These are modular web-based presentations built using Reveal.js.

Research talks

Refgenie, PEP, and bulker 2019 September.

BiocProject: a Bioconductor-oriented project management package 2019 June.
Description of the BiocProject bioconductor package, which provides an integration between PEP and Bioconductor

Computational methods for region-based analysis of epigenome signals 2019 March.
An introduction to epigenomics and discussion of standardizing project metadata with Portable Encapsulated Projects, followed by two region-based analysis approaches, LOLA and AIList.

Bioinformatics data management and epigenome analysis methods 2019 January.
An introduction to PEP, and brief overview of PEPATAC, LOLA, and MIRA.

A modular project computing ecosystem and application to ATAC-seq data processing 2018 September.
A discussion of standardizing project metadata with Portable Encapsulated Projects and a presentation of PEPATAC, an ATAC-seq pipeline that reads standard PEP projects.

Organizing large-scale biological data around standardized projects 2018 March.
Introduction to Portable Encapsulated Projects and the pepkit system

Tools for epigenome analysis of genomic regions and data-intensive project management 2017 November.
A presentation of tools we have developed: LOLA, MIRA, and the PEP ecosystem.

Bioinformatics pipeline development and deploy with Pypiper and Looper 2017 November.
A quick overview of the basic and advanced features of our python-based pipeline workflow system. Pypiper is a user-friendly large-data informatics pipeline framework. Looper is a project manager that distributes jobs across a cluster for you. Updated to reflect the PEP division.

Single cell epigenomics 2017 April.
Intro and literature review of challenges and approaches to single-cell epigenomics analysis. Presentation for the 2017 American Foundation for AIDS Research Think Tank Meeting.

Research in the Sheffield lab 2017 February.
Brief introduction to research in the group

Epigenomics and cancer heterogeneity in Ewing sarcoma 2017 February.
Exploring DNA methylation data in a rare pediatric cancer.

Using Docker Bioconductor containers for portable, sharable, and reproducible R analysis and package development 2015 December.
2015 European Bioconductor Developers Meeting, Cambridge, UK. A guide to building, using, modifying, and sharing R environments based on Bioconductor Docker containers

Short talks

Choose your own adventure through Sheffield lab research 2021 March.
Collected introductions to a variety of lab projects: LOLA, MIRA, COCOA, Refgenie, PEP, bulker, etc.

Scattering CWL across tabular samples and Interactive computing environments from CWL 2021 January.
Introduction to looper to scatter CWL workflows across tabular data, and how bulker can create portable interactive computing environments from CWL workflows.

Refgenie and bioconductor 2020 July.
Lightning talk introducing refgenie and using it from within R

Refgenie and refget 2019 August.
Introduction to refgenie

Coordinate covariation analysis 2019 June.
Short talk introducing the COCOA bioconductor package.

ATAC-seq pipeline processing 2018 September.
A presentation of PEPATAC, an ATAC-seq pipeline that reads standard PEP projects.

Methylation-based Inference of Regulatory Activity 2018 July.
Short talk introducing the MIRA bioconductor package.

Locus overlap analysis 2018 July.
Short talk introducing the LOLA bioconductor package.

Augmented Interval List 2018 July.

Educational lectures

Open chromatin and ATAC-seq 2020 April.
Overview of open chromatin and ATAC sequencing

ATAC-seq analysis via pipeline 2020 April.
Introduction to pipelines in general, and PEPATAC, an ATAC-seq pipeline.

Downstream ATAC-seq analysis 2020 April.
Overview of tools and methods for downstream ATAC-seq analysis

DNA methylation and bisulfite-seq 2019 June.
Overview of DNA methylation and bisulfite sequencing

What is epigenetics? 2019 June.
A historical and philosophical introduction to epigenetics and epigenomics.

Epigenome tools: ATAC-seq and Bisulfite-seq 2019 March.
Overview of epigenomics; basics and applications of ATAC-seq and Bisulfite-seq.

Collaborative software development 2019 March.
Discussion of the layers of collaboration in software development and introduction to git and GitHub.

ATAC-seq pipeline processing 2018 September.
A presentation of PEPATAC, an ATAC-seq pipeline that reads standard PEP projects.

Clarity: Strategies for revising scientific writing 2017 July.
Presentation highlighting common issues with scientific writing and how to solve them.