PeteHaitch/japan2015
A blog of my trip to Japan.
Developer Profile
PeteHaitch
Discovered public repositories for PeteHaitch in the GitHub catalog.
PeteHaitch/phd_thesis_analyses
Analyses accompanying each chapter of my PhD
PeteHaitch/BioCpkgA
Public repository.
PeteHaitch/CRANpkgB
Public repository.
PeteHaitch/CRANpkgA
Public repository.
PeteHaitch/BiocEurope_2015_presentation
Presentation given at European Bioconductor Developers' Meeting (12th-13th January 2015, Heidelberg, Germany)
PeteHaitch/methsim
An R package to simulate DNA methylation data.
PeteHaitch/MethylationTuples
An R package for analysing, managing and visualising methylation patterns at genomic tuples.
PeteHaitch/personal_website
Public repository.
PeteHaitch/so-simple-theme
A simple and clean responsive Jekyll theme for words and photos.
PeteHaitch/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/).
PeteHaitch/Lorne_Genome_2014_meeting_report
Meeting report for Genome Biology on the Lorne Genome Conference 2014
PeteHaitch/phd_thesis
My PhD thesis
PeteHaitch/cometh
An R package with tools for analysing, managing and visualising co-methylation data. Loosely speaking, co-methylation is the correlation structure of DNA methylation.
PeteHaitch/bismark_v0.8.1
Branch of bismark (v0.8.1) to implement some of my ideas regarding FLAG values in SAM/BAM files
PeteHaitch/Correct-Bismark-SAM-BAM-FLAGs
A Python script to "correct" the FLAGs in a SAM/BAM generated by Bismark to comply with the SAM specifications. Specifically, correct the strand information in the FLAG and add a custom tag XS:Z:<value> to encode which DNA-strand the read is informative for, where <value> = OT, CTOT, OB or CTOB.
PeteHaitch/methtuple
methtuple is a methylation caller for methylation events that co-occur on the same DNA fragment from high-throughput bisulfite sequencing data, such as methylC-seq.
PeteHaitch/XGWAS
R code for paper: Hickey, P. F. and Bahlo, M. X chromosome association testing in genome wide association studies. Genet Epidemiol. 2011 Nov;35(7):664-70. doi: 10.1002/gepi.20616. Epub 2011 Aug 4
PeteHaitch/dbSNP2VCF
A (simplistic) Perl script to create a VCF file from a dbSNP flat database.
PeteHaitch/Lister2BAM
A collection of Python scripts to convert Lister-style alignment files from Lister et al. Nature (2009 and 2011) to BAM format.