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dpeerlab / Harmony

Harmony framework for connecting scRNA-seq data from discrete time points
GNU General Public License v2.0
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load 10X data #2

Closed jphe closed 4 years ago

jphe commented 5 years ago

Hi,

I'm trying to use harmony for my own 10X scRNAseq data, for the test data it is a csv file, I'm wondering how can I load 10X data into harmony? should I transfer it into a csv? or dose it possible to use any output from scanpy?

Thanks, Jphe

awnimo commented 5 years ago

Hi,

Sorry for the late response.

Currently, Harmony reads in csv files of counts matrices from multiple time points. You should convert your 10X data to csv files before using Harmony

We are working on integrating Harmony into Scanpy framework as an external module, and soon can be used to handle AnnData from multiple time points as input from scanpy.AnnData objects.

awnimo commented 4 years ago

Hi @jphe Just wanted to followup on this and let you know that Harmony has been integrated into Scanpy and works with AnnData structures, conditional on installing the latest release of harmony