own plots via plot() on a pvclust object, this plots the dendrogram in base R. For readability and customisability reasons I prefer using the packages ggplot2 and ggtree for making my figures. However, I was having a hard time to extract the node uncertainty values from the pvclust object and integrate them into a generic R phylo object for plotting the dendrogram in ggtree.

‘Tidy’ Pop-Gen PCA plotting in R

less than 1 minute read

Published:

Many people in the human population-genetics groups in my department at MPI-SHH use a propetiary Mac specific program to make their figures of PCAs (principle component analysis). Some of the members of these groups however do not have Macs and were struggling to recreate some of the plots their collegues were making.

Updating a Github Pages Theme Through a Repo Merge

1 minute read

Published:

I am new to Git and Github, and so I am still very much learning on the fly. Today I noticed the original repository for the theme of this website had added updates, so I thought to apply them to my own repository.

how-to

How-to: Simple ‘change over time’ maps in R

4 minute read

Published:

In Archaeology, or other disciplines that looking through deep time, you often want to represent change through time. A simple example of this, is representing the location different archaeological sites through different cultural periods.

jekyll

pvclust Node Values In ggtree

3 minute read

Published:

I recently was using the R package pvclust to test the ‘robusticity’ of clusters in a microbiome-related clustering analysis. While pvclust provides it’s own plots via plot() on a pvclust object, this plots the dendrogram in base R. For readability and customisability reasons I prefer using the packages ggplot2 and ggtree for making my figures. However, I was having a hard time to extract the node uncertainty values from the pvclust object and integrate them into a generic R phylo object for plotting the dendrogram in ggtree.

‘Tidy’ Pop-Gen PCA plotting in R

less than 1 minute read

Published:

Many people in the human population-genetics groups in my department at MPI-SHH use a propetiary Mac specific program to make their figures of PCAs (principle component analysis). Some of the members of these groups however do not have Macs and were struggling to recreate some of the plots their collegues were making.

Updating a Github Pages Theme Through a Repo Merge

1 minute read

Published:

I am new to Git and Github, and so I am still very much learning on the fly. Today I noticed the original repository for the theme of this website had added updates, so I thought to apply them to my own repository.

maps

How-to: Simple ‘change over time’ maps in R

4 minute read

Published:

In Archaeology, or other disciplines that looking through deep time, you often want to represent change through time. A simple example of this, is representing the location different archaeological sites through different cultural periods.

mrbayes

How-to: cancel a MrBayes run early

2 minute read

Published:

During my M.Sc. thesis I started to use the Bayesian phylogenetic MrBayes on clusters that do not make it feasible to keep open a terminal window. This meant I had to use ‘batch mode’, meaning I could only follow the status of the MrBayes run through the log files.

ncbi

Sequin Submission to Genbank Tutorial

5 minute read

Published:

As I came to the end of my M.Sc. and writing the corresponding journal article, one thing I was aware of was that all previous papers on woolly mammoth mitchondrial genomes to NCBI’s GenBank database. To continue with this established ‘tradition’, I decided to investigate how to do this. Worringly, most people I spoke to didn’t have very positive views on this procdure, saying that it was complicated, error prone and badly documented and that it wasn’t worth my time. In fact, with a bit of help from the authors of some of the previous papers and with NCBI itself, the overall task ended up being easier than expected (admittedly after a considerable bit of trial and error).

phylogenetics

How-to: cancel a MrBayes run early

2 minute read

Published:

During my M.Sc. thesis I started to use the Bayesian phylogenetic MrBayes on clusters that do not make it feasible to keep open a terminal window. This meant I had to use ‘batch mode’, meaning I could only follow the status of the MrBayes run through the log files.

r

How-to: Simple ‘change over time’ maps in R

4 minute read

Published:

In Archaeology, or other disciplines that looking through deep time, you often want to represent change through time. A simple example of this, is representing the location different archaeological sites through different cultural periods.

theme

pvclust Node Values In ggtree

3 minute read

Published:

I recently was using the R package pvclust to test the ‘robusticity’ of clusters in a microbiome-related clustering analysis. While pvclust provides it’s own plots via plot() on a pvclust object, this plots the dendrogram in base R. For readability and customisability reasons I prefer using the packages ggplot2 and ggtree for making my figures. However, I was having a hard time to extract the node uncertainty values from the pvclust object and integrate them into a generic R phylo object for plotting the dendrogram in ggtree.

‘Tidy’ Pop-Gen PCA plotting in R

less than 1 minute read

Published:

Many people in the human population-genetics groups in my department at MPI-SHH use a propetiary Mac specific program to make their figures of PCAs (principle component analysis). Some of the members of these groups however do not have Macs and were struggling to recreate some of the plots their collegues were making.

Updating a Github Pages Theme Through a Repo Merge

1 minute read

Published:

I am new to Git and Github, and so I am still very much learning on the fly. Today I noticed the original repository for the theme of this website had added updates, so I thought to apply them to my own repository.

tutorial

pvclust Node Values In ggtree

3 minute read

Published:

I recently was using the R package pvclust to test the ‘robusticity’ of clusters in a microbiome-related clustering analysis. While pvclust provides it’s own plots via plot() on a pvclust object, this plots the dendrogram in base R. For readability and customisability reasons I prefer using the packages ggplot2 and ggtree for making my figures. However, I was having a hard time to extract the node uncertainty values from the pvclust object and integrate them into a generic R phylo object for plotting the dendrogram in ggtree.

‘Tidy’ Pop-Gen PCA plotting in R

less than 1 minute read

Published:

Many people in the human population-genetics groups in my department at MPI-SHH use a propetiary Mac specific program to make their figures of PCAs (principle component analysis). Some of the members of these groups however do not have Macs and were struggling to recreate some of the plots their collegues were making.

Updating a Github Pages Theme Through a Repo Merge

1 minute read

Published:

I am new to Git and Github, and so I am still very much learning on the fly. Today I noticed the original repository for the theme of this website had added updates, so I thought to apply them to my own repository.

Sequin Submission to Genbank Tutorial

5 minute read

Published:

As I came to the end of my M.Sc. and writing the corresponding journal article, one thing I was aware of was that all previous papers on woolly mammoth mitchondrial genomes to NCBI’s GenBank database. To continue with this established ‘tradition’, I decided to investigate how to do this. Worringly, most people I spoke to didn’t have very positive views on this procdure, saying that it was complicated, error prone and badly documented and that it wasn’t worth my time. In fact, with a bit of help from the authors of some of the previous papers and with NCBI itself, the overall task ended up being easier than expected (admittedly after a considerable bit of trial and error).

website

pvclust Node Values In ggtree

3 minute read

Published:

I recently was using the R package pvclust to test the ‘robusticity’ of clusters in a microbiome-related clustering analysis. While pvclust provides it’s own plots via plot() on a pvclust object, this plots the dendrogram in base R. For readability and customisability reasons I prefer using the packages ggplot2 and ggtree for making my figures. However, I was having a hard time to extract the node uncertainty values from the pvclust object and integrate them into a generic R phylo object for plotting the dendrogram in ggtree.

‘Tidy’ Pop-Gen PCA plotting in R

less than 1 minute read

Published:

Many people in the human population-genetics groups in my department at MPI-SHH use a propetiary Mac specific program to make their figures of PCAs (principle component analysis). Some of the members of these groups however do not have Macs and were struggling to recreate some of the plots their collegues were making.

Updating a Github Pages Theme Through a Repo Merge

1 minute read

Published:

I am new to Git and Github, and so I am still very much learning on the fly. Today I noticed the original repository for the theme of this website had added updates, so I thought to apply them to my own repository.