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392 results for “tutorial”
AnnData object for case study tutorials
<p>This dataset works for the Filter, Plot & Explore tutorial: https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-case_basic-pipeline/tutorial.html</p>
AI tutorial data
<p>Preprocessing demo</p>
Training data for the "Metabarcoding/eDNA through Obitools" tutorial
<p>Training dataset for Obitools tutorial using Galaxy.</p>
WESTPA 2.0 haMSM restarting tutorial sample data
<p>Sample dataset for use with the WESTPA-2.0 haMSM restarting plugin tutorial.</p>
CView: tutorial 1 - overview (movie and script)
<p><strong>Overview of CView</strong></p> <p>This page contains the video tutorial, tutorial_1_overview.mp4, and accompanying script, as presented by Raquel Linheiro describing the general usage of CView. Further details about the software can be obtained from our manuscript <a href="https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0259726">CView: A network based tool for enhanced alignment visualization</a>.</p> <p> </p> <p><strong>Other Tutorials</strong></p> <p>A general demonstration of how variants can be identified using CView is available <a href="https://zenodo.org/record/6514972">here</a>.</p> <p> </p> <p><strong>Case Study Data</strong></p> <p>The alignment used for the case study described within the manuscript is available <a href="https://zenodo.org/record/6475666">here</a>.</p> <p> </p> <p>A poster sumarization presented at <a href="https://www.iscb.org/ismb2022">ISMB 2022</a> is available <a href="https://doi.org/10.5281/zenodo.6798044">here</a>.</p> <p>The CView project page is located at: <a href="https://sourceforge.net/projects/cview/">https://sourceforge.net/projects/cview/</a>. </p> <p> </p> <p>Related software to this project are:<br> 1. <a href="http://sourceforge.net/projects/cstone/">CStone</a> <br> 2. <a href="http://sourceforge.net/projects/csreadgen/">CSReadGen</a><br> 3. <a href="https://sourceforge.net/projects/cview/">CView</a> <<br> 4. <a href="https://sourceforge.net/projects/chimsim/">ChimSim</a><br> 5. <a href="https://sourceforge.net/projects/tvscript/">TVScript</a></p> <p> </p> <p>General details of the project are available <a href="https://cibio.up.pt/en/projects/de-novo-based-sequence-assembly-of-next-generation-sequence-data-without-chimeras-improved-annotation-gene-expression-profiles-and-haplotype-br-reconstruction/">here</a>.</p> <p> </p> <p><strong>| linkedIn . web . orcid |</strong><br> | <a href="https://www.linkedin.com/in/raquel-linheiro-50883873/">linheiro</a> . web . <a href="https://orcid.org/0000-0003-2659-0910">orcid</a> |---| sabatino . <a href="https://cibio.up.pt/en/people/details/stephen-joseph-sabatino/">web</a> . <a href="https://orcid.org/0000-0003-2815-2375">orcid</a> |---| <a href="https://www.linkedin.com/in/diana-lobo-6aa63328/">lobo</a> . <a href="https://cibio.up.pt/en/people/details/diana-lobo/">web</a> . <a href="https://orcid.org/0000-0001-6988-9993">orcid</a> |---| <a href="https://www.linkedin.com/in/john-archer-7b872872">archer</a> . <a href="https://cibio.up.pt/en/people/details/john-archer/">web</a> . <a href="https://orcid.org/0000-0001-6212-0962">orcid</a> |</p> <p> </p>
Example data for PlotsOfData tutorial
<p>Example data for PlotsOfData tutorial</p>
Downsampled metagenomic datasets for the metaFlye tutorial
<p>Downsampled metagenomic datasets for the metaFlye tutorial</p>
Tutorial video to use the 'sm-dtw' assessment tool with simulated synthetic phyllotaxis data
<p>This tutorial explain how to use 'sm-dtw', an assessment tool which has been designed to evaluate how good a phyllotaxis measure is from a plant phenotyping experiment. To get data to play with and explore all possible case scenarios, we also designed a program to generate phyllotaxis data and simulate typical errors produced by a phenotyping experiment.</p> <p>This tutorial explains:</p> <p>1) the context in which such a tool is useful (what is a phyllotaxis measure ? What kind of phenotyping experiment ? Why do need to evaluate your results ? What are typical errors you want to detect ?)</p> <p>2) how to download and use the two programs ('sm-dtw' and the generator of phyllotaxis data)</p> <p>3) how to play with the programs thanks to pedagogical demonstrator notebooks.</p> <p>In brief, there are 3 notebooks that are meant to be run as three successive steps:</p> <ul> <li>step1 / Notebook 1: it allows anybody to simulate phyllotaxis data (pair of sequences consisting of ground truth sequences and their error-prone measures),</li> <li>step2 / Notebook 2: assess the measure performance with our new program ‘sm-dtw’ (detect errors and quantify precision)</li> <li>step3/Notebook 3: control that sm-dtw program correctly interprets the differences between the measure and its ground truth reference.</li> </ul>
GTN Tutorial: Data Manipulation Olympics
<p>Input datasets for the Galaxy Tutorial on Data manipulation</p>
16S metabarcoding tutorial
<p>Tutorial for the analysis of 16S rRNA metabarcoding sequences using the MiSeq SOP pipeline. https://github.com/AndresICM/16S-rRNA-Metabarcoding-analysis</p>
mosartwmpy tutorial data 1981-05
<p>Input data for following along with the mosartwmpy model tutorial: https://github.com/IMMM-SFA/mosartwmpy</p>
Trajectories_Jupyter_Tutorial
<p>These datasets and Jupyter notebooks are used in the single cell trajectories tutorial on the Galaxy Training Network site.</p>
Data for GNPS Tutorial
<ol> <li>Quantification file = <em>DDA_PeakArea_for_GNPS.txt</em></li> <li>MS/MS spectra file = <em>GnpsMgf_0_20228151332.mgf</em></li> </ol>
Intermediate files for dRep / inStrain tutorial
<p>Intermediate files for dRep / inStrain tutorial</p>
Cases used in EMRNA tutorial
<p>EMRNA: Accurate RNA structure determination from cryo-EM maps by deep learning and integrated modeling.</p> <p>Here stores the 4 cases used in the EMRNA tutorial.</p>
Lantern from Substance Painter tutorial
The lantern I textured following the newest Allegorithmic tutorial. Source: Objaverse 1.0 / Sketchfab
Data for the rethomics + ethoscope tutorial
<p>A toy dataset to tech readers hor to use rethomics' scopr package. See https://rethomics.github.io/scopr.html</p>
Tutorial: Sicherheitsausnahme für Internetprogramme Hinzufügen (Windows)
<p>In diesem Video zeigen wir dir, wie du eine Sicherheitsausnahme hinzufügst, um auf deinem Windows-Rechner ein aus dem Internet geladenes Programm zu starten. Im Video werden zwei mögliche Wege kurz aber Schritt-für-Schritt erklärt, sodass du sie ganz einfach nachvollziehen kannst. Da viele Programme der digitalen Geisteswissenschaften frei aus dem Internet heruntergeladen werden können, gehört das Hinzufügen von Sicherheitsausnahmen fast zu jedem Installationsprozess dieser Tools dazu.</p>
Tutorial: Sicherheitsausnahme für Internetprogramme Hinzufügen (Mac)
<p><span><span>In diesem Video zeigen wir dir, wie du eine Sicherheitsausnahme hinzufügst, um auf deinem Mac ein aus dem Internet geladenes Programm zu starten. Im Video werden zwei mögliche Wege kurz aber Schritt-für-Schritt erklärt, sodass du sie ganz einfach nachvollziehen kannst. Da viele Programme der digitalen Geisteswissenschaften frei aus dem Internet heruntergeladen werden können, gehört das Hinzufügen von Sicherheitsausnahmen fast zu jedem Installationsprozess dieser Tools dazu.</span></span></p> <div></div> <div> <div> <div></div> </div> </div> <p> </p>
Data files for Bioinformatics Tutorial May 2024
<p>These files are for use in a bioinformatics tutorial on the Galaxy platform.</p>
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.