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feiyoung / DR-SC.Analysis

Codes for analysis of DR-SC
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Human dorsolateral prefrontal cortex data #1

Open WUZHExl opened 2 years ago

WUZHExl commented 2 years ago

Hello, can you provide the data for analysis in visium_human_dorsolateral_prefrontal_Cortex.r? I can get the raw data, but I'm not sure what goes from the raw data to the data for your analysis.

Xu-010724 commented 3 months ago

Hello, can you provide the data for analysis in visium_human_dorsolateral_prefrontal_Cortex.r? I can get the raw data, but I'm not sure what goes from the raw data to the data for your analysis.

feiyoung commented 3 months ago

The data are accessible at the following GitHub repository link: https://github.com/feiyoung/DR-SC.Analysis/tree/main/data/DLPFC_data.

Xu-010724 commented 3 months ago

I know the data are accessible at the following GitHub repository link: https://github.com/feiyoung/DR-SC.Analysis/tree/main/data/DLPFC_data.But I would like to know how these data were obtained from the raw data (http://spatial.libd.org/spatialLIBD/).  

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The data are accessible at the following GitHub repository link: https://github.com/feiyoung/DR-SC.Analysis/tree/main/data/DLPFC_data.

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feiyoung commented 3 months ago

You can install spatialLIBD package in http://spatial.libd.org/spatialLIBD/, then you can download it using spatialLIBD::fetch_data(type = "spe").

class: SpatialExperiment dim: 33538 47681 metadata(0): assays(2): counts logcounts rownames(33538): ENSG00000243485 ENSG00000237613 ... ENSG00000277475 ENSG00000268674 rowData names(9): source type ... gene_search is_top_hvg colnames(47681): AAACAACGAATAGTTC-1 AAACAAGTATCTCCCA-1 ... TTGTTTCCATACAACT-1 TTGTTTGTGTAAATTC-1 colData names(69): sample_id Cluster ... array_row array_col reducedDimNames(6): PCA TSNE_perplexity50 ... TSNE_perplexity80 UMAP_neighbors15 mainExpName: NULL altExpNames(0): spatialCoords names(2) : pxl_col_in_fullres pxl_row_in_fullres imgData names(4): sample_id image_id data scaleFactor Next, you can save the data for each tissue section as a .rds file. The brain_151507_spark.Rdata is obtained by running the SPARK method to select the spatially variable genes.