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accuracy_imputation

comprehensive function for computing imputation accuracy. Accuracy has been computed as % correct, allelic error rate, correlation and correlation based on centered and scaled genotypes.

average_relatedness_between_training_validation

Computation of average genomic/pedigree relatedness/kinship/similarity between training and testing set.

awesome-r

A curated list of awesome R frameworks, packages and software.

bglr-r

blupf90tutorialstandard

A tutorial of the BLUPF90 family programs

chatgpt-prompts-for-academic-writing

This list of writing prompts covers a range of topics and tasks, including brainstorming research ideas, improving language and style, conducting literature reviews, and developing research plans.

coursesfordatascience

Course materials for the Data Science Specialization: https://www.coursera.org/specialization/jhudatascience/1

debv_garrick

Deregression based on Garrick et al. (2009). With pedigree and files containing EBVs, Deregression is undertaken and deregressed EVC, deregressed reliabilities and weights are outputted.

exercises_linearmodels_r

fimpute_and_beagle_imputation

Bash script that allows you to run BEAGLE v3, v4, and FIMPUTE using PLINK format binary input files.

free-online-r-courses

Free online R courses

fullsib_relationships

Extracting Full/half sib relationships from a relationship matrix and ploting the results

genetics_rscripts

Handy genetics-related R scripts

genstats_site

Site for Genomic Data Science Class

gnrm_genomicpedigree

Genomic relationship based on methods described in VanRaden (2008) and Forni et al. (2011). Pedigree relationship is also computed using QTLrel package. Varying approaches covering centering and scaling of G matrix is undertaken

gptstudio

GPT RStudio addins that enable GPT assisted coding, writing & analysis

gpttools

gpttools extends gptstudio for package development to help you document code, write tests, or even explain code

haplos_analysis

Using haplotype blocks defined by Haploview and phased data, build the haplotype counts (change haplotypes into copies 0,1,2). Compute Genomic relationships based on the haplotypes

instant_r_packages

R script to copy the packages installed on one computer or R version to another

linux-commands

Some useful linux, git, vim and docker commands

manhattanplot_cmplot

R script to draw Manhattan plot using CMplot package

ped_check_amat

R script to manipulate and check pedigree file and calculate the triplet format of pedigree relationship matrix (A-matrix)

stat_comp

Statistical Computing (STT 802, EPI853b)

stghn

stghn.github.io

:page_with_curl: Sajjad Toghiani's Online CV