Pinned Repositories
785Project
Single-cell RNA-seq Analysis of Metastatic Melanoma Tumors
ABCD
Code related to Activity By Contact Dynamics (ABCD)
Bioc2022nullranges
dietJuicer
dietJuicer is a lighter-weight, HPC flexible version of juicer written with snakemake
hictoolsr
An R package with a collection of useful tools for Hi-C data analysis.
loopEnrichment
Testing loop enrichment with mariner
mariner
Explore the Hi-Cs
rproject-template
This is a template for creating repoducible R projects using `docker` and `GNU Make`. The folder structure is opinionated and is designed to keep your project organized and reproducible.
nullranges
Modular package for generation of sets of ranges representing the null hypothesis. These can take the form of bootstrapped ranges (bootRanges), or set of control ranges that are matched across one or more covariates (matchRanges).
plotgardener
EricSDavis's Repositories
EricSDavis/mariner
Explore the Hi-Cs
EricSDavis/hictoolsr
An R package with a collection of useful tools for Hi-C data analysis.
EricSDavis/dietJuicer
dietJuicer is a lighter-weight, HPC flexible version of juicer written with snakemake
EricSDavis/rproject-template
This is a template for creating repoducible R projects using `docker` and `GNU Make`. The folder structure is opinionated and is designed to keep your project organized and reproducible.
EricSDavis/ABCD
Code related to Activity By Contact Dynamics (ABCD)
EricSDavis/Bioc2022nullranges
EricSDavis/loopEnrichment
Testing loop enrichment with mariner
EricSDavis/20220901_BCBStudentSeminar
BCB student seminar presentation on mariner progress.
EricSDavis/bagPipes
New and improved snakemake pipelines for RNA-seq, ChIP-seq, and ATAC-seq processing for the Phanstiel Lab
EricSDavis/confluence
EricSDavis/EPTA
Enhancer-Promoter Time-course Analysis (EPTA)
EricSDavis/GeneticsRetreat2022
Slides for Genetic Retreat talk 2022
EricSDavis/marinerData
ExperimentHub data for the mariner package
EricSDavis/matchRangesManuscript
Figures and data for the matchRanges manuscript
EricSDavis/MOPS
EricSDavis/straw
Extract data quickly from Juicebox via straw
EricSDavis/YY1P
Analysis for the YY1P project
EricSDavis/20221013_TARC
EricSDavis/Bioc2023mariner
BioC2023 workshop using mariner and plotgardener for analyzing and visualizing Hi-C genomic data.
EricSDavis/dissertationPlots
Plots created for my dissertation presentation
EricSDavis/EricSDavis
EricSDavis/ericsdavis.github.io
EricSDavis/GeneticsRetreat2022Plots
Plots for the Genetics Retreat talk
EricSDavis/HowToHic
Quarto presentation about how to read and interpret a Hi-C plot
EricSDavis/mariner2
EricSDavis/mariner3
EricSDavis/marinerBenchmark
Benchmarking pullHic functions
EricSDavis/marinerFigures
Code for generating figures or parts of figures for the mariner manuscript
EricSDavis/nci_phasesep_talk
for Doug's 2022 NCI Biology & Biophysics of the Nucleus Symposium (Phase Separation & Condensates II Session)
EricSDavis/vindhya2