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title: "Bioconductor Notes, Winter 2024" | ||
date: "2023-02-24" | ||
abstract: > | ||
We discuss general project news. | ||
author: | ||
- name: Maria Doyle, Bioconductor Community Manager | ||
affiliation: University of Limerick | ||
- name: Bioconductor Core Developer Team | ||
affiliation: Dana-Farber Cancer Institute, Roswell Park Comprehensive Cancer Center, City University of New York, Fred Hutchinson Cancer Research Center, Mass General Brigham | ||
execute: | ||
echo: false | ||
warning: false | ||
message: false | ||
--- | ||
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# Introduction | ||
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[Bioconductor](https://bioconductor.org) provides | ||
tools for the analysis and comprehension of high-throughput genomic | ||
data. The project has entered its twentieth year, with funding | ||
for core development and infrastructure maintenance secured | ||
through 2025 (NIH NHGRI 2U24HG004059). Additional support is provided | ||
by NIH NCI, Chan-Zuckerberg Initiative, National Science Foundation, | ||
Microsoft, and Amazon. In this news report, we give some updates on | ||
core team and project activities. | ||
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# Software | ||
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```{r lkdat,results="hide",echo=FALSE} | ||
curR = "4.4" | ||
nsoft = 2289 | ||
nexp = 431 | ||
nanno = 928 | ||
nwkfl = 30 | ||
nbooks = 5 | ||
``` | ||
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The current Bioconductor release is [3.20](https://bioconductor.org/news/bioc_3_20_release/). It is | ||
compatible with R `r curR` and consists of `r nsoft` software packages, `r nexp` | ||
experiment data packages, `r nanno` up-to-date annotation packages, `r nwkfl` | ||
workflows, and `r nbooks` books. \href{https://bioconductor.org/books/release/}{Books} are | ||
built regularly from source and therefore fully | ||
reproducible; an example is the | ||
community-developed [Orchestrating Single-Cell Analysis with Bioconductor](https://bioconductor.org/books/release/OSCA/). | ||
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## Bioconductor in Python! | ||
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We're excited to introduce [BiocPy](https://www.github.com/biocpy), a project aimed at enabling Bioconductor workflows in Python. Analysts today use a variety of languages in their workflows, including R/Bioconductor for statistical analysis and Python for imaging or machine learning tasks. BiocPy aims to facilitate interoperability between R and Python by providing standardized data structures based on existing Bioconductor data structures. These include genomic ranges for interval based operations, summarized experiments and other derivatives for analyzing genomic experiments. To learn more, visit the [BiocPy](https://github.com/biocpy) GitHub organization. | ||
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# Core team updates | ||
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What's new for core? | ||
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## Partnering with Outreachy | ||
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Bioconductor will also participate in Outreachy's FIXME | ||
internship round to offer internships with Bioconductor community projects. | ||
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# Conferences | ||
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Links on conferences? | ||
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# Blog | ||
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New blog entries to mention? | ||
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# Boards updates | ||
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## Community Advisory Board | ||
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Update? | ||
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<!-- | ||
- The [Community Advisory Board](https://bioconductor.org/about/community-advisory-board/) (CAB) are voting in new members. Outgoing members are Susan Holmes, Leonardo Collado-Torres, Yagoub A. I. Adam, Matt Ritchie, Benilton Carvalho, we gratefully thank them for their service. | ||
- There is a Call for Bioconductor Community-Led events supported by the CAB. | ||
Apply in [this form](https://forms.gle/oTHp26TG3eP9q4eE7) | ||
--> | ||
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# Committees and Working groups updates | ||
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If you are interested in becoming involved with one of these groups please contact the group leader(s). | ||
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Updates? | ||
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<!-- | ||
- [Cloud Methods](https://workinggroups.bioconductor.org/currently-active-working-groups-committees.html#cloud-methods) | ||
held their first meeting Feb 2023. The working group will meet monthly to | ||
develop standards and tools for the Bioconductor community related to the | ||
cloud. | ||
- [Social media working group](https://workinggroups.bioconductor.org/currently-active-working-groups-committees.html#social-media). | ||
A new group, started in Feb 2023, have set up | ||
[Bioconductor Mastodon acccount](https://genomic.social/@bioconductor). | ||
- [Teaching Committee](https://workinggroups.bioconductor.org/currently-active-working-groups-committees.html#education) | ||
- Are planning a hackathon for the | ||
[Bioconductor Carpentries RNA-seq lesson](https://carpentries-incubator.github.io/bioc-rnaseq/). | ||
- Will be participating in | ||
[Galaxy Training Smorgasbord 2023](https://gallantries.github.io/video-library/events/smorgasbord3/), | ||
a free online global event, May 22-26. | ||
- [Website working group]([https://workinggroups.bioconductor.org/currently-active-working-groups-committees.html#website) | ||
are planning the redesign of [bioconductor.org](bioconductor.org). | ||
--> | ||
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# Other | ||
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- Summer school *"Statistical Data Analysis for Genome-Scale Biology"* [CSAMA 2023](https://csama2023.bioconductor.eu/) in Bressanone-Brixen, Italy, June 11-16 2023. Application deadline May 15. | ||
- Course *"Statistical Analysis of Genome Scale Data"* at [CSHL](https://meetings.cshl.edu/courses.aspx?course=C-DATA&year=23) in New York, USA, June 30 - July 13 2023. Application deadline March 15. | ||
- Workshop *"Opportunities for Bioconductor and ELIXIR communities to co-develop training infrastructure"* accepted for the [ELIXIR All Hands meeting](https://elixir-europe.org/events/elixir-all-hands-2023) in Dublin, Ireland, June 5-8 2023. | ||
- Workshop *"Orchestrating Large-Scale Single-Cell Analysis with Bioconductor"* accepted for [ISMB/ECCB 2023](https://www.iscb.org/ismbeccb2023-programme/tutorials#ip4) in Lyon, France, July 23 2023. | ||
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# Using Bioconductor | ||
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Start using | ||
Bioconductor by installing the most recent version of R and evaluating | ||
the commands | ||
``` | ||
if (!requireNamespace("BiocManager", quietly = TRUE)) | ||
install.packages("BiocManager") | ||
BiocManager::install() | ||
``` | ||
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Install additional packages and dependencies, | ||
e.g., [SingleCellExperiment](https://bioconductor.org/packages/SingleCellExperiment), with | ||
``` | ||
BiocManager::install("SingleCellExperiment") | ||
``` | ||
[Docker](https://bioconductor.org/help/docker/) | ||
images provides a very effective on-ramp for power users to rapidly | ||
obtain access to standardized and scalable computing environments. | ||
Key resources include: | ||
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- [bioconductor.org](https://bioconductor.org) to install, | ||
learn, use, and develop Bioconductor packages. | ||
- A list of [available software](https://bioconductor.org/packages) | ||
linking to pages describing each package. | ||
- A question-and-answer style | ||
[user support site](https://support.bioconductor.org) and | ||
developer-oriented [mailing list](https://stat.ethz.ch/mailman/listinfo/bioc-devel). | ||
- A community slack workspace ([sign up](https://slack.bioconductor.org)) | ||
for extended technical discussion. | ||
- The [F1000Research Bioconductor gateway](https://f1000research.com/gateways/bioconductor) | ||
for peer-reviewed Bioconductor workflows as well as conference contributions. | ||
- The [Bioconductor YouTube](https://www.youtube.com/user/bioconductor) | ||
channel includes recordings of keynote and talks from recent | ||
conferences including BioC2022, EuroBioC2022, and BiocAsia2021, in addition to | ||
video recordings of training courses. | ||
- Our [package submission](https://github.com/Bioconductor/Contributions) | ||
repository for open technical review of new packages. | ||
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Upcoming and recently completed events are browsable at our | ||
[events page](https://bioconductor.org/help/events/). | ||
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The [Technical](https://bioconductor.org/about/technical-advisory-board/) | ||
and and [Community](https://bioconductor.org/about/community-advisory-board/) | ||
Advisory Boards provide guidance to ensure that the project addresses | ||
leading-edge biological problems with advanced technical approaches, | ||
and adopts practices (such as a | ||
project-wide [Code of Conduct](https://bioconductor.org/about/code-of-conduct/)) | ||
that encourages all to participate. We look forward to | ||
welcoming you! |
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