Ashley S Doane's repositories
chromfx
ATAC-seq tools R package
dotfiles
:wrench: .files, including ~/.macos — sensible hacker defaults for macOS
fishHook
R package for applying Gamma-Poisson regression to identify statistical enrichment or depletion of somatic mutations in regions after correcting for genomic covariates.
genevector
Vector representations of gene co-expression in single cell RNAseq.
gGnome
R API for browsing, analyzing, and manipulating reference-aligned genome graphs in a GenomicRanges framework
GSEA_R
Updated implementation of the GSEA-P R application for modern R distributions
gTrack
R package for visualizing complex and multi-track 1D and 2D genomic data in GenomicRanges framework
GxG
Scalable GenomicRanges based class for storing, manipulating, and querying genomic matrices and pairwise features.
h2o-tutorials
Tutorials and training material for the H2O Machine Learning Platform
khtools
R package for misc tools
LowRankModels.jl
LowRankModels.jl is a julia package for modeling and fitting generalized low rank models.
mintscripts
collection of scripts for mint-ChIP processing
NeoLoopFinder
A computation framework for genome-wide detection of enhancer-hijacking events from chromatin interaction data in re-arranged genomes
NucleoATACR
R package for reading in & working with NucleoATAC outputs
rBMF
:exclamation: This is a read-only mirror of the CRAN R package repository. rBMF — Boolean Matrix Factorization
realign.nf
nextflow pipeline for bam file realignment
sarek
Analysis pipeline to detect germline or somatic variants from WGS / targeted sequencing
SignatureAnalyzer
Updated SignatureAnalyzer-GPU with mutational spectra & RNA expression compatibility.
tcri
Information Theoretic Framework for Paired Single Cell Gene Expression and TCR Sequencing