GitHunt

Chase W. Nelson 倪誠志

chasewnelson

Research Fellow at NCI-NIH | Visiting Scientist at AMNH | Bioinformatics, cancer, molecular evolution, overlapping genes, population genetics, viruses

Languages

Perl44%R33%Python22%

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Top Repositories

Repositories

9
CH
chasewnelson/SNPGenie

Program for estimating πN/πS, dN/dS, and other diversity measures from next-generation sequencing data

Perl12137Updated 3 weeks ago
diversity-measurementdndsdnds-estimationevolutionevolutionary-parametersfasta-sequencesmolecular-evolutionnatural-selectionnei-gojoborinext-generation-sequencingnucleotidenucleotide-diversityperlpopulation-geneticssequence-analysissnp-reportsubstitution-ratevcfvcf-files
CH
chasewnelson/VCFgenie

Program for reproducibly filtering VCF files and eliminating false positive variants

Python00Updated 1 month ago
CH
chasewnelson/EBT

Evolutionary Bioinformatics Toolkit (EBT)

Perl124Updated 3 months ago
dna-sequencesfastafasta-sequencesgffgtfperlsequencesequence-alignmentvcfvcf-files
CH
chasewnelson/OLGenie

Program for estimating dN/dS in overlapping genes (OLGs)

Perl143Updated 4 months ago
dndsdnds-estimationmolecular-evolutionnatural-selectionnei-gojoborineutral-evolutionoverlappingoverlapping-genesperlpositive-selectionpurifying-selectionselection
CH
chasewnelson/SARS-CoV-2-ORF3d

Supplementary scripts for Nelson et al. (2020) paper on ORF3d

R54Updated 6 months ago
between-hostbiopythoncovid-19olgenieorf3doverlapping-genesperlpythonrsars-cov-2snpgeniewithin-host
CH
chasewnelson/HPV16-molecular-evolution

Supplementary material for study of HPV16 molecular evolution

Python00Updated 1 year ago
CH
chasewnelson/Taiwan-COVID-19

Analysis and visualization of Taiwan’s COVID-19 data

R284Updated 1 year ago
covid-19epidemiologyrsars-cov-2taiwanvisualization
CH
chasewnelson/Soni-response

Scripts, analysis code, input data, and intermediate files for response to Soni et al.

R10Updated 1 year ago
covid-19diversityevolutionevolutionary-simulationintrahostintrahost-genetic-diversitynatural-selectionnucleotidenucleotide-diversitysars-cov-2slim
CH
chasewnelson/trevolver

Program for simulating non-reversible DNA sequence evolution on a fixed bifurcating tree using trinucleotide context

Perl91Updated 2 years ago
coalescencoalescencednaevolutionevolution-simulationevolution-simulatormolecular-evolutionmutationnon-reversibleperlphylogenphylogenetic-treessimulationtrevolvertrinucleotide

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