/ Recent content on Bioconductor Hugo en-us Sat, 22 Jan 2022 00:00:00 +0000 /news/2022-01-22-call_for_abstracts_opens/ Sat, 22 Jan 2022 00:00:00 +0000 /news/2022-01-22-call_for_abstracts_opens/ <p>You can register your abstract at: <a href="https://openreview.net/group?id=bioconductor.org/BioC/2022/Conference">https://openreview.net/group?id=bioconductor.org/BioC/2022/Conference</a></p> /posts/my-first-post/ Fri, 16 Oct 2020 18:52:14 -0400 /posts/my-first-post/ <h1 id="test">test</h1> <p>test</p> /workshops-status/ Mon, 01 Jan 0001 00:00:00 +0000 /workshops-status/ <h2 id="workshops">Workshops</h2> <table> <thead> <tr> <th style="text-align: left">Workshop</th> <th style="text-align: center">Source  </th> <th style="text-align: center">Docker  </th> <th style="text-align: left">Status</th> </tr> </thead> <tbody> <tr> <td style="text-align: left"><a href="https://stemangiola.github.io/bioc2021_tidytranscriptomics">Interfacing Bioconductor with tidyverse with tidySingleCellExperiment and tidySummarisedExperiment</a>  </td> <td style="text-align: center"><a href="https://github.com/stemangiola/bioc2021_tidytranscriptomics"><img src="/img/GitHub-Mark-32px.png" alt="GitHub Mark"></a></td> <td style="text-align: center"><a href="https://hub.docker.com/r/stemangiola/bioc2021_tidytranscriptomics"><img src='/img/docker-vertical-logo-monochromatic.png' alt='Girl in a jacket' width='32' height='32'></a></td> <td style="text-align: left"><a href="https://github.com/stemangiola/bioc2021_tidytranscriptomics/actions"><img src="https://github.com/stemangiola/bioc2021_tidytranscriptomics/workflows/.github/workflows/basic_checks.yaml/badge.svg" alt="GitHub Action badge"></a></td> </tr> <tr> <td style="text-align: left"><a href="https://aedin.github.io/PCAworkshop">Dimension Reduction for Beginners</a>  </td> <td style="text-align: center"><a href="https://github.com/aedin/PCAworkshop"><img src="/img/GitHub-Mark-32px.png" alt="GitHub Mark"></a></td> <td style="text-align: center"><a href="https://hub.docker.com/r/aculhane/pcabiocworkshop2020"><img src='/img/docker-vertical-logo-monochromatic.png' alt='Girl in a jacket' width='32' height='32'></a></td> <td style="text-align: left"><a href="https://github.com/aedin/PCAworkshop/actions"><img src="https://github.com/aedin/PCAworkshop/workflows/.github/workflows/basic_checks.yaml/badge.svg" alt="GitHub Action badge"></a></td> </tr> <tr> <td style="text-align: left"><a href="https://waldronlab.github.io/MultiAssayWorkshop">Multi-omic Integration of cBioPortal and TCGA data with MultiAssayExperiment</a>  </td> <td style="text-align: center"><a href="https://github.com/waldronlab/MultiAssayWorkshop"><img src="/img/GitHub-Mark-32px.png" alt="GitHub Mark"></a></td> <td style="text-align: center"><a href="https://hub.docker.com/r/mr148/multiassayworkshop"><img src='/img/docker-vertical-logo-monochromatic.png' alt='Girl in a jacket' width='32' height='32'></a></td> <td style="text-align: left"><a href="https://github.com/waldronlab/MultiAssayWorkshop/actions"><img src="https://github.com/waldronlab/MultiAssayWorkshop/workflows/MAEWorkshopCheck/badge.svg" alt="GitHub Action badge"></a></td> </tr> <tr> <td style="text-align: left"><a href="https://PeteHaitch.github.io/BioC2021_DelayedArray_workshop">Effectively using the DelayedArray framework to support the analysis of large datasets</a>  </td> <td style="text-align: center"><a href="https://github.com/PeteHaitch/BioC2021_DelayedArray_workshop"><img src="/img/GitHub-Mark-32px.png" alt="GitHub Mark"></a></td> <td style="text-align: center"><a href="https://hub.docker.com/r/petehaitch/bioc2021_delayedarray_workshop"><img src='/img/docker-vertical-logo-monochromatic.png' alt='Girl in a jacket' width='32' height='32'></a></td> <td style="text-align: left"><a href="https://github.com/PeteHaitch/BioC2021_DelayedArray_workshop/actions"><img src="https://github.com/PeteHaitch/BioC2021_DelayedArray_workshop/workflows/.github/workflows/basic_checks.yaml/badge.svg" alt="GitHub Action badge"></a></td> </tr> <tr> <td style="text-align: left"><a href="https://jmacdon.github.io/Bioc2021Anno">Introduction to Bioconductor annotation resources</a>  </td> <td style="text-align: center"><a href="https://github.com/jmacdon/Bioc2021Anno"><img src="/img/GitHub-Mark-32px.png" alt="GitHub Mark"></a></td> <td style="text-align: center"><a href="https://hub.docker.com/r/jmacdon/bioc2021anno"><img src='/img/docker-vertical-logo-monochromatic.png' alt='Girl in a jacket' width='32' height='32'></a></td> <td style="text-align: left"><a href="https://github.com/jmacdon/Bioc2021Anno/actions"><img src="https://github.com/jmacdon/Bioc2021Anno/workflows/.github/workflows/basic_checks.yaml/badge.svg" alt="GitHub Action badge"></a></td> </tr> <tr> <td style="text-align: left"><a href="https://lgatto.github.io/QFeaturesScpWorkshop2021">Reproducing a single-cell proteomics data analysis using QFeatures and scp</a>  </td> <td style="text-align: center"><a href="https://github.com/lgatto/QFeaturesScpWorkshop2021"><img src="/img/GitHub-Mark-32px.png" alt="GitHub Mark"></a></td> <td style="text-align: center"><a href="https://hub.docker.com/r/lgatto/qfeaturesscpworkshop2021"><img src='/img/docker-vertical-logo-monochromatic.png' alt='Girl in a jacket' width='32' height='32'></a></td> <td style="text-align: left"><a href="https://github.com/lgatto/QFeaturesScpWorkshop2021/actions"><img src="https://github.com/lgatto/QFeaturesScpWorkshop2021/workflows/.github/workflows/basic_checks.yaml/badge.svg" alt="GitHub Action badge"></a></td> </tr> <tr> <td style="text-align: left"><a href="https://HectorRDB.github.io/bioc2021trajectories">Trajectory inference across conditions: differential expression and differential progression</a>  </td> <td style="text-align: center"><a href="https://github.com/HectorRDB/bioc2021trajectories"><img src="/img/GitHub-Mark-32px.png" alt="GitHub Mark"></a></td> <td style="text-align: center"><a href="https://hub.docker.com/r/HectorRDB/bioc2021trajectories"><img src='/img/docker-vertical-logo-monochromatic.png' alt='Girl in a jacket' width='32' height='32'></a></td> <td style="text-align: left"><a href="https://github.com/HectorRDB/bioc2021trajectories/actions"><img src="https://github.com/HectorRDB/bioc2021trajectories/workflows/.github/workflows/basic_checks.yaml/badge.svg" alt="GitHub Action badge"></a></td> </tr> <tr> <td style="text-align: left"><a href="https://systemPipeR.github.io/systemPipeWorkshop2021">systemPipe: Workflow and Visualization Toolkit</a>  </td> <td style="text-align: center"><a href="https://github.com/systemPipeR/systemPipeWorkshop2021"><img src="/img/GitHub-Mark-32px.png" alt="GitHub Mark"></a></td> <td style="text-align: center"><a href="https://hub.docker.com/r/systempipe/systempipeworkshop2021"><img src='/img/docker-vertical-logo-monochromatic.png' alt='Girl in a jacket' width='32' height='32'></a></td> <td style="text-align: left"><a href="https://github.com/systemPipeR/systemPipeWorkshop2021/actions"><img src="https://github.com/systemPipeR/systemPipeWorkshop2021/workflows/.github/workflows/basic_checks.yaml/badge.svg" alt="GitHub Action badge"></a></td> </tr> <tr> <td style="text-align: left"><a href="https://jdrnevich.github.io/BuildACarpentriesWorkshop">Building Carpentries-based Bioconductor Lessons</a>  </td> <td style="text-align: center"><a href="https://github.com/jdrnevich/BuildACarpentriesWorkshop"><img src="/img/GitHub-Mark-32px.png" alt="GitHub Mark"></a></td> <td style="text-align: center"><a href="https://hub.docker.com/r/jdrnevich/buildacarpentriesworkshop"><img src='/img/docker-vertical-logo-monochromatic.png' alt='Girl in a jacket' width='32' height='32'></a></td> <td style="text-align: left"><a href="https://github.com/jdrnevich/BuildACarpentriesWorkshop/actions"><img src="https://github.com/jdrnevich/BuildACarpentriesWorkshop/workflows/.github/workflows/basic_checks.yaml/badge.svg" alt="GitHub Action badge"></a></td> </tr> <tr> <td style="text-align: left"><a href="https://cmirzayi.github.io/epiforbioworkshop2021">Epidemiology for Bioinformaticians</a>  </td> <td style="text-align: center"><a href="https://github.com/cmirzayi/epiforbioworkshop2021"><img src="/img/GitHub-Mark-32px.png" alt="GitHub Mark"></a></td> <td style="text-align: center"><a href="https://hub.docker.com/r/cmirzayi/epiforbioworkshop2021"><img src='/img/docker-vertical-logo-monochromatic.png' alt='Girl in a jacket' width='32' height='32'></a></td> <td style="text-align: left"><a href="https://github.com/cmirzayi/epiforbioworkshop2021/actions"><img src="https://github.com/cmirzayi/epiforbioworkshop2021/workflows/.github/workflows/basic_checks.yaml/badge.svg" alt="GitHub Action badge"></a></td> </tr> <tr> <td style="text-align: left"><a href="https://waldronlab.github.io/AnVILWorkshop">Introduction to the Terra/AnVIL Cloud-based Genomics Platform</a>  </td> <td style="text-align: center"><a href="https://github.com/waldronlab/AnVILWorkshop"><img src="/img/GitHub-Mark-32px.png" alt="GitHub Mark"></a></td> <td style="text-align: center"><a href="https://hub.docker.com/r/shbrief/anvilworkshop"><img src='/img/docker-vertical-logo-monochromatic.png' alt='Girl in a jacket' width='32' height='32'></a></td> <td style="text-align: left"><a href="https://github.com/waldronlab/AnVILWorkshop/actions"><img src="https://github.com/waldronlab/AnVILWorkshop/workflows/.github/workflows/basic_checks.yaml/badge.svg" alt="GitHub Action badge"></a></td> </tr> </tbody> </table> <br/> <p>Find out more details on the <a href="/workshops">Workshops</a> page!</p> /conferences/ Mon, 01 Jan 0001 00:00:00 +0000 /conferences/ <h3 id="past-conferences">Past Conferences</h3> <ul> <li><a href="https://bioc2026.bioconductor.org">Bioconductor 2026</a></li> <li><a href="https://eurobioc2026.bioconductor.org">EuroBioC 2026</a></li> <li><a href="https://biocasia2025.bioconductor.org">BioC Asia 2025</a></li> <li><a href="https://gbcc2025.bioconductor.org">GBCC 2025</a></li> <li><a href="https://eurobioc2025.bioconductor.org">EuroBioC 2025</a></li> <li><a href="https://biocasia2024.bioconductor.org">BioC Asia 2024</a></li> <li><a href="https://eurobioc2024.bioconductor.org">EuroBioC 2024</a></li> <li><a href="https://biocasia2023.bioconductor.org">BioC Asia 2023</a></li> <li><a href="https://eurobioc2023.bioconductor.org">EuroBioC 2023</a></li> <li><a href="https://biocasia2022.bioconductor.org/">BioC Asia 2022</a></li> <li><a href="https://eurobioc2022.bioconductor.org/">EuroBioC 2022</a></li> <li><a href="https://bioc2022.bioconductor.org/">Bioconductor 2022</a></li> <li><a href="https://biocasia2021.bioconductor.org/">BioC Asia 2021</a></li> <li><a href="https://bioc2021.bioconductor.org/">Bioconductor 2021</a></li> <li><a href="https://eurobioc2020.bioconductor.org/">EuroBioC 2020</a></li> <li><a href="https://biocasia2020.bioconductor.org/">BioC Asia 2020</a></li> <li><a href="https://bioc2020.bioconductor.org/">Bioconductor 2020</a></li> <li><a href="https://bioc2019.bioconductor.org/">Bioconductor 2019</a></li> <li><a href="https://bioc2018.bioconductor.org/">Bioconductor 2018</a></li> <li><a href="https://bioconductor.org/help/course-materials/2017/BioC2017/">Bioconductor 2017</a></li> <li><a href="https://bioconductor.org/help/course-materials/2016/BioC2016/">Bioconductor 2016</a></li> <li><a href="https://bioconductor.org/help/course-materials/2015/BioC2015/">Bioconductor 2015</a></li> <li><a href="https://bioconductor.org/help/course-materials/2014/BioC2014/">Bioconductor 2014</a></li> <li><a href="https://bioconductor.org/help/course-materials/2013/BioC2013/">Bioconductor 2013</a></li> <li><a href="https://bioconductor.org/help/course-materials/2012/BioC2012/">Bioconductor 2012</a></li> <li><a href="https://bioconductor.org/help/course-materials/2011/BioC2011/">Bioconductor 2011</a></li> <li><a href="https://bioconductor.org/help/course-materials/2010/BioC2010/">Bioconductor 2010</a></li> <li><a href="https://bioconductor.org/help/course-materials/2009/BioC2009/">Bioconductor 2009</a></li> <li><a href="https://bioconductor.org/help/course-materials/2008/BioC2008/">Bioconductor 2008</a></li> <li><a href="https://bioconductor.org/help/course-materials/2007/BioC2007/">Bioconductor 2007</a></li> <li><a href="https://bioconductor.org/help/course-materials/2006/BioC2006/">Bioconductor 2006</a></li> <li><a href="https://bioconductor.org/help/course-materials/2005/BioC2005/">Bioconductor 2005</a></li> </ul> /code/ Mon, 01 Jan 0001 00:00:00 +0000 /code/ <p>This code of conduct was developed for the Bioconductor conferences. For more details, see the <a href="https://www.bioconductor.org/about/code-of-conduct/">Bioconductor Code of Conduct</a></p> <!-- The original Code of Conduct is copy-pasted and quoted below --> <h2 id="social-media-policy">Social media policy</h2> <p>Images and content from talks, workshops, and posters may be shared publicly through social media (Twitter, etc.). Videos will be released on the <a href="https://www.youtube.com/user/bioconductor">Youtube Bioconductor channel</a>. Please, inform the organizing committee as soon as possible if you don&rsquo;t wish your presentation material to be shared. <!--To avoid confusion, presentations not to be shared should be labeled "Do Not Share" on each slide, as should be posters.--></p> /abstracts/paper1/ Mon, 01 Jan 0001 00:00:00 +0000 /abstracts/paper1/ /contact/ Mon, 01 Jan 0001 00:00:00 +0000 /contact/ <style> .contact-page { max-width: 75%; margin: 0 auto; font-size: 17px; line-height: 1.5; } .contact-page h1 { color: #2f6b57; font-size: 36px; text-align: center; margin-bottom: 18px; } .contact-page p, .contact-page ul, .contact-page li, .contact-page a, .contact-page div { font-size: 17px; } .contact-page ul { margin-bottom: 28px; padding-left: 24px; } .contact-page li { margin-bottom: 10px; } .contact-all { border: 2px solid #8bb39d; border-radius: 12px; background-color: #f3faf6; padding: 22px; margin: 28px auto 32px auto; box-shadow: 0px 2px 6px rgba(47,107,87,0.12); } .contact-all strong { color: #2f6b57; font-size: 20px; } .contact-all a { color: #2f6b57; text-decoration: underline; font-size: 17px; } .contact-intro { margin-bottom: 24px; font-size: 17px; } .contact-card { margin-bottom: 24px; padding-bottom: 18px; border-bottom: 1px solid #d7e8de; } .contact-card strong { color: #2f6b57; font-size: 20px; } .contact-card a { color: #2f6b57; text-decoration: underline; font-size: 17px; } </style> <div class="contact-page"> <p>We would be happy to assist with any enquiries regarding <strong>BiocAsia 2026</strong>.</p> /submissions/ Mon, 01 Jan 0001 00:00:00 +0000 /submissions/ <style> ul.event-list li { margin-bottom: 20px; font-size: 16px; /* Adjust the value as needed */ } </style> <ul class="event-list"> <li><b>June 15, 2026</b>: Call for Abstracts and Workshops open</li> <li><b>July 6, 2026</b>: Registration for BiocAsia 2026 opens</li> <li><b>August 1, 2026</b>: Call for Abstracts and Workshops close</li> <li><b>August 21, 2026</b>: Notification of abstract decision</li> <!-- <li><b>October 14, 2024</b>: In-person registration closes</li> <li><b>October 31, 2024</b>: Virtual registration closes</li> --> <li><b>Nov 9, 2026</b>: Registrations Close @ 5pm!</li> <!-- <li><b>Nov 26, 2025</b>: BioCAsia x R-Ladies Networking Event</li> --> <li><b>Nov 16-20, 2026</b>: BioCAsia 2026 conference</li> <br> </ul> /package-demo/ Mon, 01 Jan 0001 00:00:00 +0000 /package-demo/ <h2 id="package-demos-on-orchestra">Package demos on orchestra</h2> <ol> <li>Go to <a href="http://app.orchestra.cancerdatasci.org" target="_blank" >Orchestra</a>.</li> <li>Log in.</li> <li>Search for the workshop of interest.</li> <li>Click &ldquo;Launch&rdquo; (may take a minute or two).</li> <li>Follow instructions.</li> </ol> <h2 id="all-package-demos-by-level">All package demos by level</h2> <h3> Beginner </h3> Recommended for starting with Bioconductor. <div class="container"> <table id="workshop-table" class="table table-bordered table-hover"> <thead> <tr> <th>Workshop</th> <th>Details</th> <th>Source</th> <th>Youtube</th> <tr> </thead> <tbody> </tbody> </table> </div> <h3> Intermediate </h3> <div class="container"> <table id="workshop-table" class="table table-bordered table-hover"> <thead> <tr> <th>Workshop</th> <th>Details</th> <th>Source</th> <th>Youtube</th> <tr> </thead> <tbody> </tbody> </table> </div> <h3> Advanced </h3> <div class="container"> <table id="workshop-table" class="table table-bordered table-hover"> <thead> <tr> <th>Workshop</th> <th>Details</th> <th>Source</th> <th>Youtube</th> <tr> </thead> <tbody> <tr> <td width="85%"><a href="../abstracts/paper2" target="_blank" title=Simultaneous&#32;profiling&#32;of&#32;the&#32;spatial&#32;distributions&#32;of&#32;multiple&#32;biological&#32;molecules&#32;at&#32;single-cell&#32;resolution&#32;has&#32;recently&#32;been&#32;enabled&#32;by&#32;the&#32;development&#32;of&#32;highly&#32;multiplexed&#32;imaging&#32;technologies.&#32;Extracting&#32;and&#32;analyzing&#32;biologically&#32;relevant&#32;information&#32;contained&#32;in&#32;complex&#32;imaging&#32;data&#32;requires&#32;the&#32;use&#32;of&#32;a&#32;diverse&#32;set&#32;of&#32;computational&#32;tools&#32;and&#32;algorithms.&#32;We&#32;developed&#32;a&#32;standardized,&#32;user-friendly,&#32;customizable,&#32;and&#32;interoperable&#32;workflow&#32;for&#32;processing&#32;and&#32;analyzing&#32;data&#32;generated&#32;by&#32;highly&#32;multiplexed&#32;imaging&#32;technologies.&#32;The&#32;steinbock&#32;framework&#32;written&#32;in&#32;python&#32;supports&#32;image&#32;pre-processing,&#32;segmentation,&#32;feature&#32;extraction,&#32;and&#32;data&#32;export&#32;in&#32;a&#32;reproducible&#32;fashion.&#32;The&#32;imcRtools&#32;R/Bioconductor&#32;package&#32;forms&#32;the&#32;bridge&#32;between&#32;image&#32;processing&#32;and&#32;single-cell&#32;analysis&#32;by&#32;directly&#32;importing&#32;data&#32;generated&#32;by&#32;steinbock.&#32;The&#32;package&#32;further&#32;supports&#32;spatial&#32;data&#32;analysis&#32;such&#32;as&#32;patch&#32;detection,&#32;interaction&#32;testing&#32;and&#32;spatial&#32;clustering,&#32;and&#32;integrates&#32;with&#32;tools&#32;developed&#32;within&#32;the&#32;Bioconductor&#32;project.&#32;Image&#32;visualization&#32;and&#32;segmentation&#32;quality&#32;control&#32;is&#32;performed&#32;using&#32;the&#32;cytomapper&#32;R/Bioconductor&#32;package.&#32;Together,&#32;the&#32;tools&#32;described&#32;in&#32;this&#32;workflow&#32;facilitate&#32;the&#32;analysis&#32;of&#32;multiplexed&#32;imaging&#32;raw&#32;data&#32;at&#32;the&#32;single-cell&#32;and&#32;spatial&#32;level.&#32; >A Framework For Multiplexed Image Processing And Spatial Analysis***</a> </td> <td style="text-align:center" width="5%"><a href="https://bodenmillergroup.github.io/demos/" target="_blank"><i class="fas fa-external-link-alt" ></i></a></td> <td style="text-align:center" width="5%"><a href="https://github.com/BodenmillerGroup/demos" target="_blank"><i class="fab fa-github" ></i></a></td> <td width="5%"></td> </tr> </tbody> </table> </div> /registration/ Mon, 01 Jan 0001 00:00:00 +0000 /registration/ <h3 id="coming-soon">Coming soon</h3> <!-- ### Registration is now open for the BioC22 conference. 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All sessions include Q&A time. | Time | | Track | | Name | |:----------------------:|---------------|------------|---------------|--------------------------| | **Monday, 7/27/2020** | &nbsp; &nbsp; | | &nbsp; &nbsp; | | | 8:00 AM | &nbsp; &nbsp; | Community | &nbsp; &nbsp; | Open breakfast meeting | --> /schedule/ Mon, 01 Jan 0001 00:00:00 +0000 /schedule/ <h3 id="coming-soon">Coming soon</h3> <!-- + [All short talks](../tags/short-talk/) + [All workshops and package demos](../workshops/) + Conference videos will appear on the [R Consortium](https://www.youtube.com/c/RConsortium) YouTube channel - subscribe! <h3> Wednesday, July 27, 2022 </h3> <div class="container"> <table id='schedule-table' class="table table-bordered table-hover"> <thead> <tr> <th>Time (PDT)</th> <th>Session</th> <th>Presenting author(s)</th> <th>Title/Event</th> <th>YouTube</th> <tr> </thead> <tbody> <tr> <td width="5%">07:30</td> <td width="12%">Opening Session</td> <td width="18%"></td> <td width="60%">Opening Session</td> <td width="5%"><a href="https://youtu.be/CBBA42w71vU" target="_blank"><i class="fab fa-youtube" ></i></a></td> </tr> <tr class="danger"> <td width="5%">08:00</td> <td width="12%">Keynote</td> <td width="18%"><a href="https://twitter.com/cendrinou" target="_blank">Sandrine Dudoit</a></td> <td width="60%">Learning from Data in Single-Cell Transcriptomics</td> <td width="5%"></td> </tr> <tr class="success"> <td width="5%">09:00</td> <td width="12%">Short talks track</td> <td width="18%"> <a href="https://twitter.com/marouenbg" target="_blank">Marouen Ben Guebila</a><br> Noriaki Sato<br> <a href="https://twitter.com/Lauren_M_Harmon" target="_blank">Lauren Marie Harmon</a><br> Jacob Morrison<br> </td> <td width="60%"><a href="../abstracts/track1" target="_blank" title=ZgotmplZ >Systems Biology/Epigenetics Track</a> </td> <td width="5%"> <br> <br> <a href="https://www.youtube.com/watch?v=64lkiAF9OrA" target="_blank"><i class="fab fa-youtube" ></i></a><br> <a href="https://www.youtube.com/watch?v=M_1EzH9mf-I" target="_blank"><i class="fab fa-youtube" ></i></a><br> </td> </tr> <tr> <td width="5%">12:00</td> <td width="12%">Lunch break</td> <td width="18%"></td> <td width="60%">Lunch Break</td> <td width="5%"></td> </tr> <tr class="info"> <td width="5%">13:15</td> <td width="12%">Package demo</td> <td width="18%"><a href="https://twitter.com/NilsEling" target="_blank">Nils Eling</a></td> <td width="60%"><a href="../abstracts/paper2" target="_blank" title=Simultaneous&#32;profiling&#32;of&#32;the&#32;spatial&#32;distributions&#32;of&#32;multiple&#32;biological&#32;molecules&#32;at&#32;single-cell&#32;resolution&#32;has&#32;recently&#32;been&#32;enabled&#32;by&#32;the&#32;development&#32;of&#32;highly&#32;multiplexed&#32;imaging&#32;technologies.&#32;Extracting&#32;and&#32;analyzing&#32;biologically&#32;relevant&#32;information&#32;contained&#32;in&#32;complex&#32;imaging&#32;data&#32;requires&#32;the&#32;use&#32;of&#32;a&#32;diverse&#32;set&#32;of&#32;computational&#32;tools&#32;and&#32;algorithms.&#32;We&#32;developed&#32;a&#32;standardized,&#32;user-friendly,&#32;customizable,&#32;and&#32;interoperable&#32;workflow&#32;for&#32;processing&#32;and&#32;analyzing&#32;data&#32;generated&#32;by&#32;highly&#32;multiplexed&#32;imaging&#32;technologies.&#32;The&#32;steinbock&#32;framework&#32;written&#32;in&#32;python&#32;supports&#32;image&#32;pre-processing,&#32;segmentation,&#32;feature&#32;extraction,&#32;and&#32;data&#32;export&#32;in&#32;a&#32;reproducible&#32;fashion.&#32;The&#32;imcRtools&#32;R/Bioconductor&#32;package&#32;forms&#32;the&#32;bridge&#32;between&#32;image&#32;processing&#32;and&#32;single-cell&#32;analysis&#32;by&#32;directly&#32;importing&#32;data&#32;generated&#32;by&#32;steinbock.&#32;The&#32;package&#32;further&#32;supports&#32;spatial&#32;data&#32;analysis&#32;such&#32;as&#32;patch&#32;detection,&#32;interaction&#32;testing&#32;and&#32;spatial&#32;clustering,&#32;and&#32;integrates&#32;with&#32;tools&#32;developed&#32;within&#32;the&#32;Bioconductor&#32;project.&#32;Image&#32;visualization&#32;and&#32;segmentation&#32;quality&#32;control&#32;is&#32;performed&#32;using&#32;the&#32;cytomapper&#32;R/Bioconductor&#32;package.&#32;Together,&#32;the&#32;tools&#32;described&#32;in&#32;this&#32;workflow&#32;facilitate&#32;the&#32;analysis&#32;of&#32;multiplexed&#32;imaging&#32;raw&#32;data&#32;at&#32;the&#32;single-cell&#32;and&#32;spatial&#32;level.&#32; >A Framework For Multiplexed Image Processing And Spatial Analysis***</a> </td> <td width="5%"></td> </tr> <tr class="warning"> <td width="5%">13:15</td> <td width="12%">Workshop</td> <td width="18%">James MacDonald</td> <td width="60%"><a href="../abstracts/paper25" target="_blank" title=There&#32;are&#32;various&#32;annotation&#32;packages&#32;provided&#32;by&#32;the&#32;Bioconductor&#32;project&#32;that&#32;can&#32;be&#32;used&#32;to&#32;incorporate&#32;additional&#32;information&#32;to&#32;results&#32;from&#32;high-throughput&#32;experiments.&#32;This&#32;can&#32;be&#32;as&#32;simple&#32;as&#32;mapping&#32;Ensembl&#32;IDs&#32;to&#32;corresponding&#32;HUGO&#32;gene&#32;symbols,&#32;to&#32;much&#32;more&#32;complex&#32;queries&#32;involving&#32;multiple&#32;data&#32;sources.&#32;In&#32;this&#32;workshop&#32;we&#32;will&#32;cover&#32;the&#32;various&#32;classes&#32;of&#32;annotation&#32;packages,&#32;what&#32;they&#32;contain,&#32;and&#32;how&#32;to&#32;use&#32;them&#32;efficiently.&#32; >Introduction to Bioconductor annotation resources*</a> </td> <td width="5%"><a href="https://www.youtube.com/watch?v=rFNBTrTcY78" target="_blank"><i class="fab fa-youtube" ></i></a></td> </tr> </tbody> <table> </div>Workshop/demo levels: * - beginner, recommended for starting with Bioconductor; ** - intermediate; *** - advanced. <h3> Thursday, July 28, 2022 </h3> <div class="container"> <table id='schedule-table' class="table table-bordered table-hover"> <thead> <tr> <th>Time (PDT)</th> <th>Session</th> <th>Presenting author(s)</th> <th>Title/Event</th> <th>YouTube</th> <tr> </thead> <tbody> </tbody> <table> </div>Workshop/demo levels: * - beginner, recommended for starting with Bioconductor; ** - intermediate; *** - advanced. <h3> Friday, July 29, 2022 </h3> <div class="container"> <table id='schedule-table' class="table table-bordered table-hover"> <thead> <tr> <th>Time (PDT)</th> <th>Session</th> <th>Presenting author(s)</th> <th>Title/Event</th> <th>YouTube</th> <tr> </thead> <tbody> </tbody> <table> </div>Workshop/demo levels: * - beginner, recommended for starting with Bioconductor; ** - intermediate; *** - advanced. --> <!--The conference will be held on the [Airmeet](https://www.airmeet.com/) virtual platform. Please, refer to the [Guide for participants](https://youtu.be/FvvZzcwlyv4) video and the [step-by-step guide how to use Airmeet](https://www.airmeet.com/hub/product-blog/step-by-step-guide-use-airmeet-for-attendees/). Please note there are no options to blur or hide your background in Airmeet; use third-party software if the blur is necessary. Keynote sessions are 50 min, Short talk sessions (four 10-min talks) are 50 min, Package demos are 45 min, Long workshops are 90 min. Sessions during the same time slot will be run in parallel. All sessions include Q&A time. We will be accepting abstracts for lightning talks during the conference. Watch for announcements on the first day on how to submit. If you would like to organize a meeting around a topic, challenge, geographical area, etc. during BioC2021, please, use [this form](https://forms.gle/s73DfbXPoVRe4FKj6) - [All short talk abstracts](../short-talks) - [All poster abstracts](../posters) - [All workshops](../workshops), [workshop status](../workshops-status) All times are in US Pacific Daylight savings Time (PDT). +3 hours = US EDT, +9 hours = Central European Summer Time, +15 hours = China Standard Time, +17 hours = Australian Eastern Standard Time. Time is presented in 24h format. ## Wednesday, August 4, 2021 | Time | Session | Title &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; | YouTube | |----------------------------|---------------------------------------------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|---------------------------------------| | 5:00 | Introduction | Intro to workshops, Icebreaker, Social/informal welcome | [video](https://youtu.be/6skphXuBbd4) | | 6:00 | Package demo | [Octavio Morante-Palacios, et al., shinyEPICo: a graphical pipeline to analyze Illumina DNA methylation arrays](../posts/paper10) | [video](https://youtu.be/pYoId4RAsMY) | | 6:00 | Package demo | [Federico Marini, et al., GeneTonic: enjoying the interpretation of your RNA-seq data analysis](../posts/paper55) | [video](https://youtu.be/lxpm3i4PNEE) | | 7:00 | Long workshop | [Aedin Culhane, Dimension Reduction for Beginners](../posts/paper27) | [video](https://youtu.be/dTNMmBpizGA) | | 7:00 | Long workshop | [Christophe Vanderaa, et al., Reproducing a single-cell proteomics data analysis using QFeatures and scp](../posts/paper78) | [video](https://youtu.be/20TxPLbyE3w) | | 7:00 | Long workshop | [Chloe Anya Mirzayi, et al., Epidemiology for Bioinformaticians](../posts/paper121) | [video](https://youtu.be/k9XdqF0WbbQ) | | 9:00 | Official welcome | Opening remarks | [video](https://youtu.be/vpBUahIF4xw) | | 9:30 | Keynote | Daniela Witten, Selective inference on trees | [video](https://youtu.be/rjFW4qaRPgs) | | 10:30 | Short talks | [Methodology and statistics](../methodology-and-statistics) track | [video](https://youtu.be/JpeXnugheAc) | | 10:30 | Short talks | [Epigenomics/Gene regulation](../epigenomics-gene-regulation) track | [video](https://youtu.be/zdHpSECaC6c) | | 11:30 | Break | Networking | | | 13:00 | Keynote | Lucia Peixoto, Reproducible Neuroscience from “omics” data analysis: a tale of sleep and learning | [video](https://youtu.be/howE6aPmOWE) | | 14:00 | Package demo | [Dario Righelli, et al., SpatialExperiment: infrastructure for spatially resolved transcriptomics data in R using Bioconductor](../posts/paper65) | [video](https://youtu.be/heO-TmRO1LE) | | 14:00 | Package demo | [Aaron Chevalier, et al., Enhanced Deconvolution and Prediction of Mutational Signatures](../posts/paper69) | [video](https://youtu.be/tmVhpeYnQ4o) | | 14:00 | Package demo | [Kai Hu, Integrated ATAC-seq Analysis with ATACseqQC / Integrated ChIP-seq Analysis with ChIPpeakAnno](../posts/paper94) | [video](https://youtu.be/oYcHEXqZa1Q) | | 15:00 | Short talks | [Transcriptomics](../transcriptomics) track | [video](https://youtu.be/3xNvgPWpnxs) | | 15:00 | Short talks | [Single-cell genomics](../single-cell-genomics) track | [video](https://youtu.be/4Pw7u-cJAYA) | | 16:00 | Break | Networking | | | 17:00 | Package demo | [Mahmoud Ahmed, et al., Chromatin segmentation analysis in R](../posts/paper90) | [video](https://youtu.be/YvhgF-qLP_I) | | 17:00 | Package demo | [Vincent James Carey, Integrative genetic epidemiology with OpenGWAS, OpenCRAVAT, and Bioconductor](../posts/paper113) | [video](https://youtu.be/_C5dTh4ARm0) | | 17:00 | Package demo | [Aaron R Wolen, et al., Infinitely Scalable Data Analysis in R with TileDB](../posts/paper49) | [video](https://youtu.be/CcL-xEIcHE8) | | 18:00 | Package demo | [Pratheepa Jeganathan, et al., Statistical methods for microbiome data analysis](../posts/paper85) | [video](https://youtu.be/SdM37jaXVh4) | | 18:00 | Package demo | [Nitesh Turaga, Fast-package installation with Bioconductor package binaries](../posts/paper76) | [video](https://youtu.be/Fd4gxJWwEbM) | | 19:00 | Package demo | [Sean K Maden, et al., Accessing, querying, and analyzing public DNAm array data compilations with recountmethylation](../posts/paper106) | [video](https://youtu.be/nTysBp4fvaw) | | 19:00 | Package demo | [David Allen Henderson, et al., Bioconductor Infrastructure Packages for NanoString Assay Data](../posts/paper73) | [video](https://youtu.be/yNqoS9Y2Sy4) | | 19:00 | Package demo | [Edward Zhao, et al., BayesSpace enables the robust characterization of spatial gene expression architecture in tissue sections at increased resolution](../posts/paper6) | [video](https://youtu.be/vQRT8myi-qs) | ## Thursday, August 5, 2021 | Time | Session | Title &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; | YouTube | |----------------------------|---------------------------------------------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|---------------------------------------| | 6:00 | Package demo | [Denes Turei, et al., OmnipathR: one package to access more than 100 signaling databases](../posts/paper115) | | | 6:00 | Package demo | [Johannes Rainer, et al., Seamless Integration of Mass Spectrometry Data from Different Sources with the Spectra Package](../posts/paper14) | [video](https://youtu.be/CNvqlK3Wgx4) | | 6:00 | Package demo | [Eleni Adam, et al., hummingbird: A package for detecting differential methylation](../posts/paper59) | [video](https://youtu.be/0GkNxjLUx7U) | | 7:00 | Long workshop | [Sehyun Oh, et al., Introduction to the Terra/AnVIL Cloud-based Genomics Platform](../posts/paper124) | [video](https://youtu.be/N83iDYE2yQM) | | 7:00 | Long workshop | [Jenny Drnevich, et al., Building Carpentries-based Bioconductor Lessons](../posts/paper112) | [video](https://youtu.be/m4ICc1yQTyY) | | 7:00 | Long workshop | [Marcel Ramos, et al., Multi-omic Integration of cBioPortal and TCGA data with MultiAssayExperiment](../posts/paper40) | [video](https://youtu.be/BY2BwYCHpUc) | | 8:45 | Meet the TAB | Meet the TAB | [video](https://youtu.be/cmvPHuWhacg) | | 9:30 | Keynote | Matthew Stephens, An invitation to a multiple testing party! | [video](https://youtu.be/zORLq07Y5vA) | | 10:30 | Short talks | [Transcriptomics](../transcriptomics-) track | [video](https://youtu.be/eqPD6IhbMhc) | | 10:30 | Short talks | [Apps and frameworks](../apps-and-frameworks) track | [video](https://youtu.be/3Vl0QtB5k-c) | | 11:30 | Break | Networking | | | 12:30 | Awards | Bioconductor award ceremony | [video](https://youtu.be/hOvBuJ-k1nM) | | 13:00 | Keynote | Gabriela de Queiroz, Building a Diverse Community: The R-Ladies Story | [video](https://youtu.be/iufMSW_gXvM) | | 14:00 | Birds-of-a-feather | [Nathan C. Sheffield, AnnotationHub 2.0: A new Bioconductor ecosystem for region data](../posts/paper100) | | | 14:00 | Career panel | | [video](https://youtu.be/XeyzuLMaKQM) | | 15:00 | Poster session | [Moderna Poster session](../posters) | | | 16:00 | Break | Networking | | | 17:00 | Short talks | [Epigenomics/Gene regulation](../epigenomics-gene-regulation-) track | [video](https://youtu.be/oZ6kDZbFo18) | | 17:00 | Short talks | [Education and frameworks](../education-and-frameworks) track | [video](https://youtu.be/p6DVdZNcUmo) | | 18:00 | Long workshop | [Peter Hickey, Effectively using the DelayedArray framework to support the analysis of large datasets](../posts/paper50) | [video](https://youtu.be/FZ8hZ4gZqTw) | | 18:00 | Long workshop | [James MacDonald, Introduction to Bioconductor annotation resources](../posts/paper68) | [video](https://youtu.be/3ABBm7BZszI) | | 18:00 | Long workshop | [Hector Roux de Bezieux, et al., Trajectory inference across conditions: differential expression and differential progression](../posts/paper80) | [video](https://youtu.be/SwDQFjmbZtg) | ## Friday, August 6, 2021 | Time | Session | Title &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; | YouTube | |----------------------------|---------------------------------------------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|---------------------------------------| | 6:00 | Poster session | [Nanostring Poster session](../posters) | | | 7:00 | Short talks | [Single-cell genomics](../single-cell-genomics-) track | [video](https://youtu.be/X6rCbXZEoPU) | | 7:00 | Short talks | [Proteomics/metabolomics](../proteomics-metabolomics) track | [video](https://youtu.be/mnfHJMKwRzc) | | 7:00 | Short talks | [Integrative analysis](../integrative-analysis) track | [video](https://youtu.be/OQ-0Aa5J4ec) | | 8:00 | Package demo | [Nils Eling, Visualisation of highly-multiplexed imaging data in R](../posts/paper1) | [video](https://youtu.be/DYYuAPcBf8s) | | 8:00 | Package demo | [Pacome Prompsy, Interactive analysis of single-cell epigenomic landscapes with ChromSCape](../posts/paper2) | [video](https://youtu.be/Illy08-W56k) | | 8:00 | Package demo | [Federico Agostinis, et al., NewWave, new R package for dimensional reduction and batch effect removal for single cell RNA-seq data](../posts/paper11) | [video](https://youtu.be/_WYS-JFdVrU) | | 8:45 | Meet the core team | | [video](https://youtu.be/O2WOTclMk18) | | 9:30 | Keynote | Amanda Haddock, Redefining the Patient's Role in the Genomics Era | [video](https://youtu.be/OqZ44OqESlM) | | 10:30 | Short talks | [Infrastructure/programming](../infrastructure-programming) track | [video](https://youtu.be/BXX-Q7HosnM) | | 10:30 | Short talks | [Microbiome/metagenomics](../microbiome-metagenomics) track | [video](https://youtu.be/Gv1ud-JG0ms) | | 11:30 | Break | Networking | | | 13:00 | Keynote | Melissa Wilson, Sex-biased genomics and methodology | [video](https://youtu.be/WPy3_IWa5gA) | | 14:00 | Meet the CAB | | [video](https://youtu.be/LTT1i_ACpxc) | | 15:00 | Lightning talks | | [video](https://youtu.be/nGQ6Y3GmYL4) | | 16:00 | Break | Networking | | | 17:00 | Package demo | [Lukas M Weber, et al., Orchestrating Spatially Resolved Transcriptomics Analysis with Bioconductor (OSTA)](../posts/paper74) | [video](https://youtu.be/dXF7Rv2UwdI) | | 17:00 | Package demo | [Nitesh Turaga, K8sredis: On-demand parallel computing Kubernetes application for Bioconductor users](../posts/paper82) | [video](https://youtu.be/D8eNwVfLJKo) | | 18:00 | Long workshop | [Daniela Cassol, et al., systemPipe: Workflow and Visualization Toolkit](../posts/paper81) | [video](https://youtu.be/_C4K7TFicDo) | | 18:00 | Long workshop | [Stefano Mangiola, et al., Interfacing Bioconductor with tidyverse with tidySingleCellExperiment and tidySummarisedExperiment](../posts/paper9) | [video](https://youtu.be/kmfIFIgVwvc) | | 19:45 | Closing remarks | Networking | [video](https://youtu.be/N7LCSUWYof0) | Change the time zone in the teamup calendar ('hamburger button' in the upper-right corner). Add this calendar to your calendar using "Preferences/iCalendar Feeds". <iframe src="https://teamup.com/ksctonvjmqxgz617gy?showProfileAndInfo=0&showSidepanel=1&showAgendaHeader=1&showAgendaDetails=0&showYearViewHeader=1" width="100%" height="800px" style="border: 1px solid #cccccc" frameborder="0"></iframe> --> /schedule_iframe/ Mon, 01 Jan 0001 00:00:00 +0000 /schedule_iframe/ <iframe src="https://teamup.com/ksctonvjmqxgz617gy?showProfileAndInfo=0&showSidepanel=1&showAgendaHeader=1&showAgendaDetails=0&showYearViewHeader=1" width="100%" height="800px" style="border: 1px solid #cccccc" frameborder="0"></iframe> /sponsors/ Mon, 01 Jan 0001 00:00:00 +0000 /sponsors/ <div class="heading text-center"> <h2> Platinum </h2> </div> <div class="container-fluid"> <div class="row"> </div> </div> <div class="heading text-center"> <h2> Gold </h2> </div> <div class="container-fluid"> <div class="row"> <div class="col-xs-12 col-sm-12 col-md-6 col-lg-6 text-center"> <div class="panel panel-default"> <div class="panel-body"> <img src="/img/clients/logo_genetech_biogen.png" class="img-responsive center-block"> <a href="https://www.gene.com/" target="_blank"> Genentech </a> & <a href = "https://www.biogen.com/" target="_blank"> Biogen </a> </div> </div> </div> </div> </div> <div class="heading text-center"> <h2> Silver </h2> </div> <div class="container-fluid"> <div class="row"> </div> </div> <div class="heading text-center"> <h2> Others </h2> </div> <div class="container-fluid"> <div class="row"> </div> </div> <!-- | | |:-----:| | **Moderna Therapeutics** | |  | | **https://www.modernatx.com/** | &nbsp; 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| | |:-----:| | **F1000** | |  | | **https://f1000research.com/** | &nbsp; | | |:-----:| | **Stickermule** | |  | | **[https://www.stickermule.com/](https://mule.to/p1yv)** | &nbsp; | | |:-----:| | **CRC Press** | |  | | **https://www.routledge.com/** | &nbsp; | | |:-----:| | **Bristol Myers Squibb** | |  | | **https://www.bms.com/** | --> <p> </p> /abstracts/track1/ Mon, 01 Jan 0001 00:00:00 +0000 /abstracts/track1/ <h1> Systems Biology/Epigenetics Track </h1> <br> /organizers/ Mon, 01 Jan 0001 00:00:00 +0000 /organizers/ <div style="display: grid; grid-template-columns: repeat(4, 1fr); gap: 30px;"> <div style="text-align: center; min-height: 280px;"> <img src="/img/organizers/EllisPatrick.png" alt="Photo of Ellis Patrick" style="max-width:150px;height:150px;"><br> <a href="https://profiles.sydney.edu.au/ellis.patrick" target="_blank" rel="noopener noreferrer"><b>Ellis Patrick</b></a><br> Associate Professor<br> The University of Sydney, Westmead Institute for Medical Research<br> Australia </div> <div style="text-align: center; min-height: 280px;"> <img src="/img/organizers/EmmaGail.jpeg" alt="Photo of Emma Gail" style="max-width:150px;height:150px;"><br> <b>Emma Gail</b><br> Training Lead<br> Melbourne Bioinformatics<br> Australia </div> <div style="text-align: center; min-height: 280px;"> <img src="/img/organizers/KozoNishida.jpeg" alt="Photo of Kozo Nishida" style="max-width:150px;height:150px;"><br> <b>Kozo Nishida</b><br> RIKEN Center for Biosystems Dynamics Research<br> Japan </div> <div style="text-align: center; min-height: 280px;"> <img src="/img/organizers/LoriShepherd.png" alt="Photo of Lori (Shepherd) Kern" style="max-width:150px;height:150px;"><br> <b>Lori (Shepherd) Kern</b><br> Bioconductor Core Team<br> Roswell Park Comprehensive Cancer Center<br> USA </div> <div style="text-align: center; min-height: 280px;"> <img src="/img/organizers/MalvikaKharbanda.jpeg" alt="Photo of Malvika Kharbanda" style="max-width:150px;height:150px;"><br> <a href="https://researchers.adelaide.edu.au/profile/malvika.kharbanda" target="_blank" rel="noopener noreferrer"><b>Malvika Kharbanda</b></a><br> PhD Candidate, Computational Systems Oncology<br> SAiGENCI<br> Australia </div> <div style="text-align: center; min-height: 280px;"> <img src="/img/organizers/MansiAggarwal.jpeg" alt="Photo of Mansi Aggarwal" style="max-width:150px;height:150px;"><br> <b>Mansi Aggarwal</b><br> Bioinformatician<br> Mass Dynamics<br> Australia </div> <div style="text-align: center; min-height: 280px;"> <img src="/img/organizers/MariaDoyle.png" alt="Photo of Maria Doyle" style="max-width:150px;height:150px;"><br> <b>Maria Doyle</b><br> Bioconductor Community Manager<br> University of Limerick<br> Ireland </div> <div style="text-align: center; min-height: 280px;"> <img src="/img/organizers/StefanoMangiola.jpeg" alt="Photo of Stefano Mangiola" style="max-width:150px;height:150px;"><br> <a href="https://researchers.adelaide.edu.au/profile/stefano.mangiola" target="_blank" rel="noopener noreferrer"><b>Stefano Mangiola</b></a><br> Group Leader, Computational Cancer Immunogenomics<br> SAiGENCI<br> Australia </div> <div style="text-align: center; min-height: 280px;"> <img src="/img/organizers/SteviePederson.png" alt="Photo of Stevie Pederson" style="max-width:150px;height:150px;"><br> <a href="https://www.telethonkids.org.au/contact-us/our-people/p/stephen-stevie-pederson/" target="_blank" rel="noopener noreferrer"><b>Stevie Pederson</b></a><br> Bioinformatician, Indigenous Genomics team<br> The Kids Research Institute<br> Australia </div> <div style="text-align: center; min-height: 280px;"> <img src="/img/organizers/YashpalRamakrishnaiah.jpeg" alt="Photo of Yashpal Ramakrishnaiah" style="max-width:150px;height:150px;"><br> <b>Yashpal Ramakrishnaiah</b><br> Postdoctoral Researcher<br> Monash University<br> Australia </div> <div style="text-align: center; min-height: 280px;"> <img src="/img/organizers/ZuguangGu.jpeg" alt="Photo of Zuguang Gu" style="max-width:150px;height:150px;"><br> <a href="https://jokergoo.github.io/about/" target="_blank" rel="noopener noreferrer"><b>Zuguang Gu</b></a><br> Shenzhen University of Advanced Technology<br> China </div> </div> /workshops/ Mon, 01 Jan 0001 00:00:00 +0000 /workshops/ <h2 id="0n-orchestra">0n orchestra</h2> <ol> <li>Go to <a href="http://app.orchestra.cancerdatasci.org" target="_blank" >Orchestra</a>.</li> <li>Log in.</li> <li>Search for the workshop of interest.</li> <li>Click &ldquo;Launch&rdquo; (may take a minute or two).</li> <li>Follow instructions.</li> </ol> <h2 id="all-workshops-and-demos-by-level">All workshops and demos by level</h2> <h3> Beginner </h3> Recommended for starting with Bioconductor. <div class="container"> <table id="workshop-table" class="table table-bordered table-hover"> <thead> <tr> <th>Session type</th> <th>Title</th> <th>Details</th> <th>Source</th> <th>Youtube</th> <tr> </thead> <tbody> <tr> <td width="5%"> Workshop </td> <td width="80%"><a href="../abstracts/paper25" target="_blank" title=There&#32;are&#32;various&#32;annotation&#32;packages&#32;provided&#32;by&#32;the&#32;Bioconductor&#32;project&#32;that&#32;can&#32;be&#32;used&#32;to&#32;incorporate&#32;additional&#32;information&#32;to&#32;results&#32;from&#32;high-throughput&#32;experiments.&#32;This&#32;can&#32;be&#32;as&#32;simple&#32;as&#32;mapping&#32;Ensembl&#32;IDs&#32;to&#32;corresponding&#32;HUGO&#32;gene&#32;symbols,&#32;to&#32;much&#32;more&#32;complex&#32;queries&#32;involving&#32;multiple&#32;data&#32;sources.&#32;In&#32;this&#32;workshop&#32;we&#32;will&#32;cover&#32;the&#32;various&#32;classes&#32;of&#32;annotation&#32;packages,&#32;what&#32;they&#32;contain,&#32;and&#32;how&#32;to&#32;use&#32;them&#32;efficiently.&#32; >Introduction to Bioconductor annotation resources*</a> </td> <td style="text-align:center" width="5%"><a href="https://jmacdon.github.io/Bioc2022Anno/" target="_blank"><i class="fas fa-external-link-alt" ></i></a></td> <td style="text-align:center" width="5%"><a href="https://github.com/jmacdon/Bioc2022Anno" target="_blank"><i class="fab fa-github" ></i></a></td> <td style="text-align:center" width="5%"><a href="https://www.youtube.com/watch?v=rFNBTrTcY78" target="_blank"><i class="fab fa-youtube" ></i></a></td> </tr> </tbody> </table> </div> <h3> Intermediate </h3> <div class="container"> <table id="workshop-table" class="table table-bordered table-hover"> <thead> <tr> <th>Session type</th> <th>Title</th> <th>Details</th> <th>Source</th> <th>Youtube</th> <tr> </thead> <tbody> </tbody> </table> </div> <h3> Advanced </h3> <div class="container"> <table id="workshop-table" class="table table-bordered table-hover"> <thead> <tr> <th>Session type</th> <th>Title</th> <th>Details</th> <th>Source</th> <th>Youtube</th> <tr> </thead> <tbody> <tr> <td width="5%"> Package demo </td> <td width="80%"><a href="../abstracts/paper2" target="_blank" title=Simultaneous&#32;profiling&#32;of&#32;the&#32;spatial&#32;distributions&#32;of&#32;multiple&#32;biological&#32;molecules&#32;at&#32;single-cell&#32;resolution&#32;has&#32;recently&#32;been&#32;enabled&#32;by&#32;the&#32;development&#32;of&#32;highly&#32;multiplexed&#32;imaging&#32;technologies.&#32;Extracting&#32;and&#32;analyzing&#32;biologically&#32;relevant&#32;information&#32;contained&#32;in&#32;complex&#32;imaging&#32;data&#32;requires&#32;the&#32;use&#32;of&#32;a&#32;diverse&#32;set&#32;of&#32;computational&#32;tools&#32;and&#32;algorithms.&#32;We&#32;developed&#32;a&#32;standardized,&#32;user-friendly,&#32;customizable,&#32;and&#32;interoperable&#32;workflow&#32;for&#32;processing&#32;and&#32;analyzing&#32;data&#32;generated&#32;by&#32;highly&#32;multiplexed&#32;imaging&#32;technologies.&#32;The&#32;steinbock&#32;framework&#32;written&#32;in&#32;python&#32;supports&#32;image&#32;pre-processing,&#32;segmentation,&#32;feature&#32;extraction,&#32;and&#32;data&#32;export&#32;in&#32;a&#32;reproducible&#32;fashion.&#32;The&#32;imcRtools&#32;R/Bioconductor&#32;package&#32;forms&#32;the&#32;bridge&#32;between&#32;image&#32;processing&#32;and&#32;single-cell&#32;analysis&#32;by&#32;directly&#32;importing&#32;data&#32;generated&#32;by&#32;steinbock.&#32;The&#32;package&#32;further&#32;supports&#32;spatial&#32;data&#32;analysis&#32;such&#32;as&#32;patch&#32;detection,&#32;interaction&#32;testing&#32;and&#32;spatial&#32;clustering,&#32;and&#32;integrates&#32;with&#32;tools&#32;developed&#32;within&#32;the&#32;Bioconductor&#32;project.&#32;Image&#32;visualization&#32;and&#32;segmentation&#32;quality&#32;control&#32;is&#32;performed&#32;using&#32;the&#32;cytomapper&#32;R/Bioconductor&#32;package.&#32;Together,&#32;the&#32;tools&#32;described&#32;in&#32;this&#32;workflow&#32;facilitate&#32;the&#32;analysis&#32;of&#32;multiplexed&#32;imaging&#32;raw&#32;data&#32;at&#32;the&#32;single-cell&#32;and&#32;spatial&#32;level.&#32; >A Framework For Multiplexed Image Processing And Spatial Analysis***</a> </td> <td style="text-align:center" width="5%"><a href="https://bodenmillergroup.github.io/demos/" target="_blank"><i class="fas fa-external-link-alt" ></i></a></td> <td style="text-align:center" width="5%"><a href="https://github.com/BodenmillerGroup/demos" target="_blank"><i class="fab fa-github" ></i></a></td> <td width="5%"></td> </tr> </tbody> </table> </div>