Comments (1)
I've added the Stereoscope results to spatial_analysis/stsc
.
I've fixed some of the paths in append_stereoscope_data.R
but some are still specific to our HPC cluster.
You might have to adjust some more paths to get the script to run (and please open a pull request if you do!) but at least you can explore the data.
Sorry about the hold up.
from brca_cell_atlas.
Related Issues (20)
- sd_amplifier set to 1.3 for de-noising? HOT 2
- Code about the gene module
- Identifying thresholds for cancer cell detection with medoids clustering HOT 2
- Single Cell Count HOT 3
- Batch Corrected Count Matrix HOT 3
- scSubtype related code,Is it possible to call directly? HOT 7
- CITE-seq data filtering HOT 1
- Request to Meta data csv file HOT 2
- About the "filtered_count_matrices.tar.gz" download on zenodo HOT 2
- Deconvolution file corresponding to 1160920F Patient counts from the zenodo repository. HOT 2
- Request for Original H&E Images for Spatial Transcriptomics Slides HOT 3
- Potentially application of ecotyper? HOT 1
- Request for gene_clusters.txt file for AUCell analysis for spatial data HOT 1
- Question about difference between AUcell & other geneset enrichment tools HOT 1
- Request for providing script for running stereoscope for spatial data
- Request for providing RData files for major,minor,subset celltypes
- Reproducing SC subtype calls HOT 2
- Garnett subtypes
- Gene Positions data for running inferCNV. HOT 1
- BAM files
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