Introduction to Linear Regression

A data scientist's first goal is to find underlying relations within the variables of a dataset. Several statistical and machine learning methods can be used to discover such relations. Once uncovered, this information can be applied to everyday problems. For example, in clinical medicine, a predictive model based on clinical data can help clinicians guide a patient's treatment by offering insights that might not have otherwise been taken into account. Simple linear regression One of the most basic methods available to [...]

Chemical Screen: Evaluating drug sensitivity

The study of the cellular response to a chemical compound is crucial to the development of new therapeutic drugs. Such an analysis is usually done by a screen experiment where the disease-specific cells (such as leukemia primary cells) are exposed to chemical compound for different concentrations. The response, in the form of sensitivity, of these cells is conventionally quantified by the IC50 or the l’EC50. Here are some notions to keep in mind when we analyze these values.  IC50/EC50 : estimate of [...]

By | February 13, 2017|Categories: Data Analysis, Uncategorized|0 Comments

Realize your Bash potential

A bioinformatician's best tool is his shell. While some have already mastered the dark arts of the bash shell, I often see beginners (and even catch myself at times!) unknowingly repeating key sequences when they could be getting the same result with a few simple built-in keybindings or programmatic shortcuts. Let's have a look at some of the most useful bash shortcuts that no self-respecting bioinformatician should be without. This is by no means an exhaustive list of what Bash has to offer but will hopefully serve to save [...]

By | May 26, 2016|Categories: Shell scripting, Uncategorized|0 Comments

[Python] Iterators vs Generators

In Python, there are iterators and generators. You probably already use iterators without even knowing that you do so. But understanding the difference between those two concepts is really important since choosing one over the other has a huge impact on memory usage. If you are working with small datasets, memory usage might not be your first concern. However, with big datasets, it is another story. So what are they exactly, iterators and generators? Iterators The process of going through [...]

By | September 18, 2015|Categories: Bioinformatics, Performance, Python, Uncategorized|0 Comments

Assessing enrichment

Working on a set of RNA-seq of AML patient samples, I stumble on gene X.  When its expression is high, 50% of the samples are mutated on gene Y, a mutation that has a prevalence of only 20% in the rest of the dataset.  Is there a link between these two observations?  Let's put some numbers on this:  among the 131 samples of the dataset, 28 show mutations on gene Y, 6 have high expression of X and 3 have both "features".  The table below is [...]

By | May 21, 2014|Categories: Uncategorized|0 Comments