An algorithm for calculating SUVmax value for PET/CT GE scanner will be described in this post. The starting point for this post is my post at Slicer 3D forum: https://discourse.slicer.org/t/pet-standard-uptake-value-computation/7491/4 Problem description: One would like to know SUV values and SUVmax for a given ROI in PET data from a GE scanner. This of course can be extracted from the […]
Loading BAM files with R
An example on how to load BAM file and preview sequence information (in R Markdown). Source code for the R Markdown Notebook is available at a GitHub repository.
Jupyter Notebook, Nginx, Ubuntu, and Docker
I wanted to learn how to configure a proxy for Jupyter Notebook with Nginx. For such test, it was easier to use dockerized environment rather than a remote server because the configuration could be simply reset to the defaults. The final, working version of the setup: nginx, Jupyter Notebook, Ubuntu, docker, is available at my GitLab repository. Source of the […]
Jupyter Notebook Server installation
Create a new user For this example, we will be using a Linux username hyperion. In order to create a new user in Linux and set up a password, use the following commands: Note: -m is required in order to create user’s home directory the command to remove the user is: userdel hyperion To make sure that the user has been created, […]
Logging GNU screen command output
Previously I described how to use GNU screen to run bash commands in background. In addition to that, if sometimes it happens that a detached command terminates before completion, we would like to have logs for that command, e.g., in order to determine why and when an error occurred. This post explains how to log the progress of a command […]
One sample t-test in Excel
Recently I needed to quickly perform a one sample t-test in an Excel spreadsheet. Unfortunately, this functionality is not implemented in Excel by default. However, I found a very nice post by Zach at Statology on how to calculate this test using some build-in Excel functions and objects. For my convenience what I did was to put the whole procedure […]
Manhattan plot for GWAS
Based on R Bioconductor Sushi package I created a step-by step guide of how to produce a Manhattan plot for a genom-wide associaction study (GWAS).
Detaching a bash command with GNU screen
Sometimes running a bash command on the server can take several hours to complete. In such cases you would like to run the command in background and close the terminal from which the command was started (without terminating the process itself). The best way to achieve that is to use GNU screen’s detaching utility. In order to run and detach […]
General linear model in Python and C
The goal of this post is to explain how to use general linear model in Python and C. It is assumed that the reader has basic understanding of the regression inference. Introduction Why are we using Python and C in this example? Python code is often said to be an “executable pseudocode”, i.e., Python syntax is relatively easy to read […]
What is ANCOVA?
In a broad term, analysis of covariance (ANCOVA) is equivalent to multiple linear regression. However, there is a difference in the context in which these two approaches are utilized.