bioconductor / bioc2021

BioC2021: Where Software and Biology Connect

BiocManager

Overview

The BiocManager package, as the modern successor package to BiocInstaller, allows users to install and manage packages from the Bioconductor project. Bioconductor focuses on the statistical analysis and comprehension of high-throughput genomic data.

Current Bioconductor packages are available on a ‘release’ version intended for every-day use, and a ‘devel’ version where new features are continually introduced. A new release version is created every six months. Using the BiocManager package helps users accurately install packages from the appropriate release.

• available() shows all packages associated with a search pattern
• install() installs and/or updates packages either CRAN or Bioconductor
• repositories() shows all package repository URL endpoints
• valid() checks and returns packages that are out-of-date or too new
• version() returns the current Bioconductor version number

Installation

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

Usage

Checking Bioconductor version currently installed

BiocManager::version()
#> [1] '3.15'

Installing Bioconductor packages

BiocManager::install(c("GenomicRanges", "SummarizedExperiment"))

Verifying a valid Bioconductor installation

BiocManager::valid()
#> [1] TRUE

More information

Please see the package vignette for more detailed information such as changing Bioconductor version, offline use, and other advanced usage.

Getting help

To report apparent bugs, create a minimal and reproducible example on GitHub.

bioc2021's Issues

Add organizers

Need names, photos, affiliations, committees. Example: https://bioc2020.bioconductor.org/organizers

rotating speaker view on website

Is it possible to have the 'Speakers' part of the main landing page automatically rotate through all the speakers (alternatively, show all the speakers on one page)? Right now, it's not immediately obvious that there are more than the four speakers shown on the first page.

Deploy to Netlify

Here are the 2 min instructions how to deploy this repository to Netlify https://youtu.be/RriEJuAMhzI. We can use the default domain for the time being - the goal is for everyone to see how it looks online and provide feedback. The e14ee7a commit adds the two speakers. @lshep

Add page with abstracts

Incorporate archetypes/partials from https://github.com/seandavi/genetics_branch_retreat_site. Or, a separate site to link to from the main.

Add page with links to previous conferences

Source from https://bioc2020.bioconductor.org/past_conferences

Add Euro/Asia BioC conferences?

Add link to abstract submission site

https://openreview.net/group?id=bioconductor.org/BioC/2021/Conference

Make speaker panels wider

Speaker panels for the 3x2 layout look narrow. I couldn't immediately find CSS formatting that would make speaker panels wider. Will continue looking, in a meantime - help wanted.

Long workshop status

This issue tracks the status of long workshops.

A passing badge is expected to reflect that the workshop:

• can be built as an R package
• can deploy pkgdown documentation to the gh-pages branch of the repository
• can push a Docker container to Docker Hub.

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Dimension Reduction for Beginners

Epidemiology for Bioinformaticians

Reproducing a single-cell proteomics data analysis using QFeatures and scp

Introduction to the Terra/AnVIL Cloud-based Genomics Platform

Building Carpentries-based Bioconductor Lessons

Multi-omic Integration of cBioPortal and TCGA data with MultiAssayExperiment

Effectively using the DelayedArray framework to support the analysis of large datasets

Introduction to Bioconductor annotation resources

Trajectory inference across conditions: differential expression and differential progression

systemPipe: Workflow and Visualization Toolkit

Interfacing Bioconductor with tidyverse with tidySingleCellExperiment and tidySummarisedExperiment

Add the dates of the conference

• The schedule page still has the dates from last year
• Also add dates to the landing page

Add sponsors

Need logos, URLs. They'll be listed on the front page. The menu page may list sponsorship info, currently copied from https://bioc2020.bioconductor.org/sponsor