Public Projects - Human NGS Data

GWAS training for ACE Mali - utilizing PLINK, a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses

An introduction to the R programming language and the components of programming including syntax, data types, dataframes and basic data analysis.

Advanced literature search in PubMed with an overview of PubMEd and exercise including general and clinical search, building queries and collections.

Cheminformatics training covering an intro to drug discovery, molecular file formats and databases, aligning molecules, QSAR, screening and de novo design.

Sequence retrieval tools (SRA)  for downling bulk geneomic or protein sequence data

Survey of molecular and population mechanisms creating and maintaining genetic diversity.

Learn about shotgun metagenomics with a visual and interactive community exploration software MEGAN6-CE

Introduction to protein databases, their contents and uses in bioinformatics research

Metagenomics overview (Shotgun metagenomics)

Introduction to Statistical Analysis in R

Introduction to Awk and Sed programming

Introduction to R markdown

Managing data and simple analyses in the Galaxy cyber-environment (Practical)

Introductory Training on Bash scripting. It covers basic concepts on programming. Students will be able to follow along to create various loops and other simple operations. Materials include the code used.

Manipulating files and data on Linux

Generating graphics in R - using ggplo2 from beginning with graphics through saving plots, themes, and facets.

Tutorial for learning to use the editor VIM for Unix. Demo to show file manipulation and basic command line operations using an editor.

Metagenomics overview (Metataxonomics)

Generating data and manipulating objects will introduce data object, structure, some useful functions to describe data, and data manipulation. (Part II - includes dplyr)

How to Check the Quality of Illumina Sequencing Reads with FastQC

A tour of primary sequence databases including NCBI, Array Express, GEO, PDB, Intro Pro, UniProt and Ensembl.

Processing of Aligned Reads for RNA-seq using R from QC and trimming, to mapping and differential analysis

Intro to NGS and Sanger Sequencing including the technology, sequencers and their applicability to differen research questions.

Introduction to UNIX editors: Vi

Introduction to UNIX and Text Editing

Basic conceps and use of UCSC Genome Browser Tutorial to visualize genomes, genes and other sequence entities in context.

Haplotype-based Association Test, Linkage Analysis for Binary Traits and Quantitative Traits

Mechanisms of Evolution including mutations, chromosomal variations and genomic variations

Python programming training covering the excellent DnaFeaturesViewer genome and protein visualization package.