Software/Apps

IGV

Browser-accessible IGV instance for viewing genomic tracks and sequence-alignment data.

PureTargetViz

Visualization utility for PureTarget outputs and target-analysis summaries.

VenomMaps

Shiny app for exploring New World pitviper distributions, niche models, and occurrence records for research, conservation, and snakebite-related medical reference.

Supplemental software: autokuenm

ToxCodAn

Toxin annotator and guide for venom gland transcriptomics.

ToxCodAn Guide to Venom Gland Transcriptomics

BiologyPhdStipends

Database and Shiny app for comparing biology PhD stipends and supporting graduate-student living-wage advocacy.

MitoSIS

Mitochondrial Species Identification System for mitochondrial genome assembly and sample contamination or mislabeling checks.

CoordinateMapper

Shiny app for quickly plotting and checking geographic coordinates.

PhyProbe

Pipeline for extracting phylogenetic loci from next-generation sequencing datasets, including RNA-seq, whole-genome, and target-capture data.

TransMap

Pipeline for cross-species comparative transcriptome analyses using homology-weighted transcriptome expression mapping.

Walter

Bioinformatics utility repository for workflow support and sequence-analysis tasks.

pyVAE

Modified popVAE-style variational autoencoder for generalized multidimensional data such as transcriptome expression matrices.

HelixText

Convert text into DNA sequences for fun.

BaseModViewer

Visualize modified-base annotations from BAM MM tags.