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BioC2022 conference material

Home Page: https://bioc2022.bioconductor.org/

License: MIT License

HTML 54.10% CSS 40.95% JavaScript 4.63% Shell 0.11% R 0.21%

bioc2022's Introduction

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valid() checks and returns packages that are out-of-date or too new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.

bioc2022's People

Contributors

Stargazers

Watchers

Forkers

aedin lwaldron csoneson nturaga antony-gitau kozo2 kevinrue mikelove jdrnevich memo1986 kinkir

bioc2022's Issues

Order sponsors by level

Order by donation level 82d8b3
Add headers 7bc6db4

Modular schedule

Previously, schedule was hard-coded in Markdown, like https://bioc2021.bioconductor.org/schedule/. Can we make the schedule page auto-populating from a YAML file?

Each record should contain date, time, session type, presenting author, social media handle, presentation title, GitHub link or abstract, Youtube link. Titles may be linked to GitHub/abstracts, or, if possible, abstracts may pop up when hovering over title. Entries may be colored by session type. Parallel sessions may be listed one after another.

Current schedule. @sdgamboa , can you help?

Modular Sponsors page

Currently, the Sponsors page is a hard-coded Markdown table. Can we make it modular with shortcodes/partials, like the Organizers page? @sdgamboa

Organizers page is empty

create a template repository for other regional conferences

It'd be good to have a template repository similar to https://github.com/seandavi/BuildABiocWorkshop for other conferences to use.

BioC 2022 logo

It looks like we don't have the hex sticker for the BioC2022 conference. @jorainer, can you, please, help? Since it is planned in Seattle/virtual, maybe, reuse the awesome drafts for the BioC2021 conference?

Add links to shortcode

Modify the current shortcode to allow to include as many links as required for each abstract/author.

Incorrect reference to Bioc2021 in form submission

https://bioc2022.bioconductor.org/submissions/ mentions

[Access the BioC2021 Conference submission portal at https://openreview.net/group?id=bioconductor.org/BioC/2022/Conference](https://openreview.net/group?id=bioconductor.org/BioC/2022/Conference)

but it's BioC022. Also, this is not formatted as a link.

Pending tasks

Add a webpage for workshops with orchestra instructions.
Add a webpage for talks and package demos.
Add Twitter handles to authors of the tracks in the schedule.
Increase overall font size.
Fix combined logo link.

Make the organizers page modular

Currently, the page is a hard-coded Markdown table.

Adding-removing-sorting organizers is difficult.

Implement a more modular format using Hugo functionality.

Update submission page about virtual posters

The submission page only mentions virtual posters and that they will be presented in a separate remote session - clarify based on the decision on poster format.

Short talk videos not showing

Short talk tracks contain several talks, e.g., RNA Track. Many now have Youtube videos, added to their yaml files, e.g., day2_0900_Shorttalk_paper15.yaml. But for them, the Youtube links never show up. Can they be shown on the schedule? And/or individual abstracts? @sdgamboa, can you look into it?

Fixes required in the spreadsheet of metadata

@mdozmorov, @Krithika-Bhuvan

Some notes regarding the metadata spreadsheet: https://docs.google.com/spreadsheets/d/1tGtGffcbCRxQFjE3ej42IcWlN4FJCsuQeZvETt9g0oA/edit#gid=0

I noticed that the field authors only include one author and et al in the table of metadata. I think that all authors should be included in this field since we have the information.
Sometimes the information is mixed (see c3e5b3a and lines 27 and 28 in the metadata table). We should fix these in the tables and in the data yaml. And look for other cases.
Affiliations are missing for some authors in the table.

Update schedule item "Meet the CAB"

I'll prepare a PR later, but for now an issue as a reminder to myself.

Feedback from CAB meeting:

Spell out and add a link "Meet the [Community Advisory Board][url]"