Modeling ICU Patient Trajectories
Modeling Intensive Care Unit Patients Trajectories by leveraging data from the mimic-iii dataset (work in progress, check the attached PDF for some preliminary results: damiano_fantini_week2demo_v3).
Editing Video files using ffmpeg
In linux (Ububtu), ffmpeg is a very convenient tool for manipulating video files. For example, it is possible to use ffmpeg to extract audio tracks or video streams form a file, and combine them together, using only few lines of…
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Calling Variants using WES data and samtools + bcftools
This is a very short tutorial discussing how to call variants using samtools and bcftools from BAM files in the context of a Whole Exome Sequencing (WES) experiment. All the following steps assume you are working in a Linux environment….
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Deciphering Mutational Signatures with R, Amazon EC2 and the mutSignatures package
Important Notice!! This page is currently a placeholder while the mutSignatures R package is undergoing a major upgrade. Sorry for the inconvenience! A paper is (hopefully) getting accepted soon, and then this page will finally have the tutorial about how…
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Translating MATLAB’s silhouette() function to R
Many MATLAB functions are readily translatable to R, but of course this is not always true. While translating a MATLAB script into R, I run into the following problem. I couldn’t find an R function that could replace MATLAB’s silhouette()…
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Retrieve homolog genes using biomaRt
Homolog genes are genes descending from a common ancestral DNA sequence. Homolog genes in different species (i.e., genes that evolved from a common ancestral gene by speciation) are referred to as ortholog genes and usually retain a very similar function…
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Seatmap charts with ggplot2
This is a short tutorial for creating “geom tile” charts with ggplot2. These type of plots are similar to heat maps, but they picture a variable featuring a discrete number of possible levels (categories) instead of continuous numeric values. I…
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Boxplots with ggplot2
This is a short tutorial for creating boxplots with ggplot2. The tutorial will focus on: data preparation for plotting with ggplot2 differences between the standard R plotting system and ggplot2 using geom_boxplot to create a simple boxplot with ggplot2 and…
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Web Radios boosting coding productivity
How do you stay focused while coding? How do you cope with the noises of an open workspace or with the chitchat of the other customers of your favorite coffee shop? That’s easy.. Just listen to some good chill-out music…
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Analyzing TCGA Data in R via the TCGAretriever package
Brief introduction about TCGA, cBioPortal and the Cancer Genomic Data Server (CGDS) The Cancer Genome Atlas (TCGA) is a program aimed at improving the understanding of the molecular basis of cancer. TCGA stores multidimensional genomic data sets generated by analysis…
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Predicting HIV progression and treatment response
Project Goal and Data Understanding The goal of this project is to predict patients response to the anti-HIV treatment based on a very limited number of measured parameters. The dataset was retrieved from Kaggle (https://www.kaggle.com/c/hivprogression). Dataset includes information about a…
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Fluorescence
ImageJ is one of my favourite image-analysis programs. ImageJ is free, it is compatible with all major operating systems (it is written in Java) and it is very powerful. Here I am showing how to use ImageJ for the analysis…
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Basic configuration of an IGV Data Server
Setting up an IGV Data Server allows IGV users to access and explore genomic datasets located elsewhere online or on a local area network. To configure a Data Server, we need to inform IGV about where the genomic data files…
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