Software

• spicyR (http://www.bioconductor.org/packages/devel/bioc/html/spicyR.html)
  Provides a series of functions to aid in the analysis of both immunofluorescence and mass cytometry imaging data as well as other assays that can deeply phenotype individual cells and their spatial location.


• lisaClust (http://www.bioconductor.org/packages/devel/bioc/html/lisaClust.html)
  Provides a series of functions to identify and visualise regions of tissue where spatial associations between cell-types is similar. This package can be used to provide a high-level summary of cell-type colocalization in multiplexed imaging data that has been segmented at a single-cell resolution.


• simpleSeg (http://www.bioconductor.org/packages/release/bioc/html/simpleSeg.html)
  Provides provides a structured pipeline for segmentation of cellular tiff stacks and the normalization of features, priming cells for classification / clustering.


• FuseSOM (http://www.bioconductor.org/packages/release/bioc/html/FuseSOM.html)
  Provides a pipeline for the clustering of highly multiplexed in situ imaging cytometry assays. This pipeline uses the Self Organizing Map architecture coupled with Multiview hierarchical clustering.


• Statial (http://www.bioconductor.org/packages/release/bioc/html/Statial.html)
  Statial is a suite of functions for identifying changes in cell state. These features can be used to explore how the structure and function of different cell types may be altered by the agents they are surrounded with.


• ClassifyR (https://www.bioconductor.org/packages/devel/bioc/html/ClassifyR.html)
  Provides a series of functions to identify and visualise regions of tissue where spatial associations between cell-types is similar. This package can be used to provide a high-level summary of cell-type colocalization in multiplexed imaging data that has been segmented at a single-cell resolution.


• scMerge (https://bioconductor.org/packages/release/bioc/html/scMerge.html)
  scMerge leverages factor analysis, stably expressed genes (SEGs) and (pseudo-) replicates to remove unwanted variations and merge multiple scRNA-Seq data. This package contains all the necessary functions in the scMerge pipeline, including the identification of SEGs, replication-identification methods, and merging of scRNA-Seq data.


• AFid (https://ellispatrick.github.io/AFid/)
  A method implemented in ImageJ, Matlab and R that identifies and removes autofluorescent signals from multi-channel images post acquisition.


• DCARS (https://github.com/shazanfar/DCARS/)
  An R package for performing differential correlation across ranked samples developed by Shila Ghazanfar.


• dialects (https://github.com/madeleineotway/dialects/)
  An R package for converting SWATH-MS spectral reference libraries (SRLs) between species developed by Madeleine Otway.


• directPA (http://cran.r-project.org/web/packages/directPA/)
  An R package for pathway analysis in experiments with multiple perturbation designs. For more information about this package please see our publication.


• edgeBundleR (https://cran.r-project.org/web/packages/edgebundleR)
  An R package that Garth Tarr and I wrote for plotting a circular network graph with “bundled” edges. This package allows R users to easily create a hierarchical edge bundle plot. The underlying D3 code was adapted from Mike Bostock’s examples (see here or here) and the package is based on the htmlwidgets framework.


• sydSeq (https://github.com/ellispatrick/sydSeq/)
  An R package containing the functions exClust, TshrinkPlus and pMim. An example illustrating how to use pMim can be found here.

Shiny applications