scanpy_usage

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I am wondering how to match the barcodes from text file to the barcodes from csv file in order to generate figure with the cell types assigned to each cluster?...

Kristina1234444

updated visualization examples

3

Updated the visualizations notebook to reflect the latest scanpy modifications (https://github.com/theislab/scanpy/pull/425/)

fidelram

I'm using [this tutorial](https://github.com/theislab/scanpy_usage/blob/master/171111_SPRING_export/SPRING_export.ipynb) for exporting adata object to SPRING input. First suggestion to update this tutorial, I had to modify this slightly per the updates in the command: `sc.external.exporting.spring_project(adata,...

nroak

memory

2

Hi, I am trying to run the full 1.3M 10X mouse cell dataset (using the 1M_neurons_filtered_gene_bc_matrices_h5.h5 file from 10X website). I have 126GB RAM and Intel® Xeon(R) W-2123 CPU @...

ShobiStassen

Hi, I am having an issue exporting my h5ad file to spring for visualization. I have been following the [spring export tutorial](https://github.com/theislab/scanpy_usage/tree/master/171111_SPRING_export) but every time I try to run `sc.export_to.spring_project`...

sfortma2

Cannot open louvain.csv.gz

2

Hi, I have downloaded the louvain.csv.gz file. But I cannot extract it. Tried gunzip, reading it through python and R but getting the error that it is Not a gzipped...

BSharmi

can't replicate 170505_seurat/seurat.ipynb notebook

6

I tried to replicate the .. notebook using scanpy but I got some different results (see notebook [here](https://github.com/fidelram/scanpy_usage/blob/master/170505_seurat/seurat.ipynb)): 1. The tsne plot looks different (although similar groups can be seen)....

fidelram