Pinned Repositories
CARD-VNTR
Tandem repeat analysis for the CARD consortium
Ctyper
Genotyping of paralog specific gene types
danbing-tk
Toolkit for VNTR genotyping and repeat-pan genome graph construction
devas
Deep learning validation of SV calls
hmcnc
Hidden Markov Model based Copy number caller
LRA
Long read aligner
SegDupAnnotation
SegDupAnnotation2
Count gene duplications.
TT-Mars
Structural Variants Assessment Based on Haplotype-resolved Assemblies
vamos
VNTR annotation using motif selection
ChaissonLab's Repositories
ChaissonLab/LRA
Long read aligner
ChaissonLab/vamos
VNTR annotation using motif selection
ChaissonLab/danbing-tk
Toolkit for VNTR genotyping and repeat-pan genome graph construction
ChaissonLab/TT-Mars
Structural Variants Assessment Based on Haplotype-resolved Assemblies
ChaissonLab/hmcnc
Hidden Markov Model based Copy number caller
ChaissonLab/SegDupAnnotation
ChaissonLab/Ctyper
Genotyping of paralog specific gene types
ChaissonLab/devas
Deep learning validation of SV calls
ChaissonLab/SegDupAnnotation2
Count gene duplications.
ChaissonLab/CARD-VNTR
Tandem repeat analysis for the CARD consortium
ChaissonLab/AssemblyAnalysis
ChaissonLab/chaissonlab.github.io
Start page for lab website.
ChaissonLab/danbing-tk_rxiv
Genome-wide genotyping of VNTRs from short-read datasets with haplotype-resolved database
ChaissonLab/eMotif_manuscript_analysis_scripts
Analysis scripts associated with the manuscript "The motif composition of variable-number tandem repeats impacts gene expression", including bias correction, eQTL mapping, fine-mapping, and genome folding prediction.
ChaissonLab/GenomeIndex
paths to genome data -> download
ChaissonLab/hgsvg
Analysis code for 1kg
ChaissonLab/PartitionedAssembly
Simple phase partitioned pipeline
ChaissonLab/rare-var-scratch
ChaissonLab/ScreenInversions
Simple code to look for inversions in local assemblies.
ChaissonLab/sedef
Identification of segmental duplications in the genome
ChaissonLab/vamos-somatic
A wdl file for generating per-read calls for tandem repeats in long-read data.
ChaissonLab/bioconda-recipes
Conda recipes for the bioconda channel.
ChaissonLab/GTEx-tools
Small tool-list for gtex
ChaissonLab/L1Scan
Scan a bam file for l1 insertions.
ChaissonLab/mcst
Simple sam manipulation code. Includes inversion finding.
ChaissonLab/RepeatMasking
A snakefile to run repeatmasker on genomes in a scatter/gather approach.