When life gives you big challenges, just say "It's a peanut! 🥜" and watch them become as small as one!
A comprehensive toolkit for Population & Quantitative Genetics Analysis
Dedicated to the giants whose shoulders we stand on:
G.J. Mendel and D.S. Falconer
- Inbreeding Coefficients
- F_GRM (GRM-based inbreeding)
- F_UNI (Uniting gametes correlation)
- F_HOM (Homozygosity-based)
- Principal Component Analysis (PCA)
- Genome-Wide Association Studies (GWAS)
- Genetic Data Management
- Format conversions (PLINK/VCF)
- Sample management
- Data merging
- Quality control
- Genome Annotation
- Feature annotation
- Distribution visualization
- GFF/GTF processing
- Effective Population Size (Ne)
- Genetic Diversity Suite
- H_O & H_E (Heterozygosity metrics)
- Allelic Richness
- F_ST & G_ST (Fixation indices)
- Population Differentiation Tools
- Pairwise F_ST
- AMOVA analysis
- Linkage Disequilibrium (LD)
- LD decay curves
- r² and D' calculations
- Admixture Analysis
- Selection Signatures
- iHS scores
- XP-EHH analysis
- Tajima's D
- Quantitative Genetics
- Additive Genetic Variance
- Breeding Values
- Heritability estimates
- Genetic Correlations
- ROH Analysis
- Homozygosity segments
- ROH-based metrics
- Clone this treasure chest:
git clone https://github.com/kkokay07/pq-genetics.git
- Navigate to your analysis of interest
- Follow the README.md - it's as easy as eating peanuts! 🥜
Can't find what you're looking for? No worries - it's just a peanut! 🥜
Drop me a line at [email protected] and I'll help you crack it:
- Custom metrics? Just ask!
- Special analyses? I've got you!
If you find this toolkit helpful and want to support open science and free education, consider contributing to:
UPI: 8618102886@ybl
Dr. Kanaka K. K., PhD, ARS
Scientist
School of Bioinformatics
ICAR-Indian Institute of Agricultural Biotechnology, Ranchi
Be like IIAB!: IIAB is like yogic center where all the sciences (Plant, Animal, Aquatic,Mibrobiology, IT) meet to address emerging issues in food production.
Remember: Every analysis is just a peanut waiting to be cracked! 🥜
When the data seems overwhelming - just say "It's a peanut!"
When the statistics look scary - whisper "It's a peanut!"
When the code won't run - smile and say "It's a peanut!"
🥜 It's a peanut!