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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.

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.

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

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/).

alevinqc

Create QC and summary reports for Alevin output

atena

Analysis of transposable elements

benchmarkingdelayedmatrixstats

Benchmarking the DelayedMatrixStats package

bgi_vs_illumina_benchmark

This repository contains code related to the publication "Comparative performance of the BGI and Illumina sequencing technology for single-cell RNA-sequencing" by Senabouth et al.

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

bioc2020

BioC2020: Where Software and Biology Connect

bioc2020_delayedarray_workshop

Workshop on effectively using the DelayedArray framework to support the analysis of large datasets

bioc2021_delayedarray_workshop

About Workshop on effectively using the DelayedArray framework to support the analysis of large datasets

bioc_2017_presentation

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

bioceurope_2015_presentation

Presentation given at European Bioconductor Developers' Meeting (12th-13th January 2015, Heidelberg, Germany)

bioconductor-teaching

Bioconductor teaching working group

biocpkga

biocworkshops

Workshops for learning Bioconductor

bioimagebook.github.io

An introduction to bioimage analysis - http://bioimagebook.github.io

bismark_v0.8.1

Branch of bismark (v0.8.1) to implement some of my ideas regarding FLAG values in SAM/BAM files

bsseq

Devel repository for bsseq

bwa-parclip

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

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.

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.

cranpkga

cranpkgb

dbsnp2vcf

A (simplistic) Perl script to create a VCF file from a dbSNP flat database.