If you are interested in analyzing #SingleCell #RNAseq data in #Bioconductor using #rstats, please check out our paper Orchestrating single-cell analysis (OSCA) with @Bioconductor that was published in @naturemethods this week! #genomics #scRNAseq #dataviz #methodsmatter
@Bioconductor @naturemethods OSCA is a rich, reproducible, accessible (from beginners to experts!) resource with many #scRNAseq workflows & datasets. The resource is an online #bookdown book that compiles every night to track development by the open-source and open-development @Bioconductor #rstats community
@Bioconductor @naturemethods Now, OSCA is not the only set of packages / workflows for the analysis of #scRNAseq data. #Scanpy (scanpy.readthedocs.io/en/stable/) and #Seurat (satijalab.org/seurat/) and are two incredibly popular packages in #python and #rstats, respectively.
@Bioconductor @naturemethods If you are a happy user of either of these wonderful packages and frameworks, I am not here to force you away from that happiness.
...however, if you were interested in knowing more, you might ask, what can OSCA (and the larger #rstats @Bioconductor community) offer?
...however, if you were interested in knowing more, you might ask, what can OSCA (and the larger #rstats @Bioconductor community) offer?
@Bioconductor @naturemethods I personally feel OSCA & @Bioconductor bring enormous innovation to the table: state-of-the-art, #scalable, computational #scRNAseq methods, standardized data infrastructure to enable modularity & interoperability btw packages, while maintaining robust end-user accessibility!
@Bioconductor @naturemethods So, if you want fully reproducible #rstats code to analyze #scRNAseq data using @Bioconductor packages with fantastic explanations behind many of the nuanced choices made when analyzing the type of #genomics data, I encourage you to check out our free book osca.bioconductor.org
@Bioconductor @naturemethods Finally, I want to thank my amazing coauthors, Aaron Lun, Etienne Becht, Vince Carey, Lindsay Carpp, Ludwig Geistlinger, @FedeBioinfo @KevinRUE67 @drisso1893 @CSoneson @LeviWaldron1 Herve Pages, @grimbough @wolfgangkhuber @mt_morgan & esp team co-leads @robamezquita @raphg!
@Bioconductor @naturemethods @FedeBioinfo @KevinRUE67 @drisso1893 @CSoneson @LeviWaldron1 @grimbough @wolfgangkhuber @mt_morgan @robamezquita @raphg Thank you also to all the generous funding and support of the OSCA project including @NIH @genome_gov @theNCI @Bioconductor @cziscience any so many more
@Bioconductor @naturemethods @FedeBioinfo @KevinRUE67 @drisso1893 @CSoneson @LeviWaldron1 @grimbough @wolfgangkhuber @mt_morgan @robamezquita @raphg @NIH @genome_gov @theNCI @cziscience If you want to learn more about the diverse, inclusive, and thriving #singlecell @Bioconductor community, join the Bioconductor Community Slack workspace (bioc-community.herokuapp.com) or check out the #Bioc2020 conference to be held in Boston in July 2020 (bioc2020.bioconductor.org)
