harmony

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Hello, did someone tried to use Harmony on merged objects including more than 200 samples and more than 2 M cells? Which merging and normalization approach is suggested? And which...

erosix

hello harmony team， I wonder how to get the data set cell_lines from 10X data, I would be grateful if you can provide the detailed code of 10X data to...

xuqiu-qiu

Running the `RunHarmony(seuratobject)` with seurat 4.0.3 results in the following error ```Error in UseMethod(generic = "Key", object = object) : no applicable method for 'Key' applied to an object of...

DivyaRavichandar

Thanks for your tools! I met an error like this. And I can't found the harmony results. Error: (converted from warning) Invalid name supplied, making object name syntactically valid. New...

evaniali

I have tried harmony for batch effect correction for my single-cell RNA-seq data to intergrate tumor and normal tissues, but when I used default parameter values, I found one problem...

MatsuSui

Can I split large gene matrix by rows and run harmony in parallel

1

Hi harmony group, I have a large gene expression matrix with 31734 genes by 147185 cells. As you can see from the screenshot below, running HarmonyMatrix() on the entire expression...

jiajinlongkang

General question about use case

1

Hello Harmony team, I have a single cell RNA dataset with samples from 8 different tissues. The trouble I'm having is that some of these tissues were digested enzymatically, and...

Dillon214

Corrected differential gene expression matrix

12

I've been using Harmony for batch effect integration, but I would like to be able to continue downstream analysis in Seurat using the corrected data. I read [this review](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1850-9) rating...

nshedd

Warning: Invalid name supplied

4

Thanks for the tool! When I run RunHarmony I meet a warning ：Warning: Invalid name supplied, making object name syntactically valid. New object name is Seurat..ProjectDim.RNA.harmony; see ?make.names for more...

hahahah-single

Hi, Thank you so much for this great tool! Hope you can help me with this question. I am working with a scRNA-seq dataset in which I have been using...

RolantusdataExp