GenePattern is an open source platform for reproducible bioinformatics providing access to 250+ tools for the analysis of genomic data #progammingoptional
UCSD, San Diego, CA
Joined September 2010
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GenePattern retweeted
Genomics to Notebook (g2nb): extending the electronic notebook to address the challenges of bioinformatics analysis biorxiv.org/cgi/content/shor… #biorxiv_bioinfo
GenePattern retweeted
📢 ONLINE @NatureGenet
📰 Functional landscapes of POLE and POLD1 mutations in checkpoint blockade-dependent antitumor immunity
🧑🏿🤝🧑🏼 @GeneCollector @Pheno2geno @ClevelandClinic
@CCLRI @NatlRegenMed and team
👇🏿
go.nature.com/3bYP1FH
GenePattern retweeted
#MSigDB 7.3 out now! A new sub-collection of vaccine response gene sets courtesy of HIPC, many new cell type signatures, updates for @WikiPathways, @hp_ontology, @news4go, and @reactome. Gene annotations from @ensembl 103. See gsea-msigdb.org/ for details #Bioinformatics
GenePattern retweeted
#MSigDB 7.2 out now! Includes new @WikiPathways and @hp_ontology gene sets! We've also updated @news4go, @reactome, and added a number of #SARSCoV2 sets among other miscellaneous changes. Gene annotations from @ensembl 101. See gsea-msigdb.org/ for details #Bioinformatics
GenePattern retweeted
Great virtual audience today at #ISMB2020 for the @GenePattern Notebook talk, including collection of #SingleCell #bioinformatics analysis notebooks #NCIITCR
It begins! Michael Reich giving a great talk on the very usable @GenePattern notebook. Find out more about the GenePattern notebook for single cell transcriptomic data analysis in the @F1000Research paper here 👉 f1000research.com/articles/7… #ISMB2020
GenePattern retweeted
It begins! Michael Reich giving a great talk on the very usable @GenePattern notebook. Find out more about the GenePattern notebook for single cell transcriptomic data analysis in the @F1000Research paper here 👉 f1000research.com/articles/7… #ISMB2020
GenePattern retweeted
Do you use IGV? Do you develop with igv.js? Help our proposal for renewed funding by telling us how IGV has benefited your work and why the IGV resource should be sustained. Email [email protected] or DM @igvteam by May 18, 2020 #bioinformatics #genomics #ngsdata
GenePattern retweeted
Latest work from @Anne_R1chL. We developed a tool that used systems biology models to precompute the genes needed for a cell to accomplish a metabolic task, and now you can overlay your omics data to see what your cell is doing using @GenePattern. bioRxiv: doi.org/10.1101/2020.04.26.0…
Do you want to know what does your cell really do? Then check this out => CellFie : a new framework to elucidate a cell’s metabolic functions directly from omics data. biorxiv.org/content/10.1101/…
GenePattern retweeted
Live with #msigdb 7.1! Major update to our predicted miRNA and Transcription Factor Target sets with new data from miRDB (mirdb.org/) and GTRD (gtrd.biouml.org/). Content updates from @news4go, @reactome, and Gene Symbols from @ensembl. gsea-msigdb.org
GenePattern retweeted
Happy to host @mmreich, Ted Liefeld, @edjuaro and @alextwenzel from Jill Mesirov's @UCSanDiego lab for another @GenePattern Workshop, this one entirely focused on single-cell RNA-seq analysis. Rumor has it they'll be doing this again next month @UCSF.
GenePattern retweeted
We're baaaack! Winter San Diego #Jupyter meetup is January 28. Consider signing up for a 5 min lightning talk about your favorite Jupyter extension 💻✨
meetup.com/San-Diego-Jupyter…
GenePattern retweeted
Registration is now open for the CCMI's workshop on "Single-Cell Analysis with the GenePattern Notebook Environment" featuring @mmreich and other members of the @GenePattern team - eventbrite.com/e/workshop-si…
GenePattern retweeted
IGV 2.7 released with new support for viewing data in Amazon S3 storage using native AWS authorization and authentication (thanks to @braincode and colleagues at @UMCCR for the contribution). Plus other features and fixes. See release notes at software.broadinstitute.org/… #genomics
GenePattern retweeted
San Diego and #UCSD @ProjectJupyter users: join us for our Fall Jupyter #Meetup to hear about new Jupyter-based projects and share your work meetup.com/San-Diego-Jupyter…
GenePattern retweeted
Over 2500 users have already made the jump to MSigDB 7 and GSEA 4. These major releases brought significant new #MSigDB content with updated gene sets and new @ensembl gene annotations, and improvements to GSEA architecture with OpenJDK support. Update at gsea-msigdb.org
GenePattern retweeted
Thank you @FertigLab for your ongoing collaboration! We are glad to host your cutting-edge CoGAPS #MachineLearning #singlecell analysis technique on the @GenePattern and @humancellatlas notebook workspaces!
GenePattern retweeted
Our @humancellatlas notebook workspace will let you interact easily with the HCA data from within the @GenePattern @JupyterNotebook environment hca.genepattern.org - see notebooks on querying Expression Matrix service and single-cell #RNA-seq analysis
Nice primer on the @HumanCellAtlas project, a herculean effort to chart the soft-wiring of human biology, cell by cell. Cannot wait to interact with these data
statnews.com/2019/04/23/huma…
GenePattern retweeted
Do you 💚 open+bio?
We need your help! The gender balance for our talk/posters abstracts isn't as well balanced as we'd hoped (or as previous years). Please help us spread word to get a more diverse abstract pool! Late talk applications open 'til May 15.
open-bio.org/events/bosc/sub…
GenePattern retweeted
Excited to be demonstrating our work connecting the @cziscience funded @humancellatlas to our @ProjectJupyter and @GenePattern notebook environment meetup.com/San-Diego-Jupyter… #Bioinformatics
Join us on May 8: Jupyter Notebook in Science and Education at UCSD meetup.com/San-Diego-Jupyter… #Meetup #LaJolla via @Meetup @mmreich @SDSC_UCSD @DataSciUCSD @ProjectJupyter
GenePattern retweeted
Stop by our poster at #AACR19 in section 30, board 19. Let us know how we can help with bioinformatic analysis
