Open WUZHExl opened 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.
The data are accessible at the following GitHub repository link: https://github.com/feiyoung/DR-SC.Analysis/tree/main/data/DLPFC_data.
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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------------------ 原始邮件 ------------------ 发件人: "Wei @.>; 发送时间: 2024年8月28日(星期三) 下午2:29 收件人: @.>; 抄送: @.>; @.>; 主题: Re: [feiyoung/DR-SC.Analysis] Human dorsolateral prefrontal cortex data (Issue #1)
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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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.
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.