A realistic-ish aDNA simulator
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Jul 11, 2025 - Python
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paleogenomics
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An ancient DNA genetic relatedness estimation software relying on pedigree simulations
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Aug 11, 2026 - Rust
Perform hard selective masking of ancient DNA deamination patterns, using the output misincorporation frequency estimates of MapDamage (https://ginolhac.github.io/mapDamage/)
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May 15, 2025 - Rust
grups.plots is a companion R package to grups-rs, providing with a Shiny dashboard, harboring multiple interactive visualizations, utilities and summary statistics to analyse its results
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Mar 31, 2025 - R
Visualize ancient DNA and archaeological samples on an interactive map — filter by Y-DNA, mtDNA, culture, and date.
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Mar 28, 2026 - Julia
Vous retrouverez ici mes projets scientifique en rapport avec la génomique ou mes études.
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Sep 2, 2025 - JavaScript
Scripts associated with the article "Sediment Metagenomes as Time Capsules of Lake Microbiomes"
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Oct 23, 2024 - HTML
Ancestral felid mitochondrial genome reconstruction from 83 feliform mitogenomes (5 extinct felids), with full validation and a documented retraction of its original phenotypic conclusions.
reproducible-research phylogenetics ancient-dna mitochondrial-genome ancestral-sequence-reconstruction paleogenomics comparative-biology felidae
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Sep 6, 2026
RxSexID infers biological sex from mapped reads using the Rx statistic (Skoglund et al. 2013): the ratio of X-chromosome coverage to an autosomal baseline for ancient and degraded DNA
python bioinformatics r genomics bam samtools ancient-dna sex-determination paleogenomics hakai-institute rx-statistic
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Jun 11, 2026 - Python
Reconstructing olfactory receptor repertoires across the Homo lineage using ancient DNA as templates for functional odorant receptor expression assays.
hpc regression phylogenetics vcftools bcftools olfaction cladogram heatmap-visualization human-evolution paleogenomics odorant-receptors functiona-expression functional-genetics
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Mar 3, 2026 - R
Nextflow DSL2 pipeline for ancient DNA: raw fastq to EIGENSTRAT via PALEOMIX, damage-aware clipping, pseudo-haploid genotyping and Rx sex determination (horse, EquCab3.0).
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Aug 21, 2026 - Python
TackleBox is a collection of module tools for targeted ancient DNA research.
python bash bioinformatics metagenomics ncbi gbif reference-database megan ancient-dna paleogenomics hakai-institute capture-enrichment bait-design
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Sep 3, 2026 - Python
A semi-random collection of small, useful tools for ancient DNA bioinformatics, plotting, and file summaries.
python bioinformatics r genomics metagenomics bam samtools nf-core megan utility-scripts ancient-dna paleogenomics hakai-institute mapdamage
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Jun 11, 2026 - Python
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