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Mohsin Ali
Приєднався 28 чер 2015
Hi, My name is Mohsin Ali (PhD). I go by Ali. I am deeply passionate about plants and quantitative genomics. With over five years of experience in the field of plant breeding and quantitative genetics, I have dedicated my career to exploring the intersection of these fascinating subjects.
On this channel, my goal is to provide accessible tutorials on various topics, including simple R programming, data analytics, and genetics and genomics software packages. Join me as we delve into the world of plant science and genomics together.
On this channel, my goal is to provide accessible tutorials on various topics, including simple R programming, data analytics, and genetics and genomics software packages. Join me as we delve into the world of plant science and genomics together.
Linkage disequilibrium (LD) decay plot from TASSEL LD results using R software.
This tutorial video is about the estimation and plotting of LD decay over distance from the LD results from TASSEL 5. This tutorial is only for teaching purposes.
For viewer interest, the R-script is written following Remington, et al. (2001). The R-script can be download from my GitHub page (github.com/mohsinali1990/My_scripts).
Related tutorials links are:
1. TASSEL software installation:
ua-cam.com/video/5kJGOXLKEGw/v-deo.html
2. R software and Rstudio installation:
ua-cam.com/video/QdDqzDL8oWs/v-deo.html
Like the video! why not buy me a coffee?
www.buymeacoffee.com/mohsinali90
For viewer interest, the R-script is written following Remington, et al. (2001). The R-script can be download from my GitHub page (github.com/mohsinali1990/My_scripts).
Related tutorials links are:
1. TASSEL software installation:
ua-cam.com/video/5kJGOXLKEGw/v-deo.html
2. R software and Rstudio installation:
ua-cam.com/video/QdDqzDL8oWs/v-deo.html
Like the video! why not buy me a coffee?
www.buymeacoffee.com/mohsinali90
Переглядів: 10 383
Відео
A step by step tutorial to detect population structure using STRUCTURE software.
Переглядів 18 тис.3 роки тому
STRUCTURE is one of the Softwares that assign individuals to populations using genotype data. It is most widely used clustering software applied to cluster individual into groups. For more detail, please read following article: 1. Pritchard, Jonathan K., William Wen, and Daniel Falush. "Documentation for STRUCTURE software: Version 2." (2003). 2. Earl, Dent A. "STRUCTURE HARVESTER: a website an...
SNP quality control and PCA analysis with Plink Software in RStudio.
Переглядів 12 тис.3 роки тому
PLINK command-line program, which easily handles large-scale SNP dataset. This software involve running several commands (or options), e.g. to produce summary statistics on missing data, to exclude some SNPs based on these results, to run an association analysis. Each command involves a separate instantiation of plink - note that PLINK does not remember any parameter settings between different ...
Background music for productive work.
Переглядів 1083 роки тому
Play this music while working on a coding project. This music will boost your concentration.
mrMLM (multi-locus random-SNP-effect mixed linear Model) tools for genome-wide association study.
Переглядів 4,1 тис.3 роки тому
"mrMLM" is one of the R packages which led the user to conduct GWAS analysis. The association analysis proceeds under the framework of multi-locus random-SNP-effect mixed linear model (mrMLM). There are seven approaches implemented in mrMLM.GUI package to detect QTNs. For more detail on mrMLM R package please see the following link: cran.r-project.org/web/packages/mrMLM.GUI/index.html. In this ...
Convert SNP data from one format to another in few clicks. Part 1| HapMap | VCF | Plink
Переглядів 6 тис.3 роки тому
In this tutorial, I used TASSEL software to convert SNP data into different data formats (e.g., VCF and Plink). The TASSEL tutoriL data was used for this tutorial (tassel.bitbucket.io/docs/TASSELTutorialData5.zip). However, there many other software's that could be used to transform genotypic data into different format. GWAS analysis using TASSEL software: ua-cam.com/video/5kJGOXLKEGw/v-deo.htm...
GWAS analysis using rMVP package in R software.
Переглядів 9 тис.3 роки тому
rMVP (Memory-Efficient, Visualize-Enhanced, Parallel-Accelerated GWAS Tool) is one of widely used tool to perform GWAS analysis. This package can (1) handle and process large data, (2) evaluate population genetic structure, (3) compute variance components, (4) implement parallel-accelerated association tests of SNPs through three statistical models (GLM, MLM and FarmCPU), (5) enhance visualizat...
Background music for concentration.
Переглядів 583 роки тому
Background music for deep focus and concentration.
Haplotype-based GWAS analysis using rtm-gwas software. A quick GWAS tutorial
Переглядів 2,1 тис.3 роки тому
RTM-GWAS (restricted two-stage, multi-locus, mutli-allele GWAS) is a novel approach to detect whole-genome QTL alleles controlling target traits in plants. In this tutorial, I will show you how haplotype-based GWAS is performed using RTM-GWAS software. RTM-GWAS software download link: github.com/njau-sri/rtm-gwas For more details, see RTM-GWAS software help page: gitee.com/njau-sri/rtm-gwas/wik...
20 Minutes relaxing background music for stress relief.
Переглядів 853 роки тому
Music for relaxation and stress relief.
ANOVA of multi-environmental trails using QTL IciMapping software. Heritability-Variance Comps-BLUEs
Переглядів 1,2 тис.3 роки тому
QTL IciMapping: Integrated Software for Building Genetic Linkage Maps and Mapping Quantitative Trait Genes. In this tutorial, I used AOV functionality of QTL IciMapping software. In functionality AOV, ANOVA analysis was implemented. Unbalanced data (or phenotypic data with missing) can also be analyzed. For more detail, please see software manual.
Imputation of missing data using Beagle software.
Переглядів 6 тис.3 роки тому
Beagle is a Java-based software for phasing genotypes and for imputing ungenotyped markers (i.e., missing data in the SNP matrix). In this tutorial, i am using TutorialData from TASSEL software. Moreover, TASSEL software can also impute missing data. TASSEL imputation tutorial: ua-cam.com/video/5kJGOXLKEGw/v-deo.html For detailed information about the imputation of missing data, please visit Be...
Genome-wide Association Study (GWAS) analysis in TASSEL Software (GUI).
Переглядів 18 тис.3 роки тому
TASSEL is one of the statistical software's to conduct association mapping such as General Linear Model (GLM) and Mixed Linear Model (MLM). In this tutorial, I will show you how to install TASSEL software and preprocess SNPs to run association analysis in TASSEL. For detailed information about TASSEL, please visit: www.maizegenetics.net/tassel. R-script to plot GWAS results link: github.com/moh...
Genetic analysis with PowerMarker software | step by step tutorial
Переглядів 13 тис.3 роки тому
PowerMarker is a comprehensive software package for genetic marker data analysis, designed especially for SSR/SNP data analysis. PowerMarker builds a powerful user interface around both new and traditional statistical methods for population genetic analysis. In this video, i have just covered estimation of basic population parameters such as genetic diversity, hetrozygosity and polymorphic info...
Installing Linux subsystem on windows 10 | A step by step tutorial
Переглядів 4043 роки тому
Install Ubuntu Linux subsystem in windows 10 easily. #Linux #Windows10 #tutorial #mohsinali #installation
Download and install R software for beginners | tutorial
Переглядів 2443 роки тому
Download and install R software for beginners | tutorial