Machine Learning for COVID-19 Data Analysis Project

This repository gives an overview of my teaching activities. Links to slides and data sets are included. Feel free to re-use my content.

The SpeciesPrimer pipeline is intended to help researchers finding specific primer pairs for the detection and quantification of bacterial species in complex ecosystems.

Design degenerated primers on highly variable alignments for full genome sequencing or qPCR. Specifically developed for viruses.

A PCR primer tool for DNA assembly flows

Acconeer Exploration Tool

High throughput In-silico PCR

Wetlab Calculator

In Silico PCR for Python3

A tool in order to accurately remove primer sequences from NGS reads in an amplicon experiment

multiPrime is a mismatch-tolerant minimal primer set design tool for large and diverse sequences (e.g. Virus). Here is a web-based version (test: http://multiPrime.cn))

Basecalling, alignment, assembly and deconvolution of Sanger Chromatogram trace files

This is a user space TSS for TPM 2.0. It implements the functionality equivalent to (but not API compatible with) the TCG TSS working group's ESAPI, SAPI, and TCTI API's (and perhaps more) but with a hopefully simpler interface.

PCR Primer Quality Control

A simple, ready-to-use PCR calculator for my Lab colleagues and me.

This project explores interpretable machine learning models using Decision Trees for classification and LASSO, Ridge Regression, PCR, and Boosting techniques for regression, applied to Acute Inflammations and Communities and Crime datasets, focusing on model interpretability, feature analysis, and optimization.

Ampseer examines reads in fastq format and identifies which multiplex PCR primer set was used to generate the SARS-CoV-2 sequencing library they are read from. It is intended to differentiate between ARTIC v3, ARTIC v4, ARTIC v4.1, VarSkip 1a, VarSkip 2, Midnight and VarSkip Long primer sets sequenced by Illumina or ONT.

Parsing, Manipulation, and Visualization of Metabarcoding/Taxonomic data

Clermont PCR method In-Silico

Online PCR simulator, Tm calculator and primer designer and more!