There are many packages on Bioconductor, CRAN and GitHub to build and improve workflows. Here are the essentials. Rafael Gottardo leads a fabulous team (Greg Finak, Mike Jiang, Jake Wagner) that develops the core packages for flow cytometry. These packages provide examples (vignettes). Looking at the results of those packages is valuable, at least to […]
Main workflows to start with are: the pipeline from Nowicka et al. from Mark Robinson’s lab. the primer of BioSurf for the data scientist (R pipeline). See also the valuable primer for the cytometrist. Mark Robinson’s lab does a great job developing package and workflows: CATALYST (Cytometry dATa anALYSis Tools) allows Preprocessing and Differential discovery. […]
Here is the place to start with R with the goal to analyze cytometry data. Christopher Hall provides nice resources to start and improve R handout.pdf from zero to R basics to visualize, gate, tSNE… R flow cytometry course Scripts for cytometry Lukas Weber provides simple scripts, Rtsne-example and FlowSOM-Rtsne-example, and scripts from a CyTOF-workshop-2017. Nello Blaser […]
There is an increasing interest in analyzing cytometry data with R. R is not intuitive and the learning curve is not fast. But there are rewards: You can easily repeat and tweak an analysis because the analysis is a script, that is a text file with commands to run and achieve the analysis. This is […]