Repository for pipeline code
☆26Feb 28, 2024Updated 2 years ago
Alternatives and similar repositories for PPP
Users that are interested in PPP are comparing it to the libraries listed below
Sorting:
- A tool for estimating time-dependent migration rates based on cross-/within-population coalescent rates from MSMC☆16Apr 6, 2025Updated 11 months ago
- Code associated with the manuscript "A complete reference genome improves analysis of human genetic variation".☆17Jan 17, 2023Updated 3 years ago
- Main scripts and commands used to analyze goat population genetic and domestication☆19Mar 25, 2019Updated 6 years ago
- Leroy & Rougemont - “learning-by-doing” introduction to population genomics - scripts☆21Oct 2, 2019Updated 6 years ago
- Repository☆10Oct 23, 2024Updated last year
- Script for removing or counting invariant sites for the RAxML ascertainment bias corrections☆16Oct 12, 2024Updated last year
- Site frequency spectrum estimation based on window expectation-maximisation algorithm☆16May 19, 2023Updated 2 years ago
- A graph-based pipeline used to call/genotype snvs/indels/SVs from NGS data☆17Aug 30, 2025Updated 6 months ago
- Streamlined duo/trio analysis and pedigree haplotyping: from VCF to interactive HTML☆15Oct 30, 2024Updated last year
- The Vertebrate Genomes Project Mitogenome Assembly Pipeline☆19Mar 26, 2023Updated 2 years ago
- Homologizer: phasing gene copies into polyploid subgenomes☆11Feb 3, 2026Updated last month
- Bash scripts and data used in pantranscriptomic paper☆24Oct 21, 2022Updated 3 years ago
- Teaching modules for Human Genome Variation Lab.☆21Jun 6, 2025Updated 9 months ago
- R functions for generating site frequency spectra (SFS) from a VCF file.☆28Feb 13, 2020Updated 6 years ago
- SINE annotation tool for plant genomes☆19Jan 21, 2024Updated 2 years ago
- ☆21Feb 1, 2026Updated last month
- Snakemake workflow for Illumina RNA-sequencing experiments - extract population genomic signals from RNA-Seq data☆18Feb 17, 2026Updated last month
- ☆13Sep 11, 2025Updated 6 months ago
- RNA-seq analysis scripts☆16Jan 8, 2026Updated 2 months ago
- [mu]tation [s]pectrum [h]istory [i]nference☆27Jan 9, 2025Updated last year
- An R package for plotting GWAS results from the GAPIT package☆14Oct 9, 2025Updated 5 months ago
- Fast calculation of Patterson's D (ABBA-BABA) and the f4-ratio statistics across many populations/species☆186Dec 19, 2024Updated last year
- GONE: Scripts, programs and an example data set☆52Jul 20, 2025Updated 8 months ago
- CPANG19 - Computational PANGenomics (2019)☆12May 7, 2020Updated 5 years ago
- ☆18Dec 15, 2021Updated 4 years ago
- Reference bias measuring toolkit☆20Mar 12, 2026Updated last week
- ggplot2-based Manhattan plot☆12Oct 18, 2022Updated 3 years ago
- RIESLING: Super-enhancer identification. (Rapid Identification of EnhancerS LInked to Nearby Genes)☆10Jun 28, 2018Updated 7 years ago
- A mosaic genome painting tool for plant genomes☆18Mar 4, 2025Updated last year
- The pipelines were built in the project resolving the genome of a diploid potato. Most of the scripts were sepcially designed to perform …☆23Jul 4, 2023Updated 2 years ago
- Versatile tool for detecting selective sweeps with a variety of ages, strengths, starting allele frequencies, and completeness.☆15Feb 16, 2026Updated last month
- ☆12Nov 23, 2020Updated 5 years ago
- Readme☆10Mar 15, 2020Updated 6 years ago
- Unzip assembly graphs with Hi-C data and/or long reads.☆27Sep 20, 2024Updated last year
- A course with Jupyter Notebooks for Computational Population Genetics☆10Sep 4, 2022Updated 3 years ago
- Pipeline to perform the allele-specific expression analysis (based on the work by Skelly et al. 2011)☆12May 22, 2025Updated 10 months ago
- ☆13May 16, 2016Updated 9 years ago
- PanEffect is a JavaScript framework to explore variant effects across a pangenome. The tool has two views that allows a user to (1) expl…☆13Jan 30, 2024Updated 2 years ago
- ☆17Feb 11, 2026Updated last month