Data handling

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The BD2K Guide to the Fundamentals of Data Science Series
#Lecture/Webinar
Submitted by rehabbashaaree@gmail.com - Sun, 10/02/2016 - 22:35

It is about big data in Medicine!

PLINK v1.90
#MOOC
Submitted by b.mlotshwa@hotmail.co.uk - Thu, 06/23/2016 - 23:10

The focus of PLINK is purely on analysis of genotype/phenotype data. using PLINK, researchers can read data in a variety of formats, recode and reorder files, merge two or more files, extract subsets (SNPs or individuals), flip strand of SNPs and compress data in a binary file format. PLINK also enables researchers to perform summary statistics for quality control, detect population…

EMBO Practical Course on Analysis of High-Throughput Sequencing Data
#MOOC
Submitted by b.mlotshwa@hotmail.co.uk - Thu, 06/23/2016 - 22:54

Familiarity with the technology and biological use cases of high throughput sequencing is required, as is some experience with R/Bioconductor. The lectures give insight into how biological knowledge can be generated from RNA-Seq and ChIP-Seq experiments and illustrate different ways of analysing such data. Practicals consist of computer exercises that will enable the participants to apply…

eBiomics: Good practices and specific methods for using bioinformatics resources
#MOOC
Submitted by b.mlotshwa@hotmail.co.uk - Thu, 06/23/2016 - 22:51

eBiomics is composed of several interconnected sections that can be accessed through different interactive activities. The 5 main sections of the website are: Resources ( a catalogue of selected databases and data analysis software that are briefly described and illustrated with examples); Conceptual flowcharts (a collection of clickable images picturing typical data analysis flows in…

EBI: Next Generation Sequencing Practical Course
#MOOC
Submitted by b.mlotshwa@hotmail.co.uk - Thu, 06/23/2016 - 22:49

This course is designed to impart the following objectives: understanding of some principles behind NGS; knowledge of the challenges created by NGS; knowledge of how to submit and retrieve NGS data to and from databases and understanding the uses of NGS data in whole genome assembly, gene expression analysis, genome annotation, gene regulation analysis and variation studies.

Genephony
#Software
Submitted by kgurwitz@gmail.com - Fri, 04/15/2016 - 23:15

'Genephony is an online tool for the manipulation of large datasets of genomic information. It can be used as a browser for genomic data, as a high-throughput annotation tool, and as a knowledge discovery tool.' - from the website

LEfSe
#Software
Submitted by kgurwitz@gmail.com - Fri, 04/08/2016 - 23:27

In determining differences between two or more biological conditions, LEfSe "emphasizes both statistical significance and biological relevance, allowing researchers to identify differentially abundant features that are also consistent with biologically meaningful categories (subclasses). LEfSe first robustly identifies features that are statistically different among biological classes. It then…

MetaPhIAn2
#Software
Submitted by kgurwitz@gmail.com - Fri, 04/08/2016 - 23:22

"a computational tool for profiling the composition of microbial communities (Bacteria, Archaea, Eukaryotes and Viruses) from metagenomic shotgun sequencing data with species level resolution." - from the website
Workflow available in Galaxy.

HUMAnN2
#Software
Submitted by kgurwitz@gmail.com - Fri, 04/08/2016 - 23:18

"HUMAnN is a pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data." - from the website. This tool uses 'functional profiling' to ask "What are the microbes in my community-of-interest doing (or capable of doing)?"

VarElect
#Software
Submitted by kgurwitz@gmail.com - Fri, 04/08/2016 - 23:17

*Interpret next generation sequencing results
*Identify & Prioritize genes and variants according to their relevance to diseases and phenotypes of interest
*Explore relationships between genes and gene variants and selected diseases or phenotypes via relevant pathways, interaction networks and publications
*Discover biomarkers for diseases
-from the website.

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