Dr. Sultan Mia's repositories
cider-vs-dessert
This repository contains data and scripts used to repoduce analyses in the manuscript "Quantifying the differences between cider and dessert apples".
GPU-accelerated-guppy-basecalling
GPU-accelerated guppy basecalling and demultiplexing on Linux
shell-genomics
Introduction to the Command Line for Genomics
SOAPnuke
A Tool for integrated Quality Control and Preprocessing on FASTQ or BAM/CRAM files
PyBSASeq
A novel algorithm for BSA-Seq data analysis
minimalmarkers
Code for choosing the minimal set of genetic markers needed to differentiate all samples in a genotyping dataset
LongRead_tutorials
Workflows and tutorials for LongRead analysis with specific focus on Oxford Nanopore data
snphub
A Shiny-based server framework for retrieving, analyzing and visualizing the large genomic variations data in a lab.
learning-resource-links
An awesome list of learning resources for bioinformatics, genomics and computational biology
common_analyses
Repository of common bioinformatics scripts
bookdown-demo
A minimal book example using bookdown
CV
My curriculum vitae.
Rnotebook_Self-incompatibility
Apple S-allele
abc-phenomics
Phenotypic analysis of 1119 apple accessions within the ABC.
bioruby-polyploid-tools
Library and tools to deal with polyploid genomics
submission_checklist
A checklist to help you avoid all those minor errors when submitting a scientific manuscript
TBtools
GUI/CommandLine Tool Box for biologistists to utilize NGS data.
Intro-to-rnaseq-hpc-O2
This repository has teaching materials for a 2 and 3-day Introduction to RNA-sequencing data analysis workshop using the O2 Cluster
Heritability
Heritability in plant breeding - R and SAS code examples
Things-a-scientist-is-suppposed-to-know
A comprehensive and long list of things a modern scientist is supposed to know
Pedimap
Pedimap: software for the visualization of genetic and phenotypic data in pedigrees
TASSEL-workshop
This site contains sample files and instructions for the TASSEL workshop hosted by the UMN Plant Breeding Center.
Seedling_Select
Seedling Select is a cost modeling tool to estimate seedling selection cost for tree fruit breeding programs.
CMplot
📊 Circular and Rectangular Manhattan Plot
rstatix
Pipe-friendly Framework for Basic Statistical Tests in R
genomics-tutorial-_sscheiem
Sphinx documentation source for a computational genomics tutorial.
Cat-Does-Plant
Cat doing plant science.