Blog – Data Detective

Part II - Lost in translation

In this section I will try to translate, or at least give enough clues on how to read a job ad from an company. The approach I prefer is to pick a couple of real job…

António Domingues

Part I - Should I stay or should I go

I will start this series answering what I feel is a relevant question: Is it possible to stay in academia without being a professor?

António Domingues

Help. I am a bioinformatician looking for a job

Usually a Data Science job, and I am here to help you. In the past year or so I have been doing a lot of mentoring with bioinformaticians / data scientists who are looking…

António Domingues

Convert multiple mercurial repos to git

For historical reasons many of my I have dozens of version-controlled projects using mercurial (hg) hosted on Bitbucket. Since Bitbucket not only discontinued support for…

António Domingues

Improving database performance

I am a bit of a DB n00b but for a project I had to setup and query an rather larger sqlite database from an existing dump and schema. Here are a couple if things I leaned…

António Domingues

My visual CV

career

R

data

viz

TLDR; I made a visual timeline of my career (CV) completely in R. Here I will show how it was done, and in the process how to hack ggplot objects, add images to plots, and…

António Domingues

Clone all repositories from a user (bitbucket) - API2.0

My post about cloning all bitbucket, originally posted on my old wordpress blog, got some attention over the internet. Well, three or four mentions. Sadly the information in…

António Domingues

How style your R code from sublime text

Let’s face it: we all write ugly R code. Either because we are in a hurry, or we copy pasted from stackoverflow, or our coding style just changed over the course of time, it…

António Domingues

My first R package - some notes

I have been toying with the idea of making an R package for sometime. To me this is the natural step after been an R user for some years now. Though I had some ideas they…

António Domingues

How to compile R in a specific location

Rstats

tutorial

terminal

linux

Recently I noticed that the Bioconductor installed in our Debian server was two versions out of date, but I use the Institutes’s server for which I am not an administrator…

António Domingues

How big is my baby?

I am a bit of a nerd and also a recent progenitor. So of course I had to find ways of analyzing the growth of my F1.

António Domingues

Filter overlapping features in bed file

How to remove overlapping coordinates in a single bed file with the restriction that these must be within a certain distance.

António Domingues

Function to find maximal coverage in multiple bigwigs II

[This is an updated version of this post with improved functions and a reproducible example]

António Domingues

Function to find maximal coverage in multiple bigwigs

I really like the package Gviz to prepare figures for presentations and publications (I have used it in B with some tidying up in inskape).

António Domingues

Sublime Text 3 set-up

I am a big fan of Sublime Text! It is a lightweight text editor, inexpensive license, and with contributions by hundreds of users, highly extensible and customizable. From a…

António Domingues

Custom chromosome sizes for pybedtools

I use pybetools a lot in my little script. One issue that I have encountered recentely was when using those scripts with a custom genome, in this case mapping to the…

António Domingues

Repeat mapping

Most of the projects I am involved with deal with mapping reads to repeat regions of the genome. Specifically transposons. While not all genomic repeats have exactly the…

António Domingues

Kill all jobs with a name

I had some jobs waiting in queue with non-consecutive job id numbers, but all with the same job name. Mistakes were made and they needed killing. A solution would be to…

António Domingues

Testing for over-representation of anything

Recently I wrote a post on how to test for chromosome over-representation on a list of genes. The solution, which I thought it was clever at the time, can be simpled to be…

António Domingues

Merge fastq sample from different lanes and rename them

This is something I need to do often and a collegue asked me how to do it herself. So the best way to share is to post it in the blog.

António Domingues

Finding the closest element to a number in a vector

A colleague came to my office the other day with an interesting question:

António Domingues

Table of results embed in a PDF

Warning: This is a rant.

António Domingues

Painless installation of R packages from source

I was minding my own business trying to add labels to a line plot in ggplot2. Then I saw that the package directlabels would solve all my problems with one single line of…

António Domingues

Testing for chromosome over-representation

Sometimes I am working on some data and notice certain biases, say differentially expressed genes appearing to originate more often from a chromosome. Or a factor binding…

António Domingues

Reminder - building blog locally with Jekyll

It took me while from moving my blog from wordpress to github pages and writing a new post. Such a long time that I forgot that to build the site locally I need to use bundle…

António Domingues

Install bioconductor packages from SVN

Due to some issues with the way DEXseq calculates the log2foldchanges I decided to re-run an analysis with the issue fixed. Since it is not yet in the development branch, an…

António Domingues

virtualenvs or: How I Learned to Stop Worrying and Love not having sudo powers in a server

Well, you might think, there is always pip install --user. Aha! Yes, that works most of the time, but not when some package upgrade (distribute for deepTools) conflicts with…

António Domingues

Clone all repositories from a user (bitbucket)

Now that I have computer, the next step is to install everything I use on daily basis, and set-up my projects space. This involves cloning all my repositories. I could do…

António Domingues

New shiny toy

Update of 11.08.2016 tldr: upgraded to 16.04 with a fresh install and everything is rosy - the system is better than ever.

António Domingues

The “p” problem in R plots, or when a dot is a font in inkscape

My graphics/figure workflow generally involves plotting something in R, saving it as a pdf (+png if writing a report with Rmarkdown), followed by some manual editing with Ink…

António Domingues

Nerd up your R

I probably spend most of my working day in an R terminal, or at least I start R often enough. Now I saw in a blog I follow a way to entertain and instruct in equal measure…

António Domingues

Rcolorbrewer pallete

I am always looking for a good quality printout of the available palettes in the RColorBrewer package. I finally decided to take matters on my own hand and create a pdf for…

António Domingues

ChIP-seq coverage analysis

It has been a long time since I wrote this post, and in between a wonderful set of tools for coverage calculation and visualization has been published: deepTools does…

António Domingues

BioPython musings

On my quest to improve my scripting skils I have just recently taken the Introduction to BioPython course at the VIB in Leuven.

António Domingues

One liners, snippets and small scripts

Often I use one liners or small scripts for useful task but I keep forgetting about those. So I’ll just put them here for future reference.

António Domingues

Calculating and plotting mapped reads - a simple R/shell script

As this is my first post I’ll start with something very simple I did recently. The problem is simple: “how many reads did does my deep-seq experiment have and how many were…

António Domingues