Cell Ranger 3.1 (latest), printed on 11/11/2019
|Prior to Cell Ranger 3.0 10x Genomics supported an R package, called rkit, that enabled users to load and manipulate 10X data. However, due to the growth of third-party tools that provide similar capabilities, this package has been deprecated and it is unable to analyze data produced by the Cell Ranger 3.0 software.|
The bioinformatics community is actively developing software to analyze Chromium Single Cell data. See below for some featured examples. These packages are not supported by 10x Genomics.
Seurat 3.0 is specifically designed to handle the type of multi-data experiments enabled by Feature Barcoding technology, and can also read the latest output file produced by Cell Ranger 3.0. Note that Seurat versions below 3.0 do not support reading the new output files produced by Cell Ranger 3.0.
Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data using R, including data produced by 10X Genomics technology.