Dr. Stefano Mangiola is leading the Computational
Cancer immunology group at the South Australian immunoGENomics Cancer
Institute (SAiGENCI). He uses single-cell and spatial technologies to
investigate the tumor microenvironment and the immune system. Beyong
data production, his focus in on the integration and modelling of
large-scale single-cell data resources. He is the author of
tidytranscriptiomics and co-leads the
tidyomics endevour.
BLUESKY: https://bsky.app/profile/stemang.bsky.social TWITTER/X: https://x.com/steman_research
Dr. Luciano Martelotto is a key figure in the field of spatial omics technology. He was previously the Scientific Director at the Single Cell Core facility at Harvard University, where he demonstrated his extensive expertise and significant contributions to the fields of single cell and spatial omics technology. Currently, he heads the Martelotto Lab located at the Adelaide Centre for Epigenetics and the South Australian immunoGENomics Cancer Institute (SAiGENCI). His lab is dedicated to the development and evaluation of new tools and methodologies for single cell and spatial omics, serving as an important incubator for innovation in these technologies. The lab engages in global collaborations and provides comprehensive support from the conceptual stage through to the analysis and delivery of results.
tidyomicsSpatialExperiment with tidy R
manipulation and visualisationIf you want to install the packages and material post-workshop, the
instructions are below. The workshop is designed for R 4.4
and Bioconductor 3.19.
# Install workshop package
#install.packages('BiocManager')
BiocManager::install("tidyomics/tidySpatialWorkshop2024", dependencies = TRUE)
# In May 2024, the following packages should be installed from github repositories, to use the latest features. In case you have them pre installed, run the following command
BiocManager::install(c("lmweber/ggspavis",
"stemangiola/tidySummarizedExperiment",
"william-hutchison/tidySpatialExperiment",
"stemangiola/tidybulk",
"stemangiola/tidygate",
"stemangiola/CuratedAtlasQueryR"),
update = FALSE)
BiocManager::install("ggcorrplot")
# Then build the vignettes
BiocManager::install("tidyomics/tidySpatialWorkshop2024", build_vignettes = TRUE, force=TRUE)
# To view vignette
library(spatialOmicsWorkshop2024)
vignette("Introduction")From command line, and enter the tidySpatialWorkshop2024 directory.
# Open the command line
git clone git@github.com:tidyomics/tidySpatialWorkshop2024.git
Alternatively download the git zipped package. Uncompress it. And enter the directory.
Postdoc, RA and PhD positions available!
Spatial and single-cell computational immunogenomics for cancer diagnosis
AI large-language models of single-cell data for cancer immunogenomics
R software engineer for tidyomics ecosystem and single-cell and spatial omic pipelines
Provide a foundational understanding of spatial omics, covering different technologies and the distinctions between imaging and sequencing in experimental and analytical contexts.
<mangiola.s at wehi.edu.au>↩︎