We offer pre-processing of data from 10x Genomics Chromium gene expression assays. We use cellranger count to map the reads to the reference genome and count the number of reads overlapping with each gene to produce a count matrix for each sample. After that, we perform a downstream analysis with a.o. the R packages Seurat and scater, resulting in quality control, transformation, dimensionality reduction and clustering.
Note that we also offer more extensive downstream analyses in the form of collaborations. Please contact us for more details.
HTML reports from an example analysis can be downloaded below.