Category Archives: Uncategorized

Docker: plugging into the jupyter/datascience-notebook

Again, quick notes for myself as this is subtly different depending on whether I am on a windows host or a linux host. Install Pulling down the datascience-notebook image is easy-peasy: $ docker pull jupyter/datascience-notebook Starting the notebook Again, this

Docker: plugging into the jupyter/datascience-notebook

Again, quick notes for myself as this is subtly different depending on whether I am on a windows host or a linux host. Install Pulling down the datascience-notebook image is easy-peasy: $ docker pull jupyter/datascience-notebook Starting the notebook Again, this

Docker – RStudio server

Quick note for myself – installing and starting RStudio via docker: install: $ docker pull rocker/rstudio starting: $ docker run -d  -p 8787:8787 rocker/rstudio accessing (from browser): localhost:8787 username and password are: rstudio

Docker – RStudio server

Quick note for myself – installing and starting RStudio via docker: install: $ docker pull rocker/rstudio starting: $ docker run -d  -p 8787:8787 rocker/rstudio accessing (from browser): localhost:8787 username and password are: rstudio

Using bcftools to merge and filter VCF files

GOALS to merge genotype calls from separate VCF files (e.g. one VCF file per sample) into one master VCF file with a column for each sample. and filter this master VCF file and extract regions of interest EDIT: have edited

Using bcftools to merge and filter VCF files

GOALS to merge genotype calls from separate VCF files (e.g. one VCF file per sample) into one master VCF file with a column for each sample. and filter this master VCF file and extract regions of interest EDIT: have edited

Quantum mechanics & purgatory

“Quantum mechanics theorises that there is unlimited number of universes. Which means, there is infinite amount of me making this talk and, infinite amount of you… listening. Think about that.” “Andrea”, Limitless, season 1, episode 18.   #hilarious!

Quantum mechanics & purgatory

“Quantum mechanics theorises that there is unlimited number of universes. Which means, there is infinite amount of me making this talk and, infinite amount of you… listening. Think about that.” “Andrea”, Limitless, season 1, episode 18.   #hilarious!

Manipulating VCF Files

In this post we are going to cover some very basic scenarios for manipulating VCF files. We will begin with a (very) brief description of the VCF format, look at how to extract targeted regions using tabix. In a future post

Manipulating VCF Files

In this post we are going to cover some very basic scenarios for manipulating VCF files. We will begin with a (very) brief description of the VCF format, look at how to extract targeted regions using tabix. In a future post

A quick sound bite on predictive analytics

Was reading this post, and this little quote jumped out: “I now know the probability of an outcome [and] what can be done to influence it in the direction that’s positive for me,’ whether that be preventing customer churn or

A quick sound bite on predictive analytics

Was reading this post, and this little quote jumped out: “I now know the probability of an outcome [and] what can be done to influence it in the direction that’s positive for me,’ whether that be preventing customer churn or

Signal extraction: fourier transform

Stretching my brain back a decade, I used to work a lot with fourier transforms (FT) which are foundational methods of analysis MRI / NMR data. FT is so powerful and versatile that is widely used across all physical sciences

Signal extraction: fourier transform

Stretching my brain back a decade, I used to work a lot with fourier transforms (FT) which are foundational methods of analysis MRI / NMR data. FT is so powerful and versatile that is widely used across all physical sciences