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2019_scworkshop

Repo for Physalia course Analysis of Single Cell RNA-Seq data

2020_scworkshop

Code and data repository for the 2020 physalia course on single cell RNA sequencing.

adaptiveattractor

The adaptive version of attractor algorithm.

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

ampliconreconstructor

Reconstructs complex variation using Bionano optical mapping data and breakpoint graph data

ampliconrepository

Website to host AmpliconSuite outputs, including AA outputs and resulting focal amplification classifications, such as ecDNA.

ampliconsuite

wrapping prepare AA, handling arguments, starting docker with correct reference files

ampliconsuiteaggregator

Aggregates the results from AmpliconSuite

ascat

ASCAT R package

bccmodels

Source files for DREAM7 BCC models

cafr

Attractor finding algorithm

ccube

Bayesian mixture models for estimating and clustering cancer cell fractions

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.

clustersv

SV clustering

cromwell

Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments

cycleviz

Visualize outputs of AmpliconArchitect and AmpliconReconstructor in Circos-style images.

depmap_omics

What you need to process the Quarterly DepMap-Omics releases from Terra

docker-ccube

ecnapp

ecsimulator

Simulate ecDNA structures with user-specified properties.

fingerprint_maps

Create "haplotype maps" of variants in order to use with Picardtools Crosscheck_Files utility, which allows for robust genotyping of functional genomic data.

gatk

Official code repository for GATK versions 4 and up

gbmatlas

glassx

GLASS consortium

hdp

R pkg for Hierarchical Dirichlet Process

heterogeneity

Code accompanying Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes

hoonbiolab.github.io

infercnv_workshop

medullo-ecdna

Code accompanying Chapman et al 2021, "The landscape of extrachromosomal circular DNA in medulloblastoma"