jluebeck
Bioinformatics post-doc at UC San Diego working in the Vineet Bafna lab. Lead developer of @AmpliconSuite.
UC San DiegoSan Diego
Pinned Repositories
AmpliconArchitect
Identify one or more connected, focally amplified genomic regions to elucidate the architecture of focal amplifications such as ecDNA.
AmpliconClassifier
Classify output of AmpliconArchitect to detect types of focal amplifications present
AmpliconSuite-pipeline
A quickstart tool for AmpliconArchitect. Performs all preliminary steps (alignment, CNV calling, seed interval detection) required prior to running AmpliconArchitect. Previously called PrepareAA.
CoRAL
Complete Reconstruction of Amplifications with Long reads
CycleViz
Visualize outputs of AmpliconArchitect and AmpliconReconstructor in Circos-style images.
bionano_tools
Helper scripts for working with Bionano data
FaNDOM
Fast Nested Distance aligner for Optical Maps
ReactionDiffusionSimulator
Simulate and visualize reaction-diffusion models and Turing patterns
ScaffoldGraphViewer
Cytoscape.js viewer for AmpliconReconstructor Scaffold Graph
WordleSolver
A maximum-entropy solution to Wordle
jluebeck's Repositories
jluebeck/ReactionDiffusionSimulator
Simulate and visualize reaction-diffusion models and Turing patterns
jluebeck/FaNDOM
Fast Nested Distance aligner for Optical Maps
jluebeck/bionano_tools
Helper scripts for working with Bionano data
jluebeck/WordleSolver
A maximum-entropy solution to Wordle
jluebeck/ScaffoldGraphViewer
Cytoscape.js viewer for AmpliconReconstructor Scaffold Graph
jluebeck/circdna
Pipeline for the identification of extrachromosomal circular DNA (ecDNA) from Circle-seq, WGS, and ATAC-seq data that were generated from cancer and other eukaryotic cells.
jluebeck/jluebeck.github.io
Github Pages template for academic personal websites, forked from mmistakes/minimal-mistakes