Chase W. Nelson 倪誠志

All

9 repositories

Soni-response
Public
Scripts, analysis code, input data, and intermediate files for response to Soni et al.
diversity evolution slim nucleotide natural-selection nucleotide-diversity covid-19 sars-cov-2 evolutionary-simulation intrahost-genetic-diversity
R
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GNU General Public License v3.0
•0•1•0•0•Updated Apr 20, 2024Apr 20, 2024
Taiwan-COVID-19
Public
Analysis and visualization of Taiwan’s COVID-19 data
visualization r taiwan epidemiology covid-19 sars-cov-2
R
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GNU General Public License v3.0
•4•28•0•0•Updated Nov 24, 2023Nov 24, 2023
SNPGenie
Public
Program for estimating πN/πS, dN/dS, and other diversity measures from next-generation sequencing data
evolution perl next-generation-sequencing vcf population-genetics dnds-estimation molecular-evolution nucleotide vcf-files diversity-measurement
Perl
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GNU General Public License v3.0
•37•109•28•0•Updated Aug 21, 2023Aug 21, 2023
OLGenie
Public
Program for estimating dN/dS in overlapping genes (OLGs)
selection overlapping dnds-estimation molecular-evolution positive-selection dnds natural-selection nei-gojobori purifying-selection neutral-evolution
Perl
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GNU General Public License v3.0
•2•13•2•0•Updated Dec 2, 2022Dec 2, 2022
HPV16-molecular-evolution
Public
Supplementary material for study of HPV16 molecular evolution
Python
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GNU General Public License v3.0
•0•0•0•0•Updated Sep 13, 2022Sep 13, 2022
VCFgenie
Public
Program for reproducibly filtering VCF files and eliminating false positive variants
Python
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GNU General Public License v3.0
•0•1•0•0•Updated Aug 25, 2022Aug 25, 2022
SARS-CoV-2-ORF3d
Public
Supplementary scripts for Nelson et al. (2020) paper on ORF3d
python r perl biopython overlapping-genes within-host covid-19 sars-cov-2 orf3d olgenie
R
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GNU General Public License v3.0
•4•5•0•0•Updated Nov 5, 2020Nov 5, 2020
trevolver
Public
Program for simulating non-reversible DNA sequence evolution on a fixed bifurcating tree using trinucleotide context
simulation evolution perl mutation phylogenetic-trees dna molecular-evolution evolution-simulation evolution-simulator coalescence
Perl
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GNU General Public License v3.0
•1•9•0•0•Updated Sep 19, 2020Sep 19, 2020
EBT
Public
Evolutionary Bioinformatics Toolkit (EBT)
perl vcf fasta gtf sequence dna-sequences sequence-alignment fasta-sequences gff vcf-files
Perl
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GNU General Public License v3.0
•4•11•1•0•Updated Jul 14, 2020Jul 14, 2020