Discover and read the best of Twitter Threads about #scanpy
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Proud of our 1st manuscript! Cell2location: a new tool that integrates single cell + spatial transcriptomics data to map tissue atlases at scale. Also new biology in brain/lymph node. Fantastic collab with @OliverStegle, lead by @vitaliikl biorxiv.org/content/10.110…
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Single cell + spatial RNAseq is highly scalable for cell atlassing. However, complex tissues present big challenges for computational methods: need to accurately map dozens of cell types including rare & fine subtypes + account for tech differences between sc/spatial data 
Enter cell2location. First, we derive cell type gene expression signatures from scRNAseq. Then, we decompose spatial data into cell type abundance maps using these reference signatures. We show c2l accurately maps two complex tissues: the mouse brain and human lymph node
We developed Visualization in Plugin on top of #cellxgene to generate violin, stacked violin, stacked bar, heatmap, volcano, embedding, dot, track, density, 2D density, sankey and dual-gene plot in high-resolution SVG/PNG format for #singlecell #rnaseq dataset #scRNAseq #scanpy
The preprint is available here
@cellxgene VIP unleashes full power of interactive visualization, plotting and analysis of #scRNA-seq data in the scale of millions of cells biorxiv.org/content/10.110…
@cellxgene VIP unleashes full power of interactive visualization, plotting and analysis of #scRNA-seq data in the scale of millions of cells biorxiv.org/content/10.110…
Want to play with cellxgene VIP live? Demo is here
cellxgenevip-ms.bxgenomics.com
Dataset: MS brain #snRNAseq dataset by @schirmerlab and #RowitchLab
cellxgenevip-ms.bxgenomics.com
Dataset: MS brain #snRNAseq dataset by @schirmerlab and #RowitchLab
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.
