sclipman
Epidemiologist & Bioinformatician, Assistant Professor at Johns Hopkins University School of Medicine
Johns Hopkins School of MedicineBaltimore, MD, USA
Pinned Repositories
Anelloflow
Bioinformatics pipeline for detecting anelloviruses present in samples using our metagenomic RCA ONT protocol
augur
Pipeline components for real-time virus analysis
Authorplea-Filenamer
Python script for automatically prefixing .docx files with the author's last name
barabasialbert
Simulation of a scale-free network using the Barabási-Albert model.
CoupledMCMC
Coupled MCMC for Beast2
EPI-ClusT
User-friendly distance-free method for defining clusters from phylogenetic trees
NGSTools
Next-Generation Sequencing(NGS) toolkits.
Phylogeography
This repository hosts code for an animated phylogeographic plot of HCV spread among PWID in India
sociospatial-baseline
This repository hosts data and code for an interactive sociospatial network visualization of baseline HIV/HCV prevalence among a cohort of people who inject drugs in New Delhi, India. Visit the link below to view the interactive figure.
SociospatialNet-Incidence
This repository hosts code for an interactive sociospatial network visualization of HIV incidence among a cohort of PWID in New Delhi, India
sclipman's Repositories
sclipman/EPI-ClusT
User-friendly distance-free method for defining clusters from phylogenetic trees
sclipman/Anelloflow
Bioinformatics pipeline for detecting anelloviruses present in samples using our metagenomic RCA ONT protocol
sclipman/Phylogeography
This repository hosts code for an animated phylogeographic plot of HCV spread among PWID in India
sclipman/augur
Pipeline components for real-time virus analysis
sclipman/Authorplea-Filenamer
Python script for automatically prefixing .docx files with the author's last name
sclipman/barabasialbert
Simulation of a scale-free network using the Barabási-Albert model.
sclipman/CoupledMCMC
Coupled MCMC for Beast2
sclipman/EV-D68
sclipman/NGSTools
Next-Generation Sequencing(NGS) toolkits.
sclipman/sociospatial-baseline
This repository hosts data and code for an interactive sociospatial network visualization of baseline HIV/HCV prevalence among a cohort of people who inject drugs in New Delhi, India. Visit the link below to view the interactive figure.
sclipman/SociospatialNet-Incidence
This repository hosts code for an interactive sociospatial network visualization of HIV incidence among a cohort of PWID in New Delhi, India
sclipman/gephi-plugins
Switch to the sigmaexporter-plugin branch (https://github.com/oxfordinternetinstitute/gephi-plugins/tree/sigmaexporter-plugin/modules/sigmaExporter) or jsonexporter-plugin branch (https://github.com/oxfordinternetinstitute/gephi-plugins/tree/jsonexporter-plugin/modules/JsonExporter) for the relevant code.
sclipman/GraphRNN
sclipman/hyphy
HyPhy: Hypothesis testing using Phylogenies
sclipman/Markdown
Google Chrome, Firefox, and Thunderbird extension that lets you write email in Markdown and render it before sending.
sclipman/PandemicPulse
Rapid, real-time monitoring of the SARS-CoV-2 pandemic and its impacts
sclipman/pgeocode
Postal code geocoding and distance calculation
sclipman/Phydelity
Inference of putative transmission phylogenetic clusters
sclipman/sclipman
Config files for my GitHub profile.
sclipman/shiver
Sequences from HIV Easily Reconstructed
sclipman/vg
tools for working with genome variation graphs