What types of data are supported by Cellenics?

I have a collaborator who wants to send me some single cell data and I hope to examine it using your platform. What format should I request this in? I think I will need raw count matrix files, sample IDs as CSV files?
Similarly, if I download scRNAseq data from GEO, what format should this be in for input into your platform?

In order to get your data into Cellenics. you’ll need the raw count matrices in the shape of three files: barcodes.tsv, features.tsv and matrix.mtx files. This is a common data type generated after processing Fastq files with either Cell Ranger or 10x Cloud. For every sample you’ll need a different set of files, and each set of files should be in a separate folder with the sample name, as shown on this slide.

Unfortunately, datasets that are available on public repositories such as GEO and ArrayExpress are often in different formats as there is no set standard. For converting data files in other formats so that they are compatible with Cellenics, you have two options:

  1. You can use the various blog posts available on our website (Blog) to guide you through the data conversion. These blog posts contain instructions and associated R code for the conversion of H5 files, Seurat objects, CSV/TSV files, and combined / multiplexed count matrices. Note that some knowledge of using R is required.
  2. If you’d like us to take care of the data file conversion for you, we can do so on a consulting basis for a fee of $235 USD per hour bioinformatics time. Please get in touch for a quote: hello@biomage.net
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