SNP chip data, PCA, and biomaRt in R (Bioinformatics S10E3) скачать в хорошем качестве

SNP chip data, PCA, and biomaRt in R (Bioinformatics S10E3)

Data analysis example of African goat SNP chip data using biomaRt. Principal Component Analysis (PCA) is used find SNPs involved in milk and meat production in African goats. After which I use biomaRt to query Ensembl for protein coding genes located near these SNPs. Lectures @ https://dannyarends.nl/bioinformatik/ Programming Assignments and Answers @ https://dannyarends.nl/bioinfo/ Playlist:    • Bioinformatics for Plant and Animal sciences   Chapters: 00:00 Welcome back and data overview 04:20 Overview of the 50K SNP genotype data 07:00 Annotation - individual goat level data, fix annotation errors and creating subsets 08:30 Clustering all 6000 animals together, relatedness between goats and breeds 13:18 Filtering down using meat and milk type and initial genotype data QC 19:16 Explanation of the Principal Component Analysis code 23:31 Running the PCA code, and explaining what happens 28:10 Analysis done, results of the PCA analysis 33:30 Connecting the R session to biomaRt and querying the goat gene database 40:34 Defining the regions based on the SNPs identified by PCA 46:23 Opening up the results, creating an overview table in MS Excel 49:59 A lot of unknown genes are present in some of the PCA identified regions 53:04 Initial excel table of the genes in the PCA identified regions This is a live-stream recording of the MSc and PhD lecture series: Bioinformatics for plant and animal sciences, given digitally during the Covid19 pandemic at the Humboldt University in Berlin organized and lectured by Dr Danny Arends. Thanks for taking an interest in my channel 😄If you've made it this far down, support me by giving a like or subscribing. Join me during my live streams Thursday afternoons on Twitch @   / dannyarends   This work is licensed under version 3.0 of the Creative Commons CC-BY license. For more information see http://creativecommons.org/licenses/b... #bioinformatics #computationalbiology #lectureseries #programmingforstudents #programmingforbeginners #molecularbiology #englishstream #msc #phd #livestream #computers #computerskills #live #assignments #statisticsfordatascience #academia #academicyoutube #datamanagement #datamanipulation #genes #pca #biomart #generegions #genotypes #SNPchip #genetics #goats