Pinned Repositories
align2rawsignal
Automatically exported from code.google.com/p/align2rawsignal
annotables
R data package for annotating/converting Gene IDs
ARchipSeq
chip-seq analysis pipeline scripts
atacflow
Analysis pipeline for ATACseq data using Nextflow
ATACseq
ATACseq data processing pipeline
ATACseqCSHL
ATAC-seq Tutorial CSHL
elementoEpigenomics
genevector
Vector representations of gene co-expression in single cell RNAseq.
RforSingularity
UniPro_Python
Unipro script
DoaneAS's Repositories
DoaneAS/atacflow
Analysis pipeline for ATACseq data using Nextflow
DoaneAS/ashnatwedding
DoaneAS/genevector
Vector representations of gene co-expression in single cell RNAseq.
DoaneAS/atacflowpooled
DoaneAS/chipseq
Chromatin immunoprecipitation (ChIP-seq) analysis using BWA and MACS2 with QC steps.
DoaneAS/chromfx
ATAC-seq tools R package
DoaneAS/configs
Config files used to define parameters specific to compute environments at different Institutions
DoaneAS/DoaneAS.github.io
DoaneAS/dotfiles
:wrench: .files, including ~/.macos — sensible hacker defaults for macOS
DoaneAS/fishHook
R package for applying Gamma-Poisson regression to identify statistical enrichment or depletion of somatic mutations in regions after correcting for genomic covariates.
DoaneAS/gGnome
R API for browsing, analyzing, and manipulating reference-aligned genome graphs in a GenomicRanges framework
DoaneAS/GSEA_R
Updated implementation of the GSEA-P R application for modern R distributions
DoaneAS/gTrack
R package for visualizing complex and multi-track 1D and 2D genomic data in GenomicRanges framework
DoaneAS/GxG
Scalable GenomicRanges based class for storing, manipulating, and querying genomic matrices and pairwise features.
DoaneAS/h2o-tutorials
Tutorials and training material for the H2O Machine Learning Platform
DoaneAS/khtools
R package for misc tools
DoaneAS/LowRankModels.jl
LowRankModels.jl is a julia package for modeling and fitting generalized low rank models.
DoaneAS/mintscripts
collection of scripts for mint-ChIP processing
DoaneAS/mskilibs
DoaneAS/NeoLoopFinder
A computation framework for genome-wide detection of enhancer-hijacking events from chromatin interaction data in re-arranged genomes
DoaneAS/NucleoATACR
R package for reading in & working with NucleoATAC outputs
DoaneAS/qqplots
DoaneAS/rBMF
:exclamation: This is a read-only mirror of the CRAN R package repository. rBMF — Boolean Matrix Factorization
DoaneAS/realign.nf
nextflow pipeline for bam file realignment
DoaneAS/reg-gen
Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.
DoaneAS/rnaflow
DoaneAS/sarek
Analysis pipeline to detect germline or somatic variants from WGS / targeted sequencing
DoaneAS/SignatureAnalyzer
Updated SignatureAnalyzer-GPU with mutational spectra & RNA expression compatibility.
DoaneAS/tcri
Information Theoretic Framework for Paired Single Cell Gene Expression and TCR Sequencing
DoaneAS/v4C