for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. http://bioconductor.org/
using Bioconductor Righelli, Weber, Crowell, et al, bioRxiv, 2021 DOI 10.1101/2021.01.27.428431 Dario Righellli Helena L Crowell @drighelli @CrowellHL Lukas M Weber @lmwebr
@PardoBree Brenda Pardo • Opportunity to lead • SpatialExperiment: common infrastructure • STexampleData: example datasets • spatialLIBD: visualization functions & shiny app • ggspavis: visualization • Pre-prints for SpatialExperiment & spatialLIBD • Some conversations with other developers to bring them into the Bioconductor world
high resolution histology images for Visium spatial transcriptomics data https://doi.org/10.1101/2021.08.04.452489 Tutorial: http://research.libd.org/VistoSeg Pipeline: https://github.com/LieberInstitute/VistoSeg Work in progress: 1. Modify pipeline to import and process multichannel Immuno Fluorescence images. 2. Extract cell type and cell morphology information and use it for downstream transcriptomics analysis. Spot Barcode X coordinate Y coordinate Tissue Present - 1 Absent - 0 Cell count %Spot covered spot1 1 2 1 3 90% spot2 1 4 0 0 0%
not GitHub) or available via pip ◦ Centered around SpatialExperiment and Visium by 10x Genomics ◦ macOS / winOS / linux • Main chapters for: ◦ Pre-processing steps: outside R ◦ Analysis steps • Workflow chapters: ◦ Illustrate the commands discussed earlier adapted for a few datasets ◦ Not standalone Bioconductor workflows http://bioconductor.org/packages/release/BiocViews.html#___Workflow ◦ One more detailed workflow on using spatialLIBD • Paper / pre-print coming soon
102 triangle 130.4 feat0002 10 30 cloud 99.1 Max (X, Y) Min (X, Y) Area ... IF Image Analysis * segment each channel * find features Challenges: * morphological features can be quite diverse * images are large * multiple tiles +
Weber @stephaniehicks Stephanie C Hicks @abspangler Abby Spangler @martinowk Keri Martinowich @CerceoPage Stephanie C Page @kr_maynard Kristen R Maynard @lcolladotor Leonardo Collado-Torres @Nick-Eagles (GH) Nicholas J Eagles Kelsey D Montgomery Sang Ho Kwon Image Analysis Expression Analysis Data Generation In collaboration with Thomas M Hyde