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GenePattern @GenePattern

GenePattern is an open source platform for reproducible bioinformatics providing access to 250 tools for the analysis of genomic data #progammingoptional

Joined September 2010
  • Tweets 703
  • Following 187
  • Followers 956
67 Photos and videos
The Genomics to Notebook (g2nb) environment is featured on the @GalaxyProject blog. Read about how to use Galaxy, IGV, and other bioinformatics tools from within a @ProjectJupyter notebook interface! galaxyproject.org/news/2025-… #nciitcr #bioinformatics

Genomics to Notebook (g2nb): extending the computational notebook

An environment that integrates Jupyter with Galaxy, allowing tools to be added as notebook cells, and providing access to thousands of bioinformatics tools from within a notebook interface.

galaxyproject.org
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Tangram is now available on GenePattern! 🎉 Map sc-RNA-seq data onto spatial gene expression data. GPU & CPU compatible for flexible workflows. 👉 CPU: t.ly/9G2lJ 👉GPU: t.ly/XO8qA 📷 GitHub: t.ly/07w-M #nciitcr @broadinstitute @NIH
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Today's ( Monday September 16, 2024) GenePattern upgrade to the cloud server, cloud.genepattern.org/gp, is complete. Please let us know on the help forum, groups.google.com/u/1/g/gene…, if you experience any issues.
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On Monday September 16, the main GenePattern public server, cloud.genepattern.org/gp, will be unavailable from 7:00 AM through 3:00 PM PST (UTC 8) to update the GenePattern software and database.
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GenePattern needs your help! We are preparing a grant proposal for the sustainment of GenePattern server & GenePattern Notebooks. An email from you will help underscore their impact when the grant is reviewed. See our post at: bit.ly/gp-needs-your-help
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GenePattern in @NatureComms! A transcriptome based molecular classification scheme for cholangiocarcinoma and subtype-derived prognostic biomarker. 2024. Nature Communications. doi.org/10.1038/s41467-024-4… #nciitcr #bioinformatics
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GenePattern and @GSEA_MSigDB in @NatureComms! Tumour-retained activated CCR7 dendritic cells are heterogeneous and regulate local anti-tumour cytolytic activity. 2024. Nature Communications. doi.org/10.1038/s41467-024-4… #nciitcr #bioinformatics
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GenePattern and @GSEA_MSigDB in @NatureComms! The tumor microenvironment shows a hierarchy of cell-cell interactions dominated by fibroblasts. 2023. Nature Communications. doi.org/10.1038/s41467-023-4… #nciitcr #bioinformatics
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The GenePattern server, cloud.genepattern.org, will be offline for maintenance on Tuesday November 7th, 2023 from 1-3pm PST (GMT-7).
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g2nb: Genomics to Notebook! A new platform that combines the accessibility and research narrative capabilities of @ProjectJupyter with the genomics tools available in @galaxyproject, @igvteam, @cytoscape, and GenePattern. youtu.be/40YEVyJnGAc #nciitcr #bioinformatics

Introducing g2nb

This video introduces the core features of g2nb and how to get star...

youtube.com
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g2nb: Genomics to Notebook extends GenePattern Notebooks to add @galaxyproject, @igvteam, @cytoscape to @ProjectJupyter for easy access to 1000s of bioinformatics tools as notebook cells g2nb.org drive.google.com/file/d/1mIP… @g2nb #bioinformatics #openscience #nciitcr
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The GenePattern server at cloud.genepattern.org will be unavailable between 1-3pm PST (UTC 8) on Monday August 28th, 2023 as it is upgraded to the latest version.
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The GenePattern server at cloud.genepattern.org will be unavailable between 2-3pm PST (UTC 8) on Monday August 7th, 2023 as it is upgraded to the latest version.
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Harmony, from the @RoychoudhuriLab, is now available on GenePattern! Harmony corrects batch effects in single-cell RNA seq datasets. Use it at rb.gy/o6a5n #nciitcr #Bioinformatics
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GenePattern is glad to join @galaxyproject, @cytoscape, and @igvteam as tools in the JupyterLab-based g2nb environment. g2nb.org #nciitcr #bioinformatics

bioRxiv Bioinfo@biorxiv_bioinfo
6 Apr 2023
Genomics to Notebook (g2nb): extending the electronic notebook to address the challenges of bioinformatics analysis biorxiv.org/cgi/content/shor… #biorxiv_bioinfo
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GenePattern retweeted
bioRxiv Bioinfo@biorxiv_bioinfo
6 Apr 2023
Genomics to Notebook (g2nb): extending the electronic notebook to address the challenges of bioinformatics analysis biorxiv.org/cgi/content/shor… #biorxiv_bioinfo
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Today's maintenance is complete and the GenePattern server at cloud.genepattern.org is once again available for use
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On Monday, March 16th from 1:00 pm to 2:00 pm PST (UTC-8) the public GenePattern server at cloud.genepattern.org/gp will be unavailable for scheduled maintenance.
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GenePattern, @galaxyproject, and @cytoscape in @IJMS_MDPI! Transcriptomic Analysis of Glycosylation and Neuroregulatory Pathways in Rodent Models in Response to Psychedelic Molecules. Oommen et al. 2023. IJMS. doi.org/10.3390/ijms24021200 #nciitcr #bioinformatics

Transcriptomic Analysis of Glycosylation and Neuroregulatory Pathways in Rodent Models in Response...

The potential for psychedelic molecules in impacting cognitive flexibility has long been supported and acknowledged across scientific reports. In the current study, an approach leveraging knowledge...

mdpi.com
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The connection between GenePattern and Globus has been restored. All systems are operating properly once again.
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