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5_ways_2d_histograms

5 Ways to do 2D Histograms in R

activelearning

Active Learning in R

an-introduction-to-applied-bioinformatics

Interactive lessons in bioinformatics.

atsnp

Large-scale testing for SNP-motif interactions.

bayesian_first_aid

Inside every classical test there is a Bayesian model trying to get out.

beamercolorthemesolarized

Beamer color theme using the Solarized palette

biocanno2016

biocgadgets

biscuit_singlecell_imm_icml_2016

R Codebase for BISCUIT: Infinite Mixture Model to cluster and impute single cells.

bnp

Some notes about bayesian non-parametrics

chipexo

ChIP-Exo is a new techonology for sequencing which obtains a higher accuracy to predict TFBS

chipexoqual

A quality control pipeline for ChIP-exo/nexus samples.

chipexoqualexample

Example data for the ChIPexoQual pacakge

chiputils

A package with basic utilities for ChIP analysis (both ChIP-seq and ChIP-exo)

cisr2021singlecellrna

UWCCC 2021 single cell RNA-seq tutorial

comp-genomics-class

Code and examples for JHU Computational Genomics class

complex-upset

A library for creating complex UpSet plots with ggplot2 geoms

crayon

R package for colored terminal output

create_bioc_package

Slides about my experience creating a bioconductor package

data.table

R's data.table package extends data.frame. More info:

deeplearningbook

MIT Deep Learning Book in PDF format

dpeak

High resolution identification of protein binding sites using PET and SET ChIP-Seq and ChIP-exo data

dpeak_example

drake_slides

slides for group meeting about using drake

ebna_analysis

ebv_nok

Repository for a study of the biological effects of EBV in epithelial cells

emogg

Emoji in ggplot2

encodeenhancerchallenge

script and data for mouse E11.5 enhancer prediction

fastqcr

fastqcr: Quality Control of Sequencing Data

fmhighld