PeteHaitch

fstArray

Leveraging 'fst' for fast on-disk matrices

phd_thesis

My PhD thesis

tutorial.450k

A 450k tutorial in the form of an R package

2015-09-08_CI-with-bioconductor

Material for presentation on using continuous integration services (e.g., Travis) when developing Bioconductor packages given on 2015-09-08 in Tokyo, Japan as part of the Asia-Pacific Bioconductor Developers' Meeting.

methsim

An R package to simulate DNA methylation data.

SparseSummarizedExperiment

An experimental R package that defines S4 classes and methods for sparse genomic data

2015-09-08_GenomicTuples-and-MethylationTuples

Material for lightning talk given on 2015-09-08 in Tokyo, Japan as part of the Asia-Pacific Bioconductor Developers' Meeting.

Aclust

This repository is merely a copy of the `Aclust` R package developed by Tamar Sofer. This version of `Aclust` was downloaded on 30 April, 2014 from [http://www.hsph.harvard.edu/tamar-sofer/packages/](http://www.hsph.harvard.edu/tamar-sofer/packages/).

DSArray

Compressed In-Memory Representation of 3-Dimensional Arrays That Contain Many Duplicate Slices

matterArray

matter back end for DelayedArray objects

repete

Miscellaneous R functions that I find useful.

bwa-parclip

An experimental hack of bwa-meth to align PAR-CLIP reads

2015-09-09_bioconductor-dna-methylation

Material for presentation on analysing DNA methylation data with Bioconductor at GIW/InCoB 2015 given on 2015-09-09 in Tokyo, Japan

2016-03-01_zero-inflated-poisson-regression

Material for presentation on zero inflated Poisson regression at Biostatistics Journal Club given on 2016-03-01

2016-06-24-BioC2016-lightning-talk

BenchmarkingDelayedMatrixStats

Benchmarking the DelayedMatrixStats package

BioC2015LargeData

package for 'Management and analysis of large genomic data' lab

BioC2018_DelayedArray_workshop

Proposed tutorial on the DelayedArray infrastructure for BioC 2018

BioC2019_DelayedArray_workshop

Workshop on the DelayedArray infrastructure for BioC 2019

BioC_2017_presentation

Presentation given at Bioconductor Developers' Meeting (26-28th, July, 2017, Boston, USA)

BiocWorkshops

Workshops for learning Bioconductor

GenomicTuples-old

Representation and Manipulation of Genomic Tuples in R

MethylationTuples

An R package for analysing, managing and visualising methylation patterns at genomic tuples.

MultiAssayExperiment

R package(s) demonstrating management of multiassay data on a set of samples

runs

Scripts for reproducing analyses of large RNA-seq datasets

slide-template-dukeu

A Xaringan slide template using the Duke University Color Pallate

system-setup

Notes on how I set up my computer

testMatrixGenerics

trimadap

Fast but inaccurate adapter trimmer for Illumina reads

usethis

Automatically Set Up Commonly Used Package and Analysis Components