biobenkj Goto Github PK

2015-09-21-genentech

Data Carpentry workshop at Genentech

2015-sep-microbial

aclust

A-Clustering functions and analysis pipeline for methylation outcome data

angus

Materials for Analyzing Next-Generation Sequencing (ANGUS) course.

archr

ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)

atacseeker

ATACseq tools for Bioconductor

bed

Bayesian Epiallele Detection (BED)

biobenkj.github.io

Personal blog

biscuit

BISulfite-seq CUI Toolkit

biscuiteer

tools for analysing Biscuit (https://huishenlab.github.io/biscuit/) output

bisplotti

Plotting package for bisulfite sequencing and methylation arrays

bonito

Bonito - A PyTorch Basecaller for Oxford Nanopore Reads

boostme

R package to impute methylation within WGBS using machine learning

bsseq

Devel repository for bsseq

cicero

combinatorialhic

Scripts + resources for analyzing combinatorial Hi-C data

compartmap

Reconstruction of higher order chromatin from scRNA-seq and scATAC-seq

compartmap_manuscript

This repository contains all the code and much of the processed data for the compartmap manuscript

complexion

R utilities to compute library complexity measures

construct

method for modeling continuous and discrete population genetic structure

conumee

Enhanced copy-number variation analysis using Illumina DNA methylation arrays -

couplenmf

covmat

Package Development for GSOC 2015

cv

Repo containing a pdf of my CV

datacarpentry

Notes and things for DC

datasets

Datasets related to the IGVF workflows

densvis

R package implementing the density-preserving data visualization tools den-SNE and densMAP

dndscv

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

dpmclust

Bayesian nonparametric clustering in R using DP-means

droplasso

Dropout Lasso