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alleloscope

Alleloscope is a method for allele-specific copy number estimation that can be applied to single cell DNA and ATAC sequencing data (separately or in combination). Allele-specific estimation allows for the more accurate delineation of copy number states and the detection of subclonal copy-neutral loss-of-heterozygosity and mirrored CNA events. On scATAC-seq data, Alleloscope allows integrative multi-omic analysis of allele-specific copy number and chromatin accessibility for the same cell.

approxbayes.jl

Approximate Bayesian Computation (ABC) algorithms for likelihood free inference in julia

bayes-bior-docker

Docker container for collection of R packages for bioinformatics and bayesian inference

cancerseqsim.jl

cinulator.jl

diffeqbayes.jl

Extension functionality which uses Stan.jl, DynamicHMC.jl, and Turing.jl to estimate the parameters to differential equations

dna-seq-gatk-variant-calling

This Snakemake pipeline implements the GATK best-practices workflow

dnds-clonesize

Snakemake pipeline to produce figures for "Measuring the distribution of fitness effects in somatic evolution by combining clonal dynamics with dN/dS ratios"

dnds-clonesize-container

dnds-clonesize-r-container

dndscv

dN/dS methods to quantify selection in cancer and somatic evolution

dpclustering.jl

Dirichilet process clustering for cancer sequencing data

fluidigm-pipeline

hmmrefs

What the Package Does (One Line, Title Case)

hscn_pipeline

julia-notebooks

lpwgs

marcjwilliams1.github.io

Github Pages template for academic personal websites, forked from mmistakes/minimal-mistakes

metadata.jl

Metadata for registered Julia packages.

neutral-tumour-evolution

neutral-tumour-evolution-werner-2018

Jupyter notebook to generate figures in Werner et al 2018 Nature Genetics

neutral-tumour-evolution-williams-2018

Jupyter notebook to produce figure from "Reply to ‘Revisiting signatures of neutral tumor evolution in the light of complexity of cancer genomic data’ "

neutralitytestr

Testing a neutral evolution model on cancer sequencing data

ng2018_bioinformatics

palimpsest

An R package for studying mutational and structural variant signatures along clonal evolution in cancer.

qdnaseq

QDNAseq package for Bioconductor

r-tidy-markdown-bio

rstudio-docker

rstudio_julia

rstudiosrvrv4