search

feiyoung / DR.SC

DR.SC: Joint dimension reduction and spatial clustering for single-cell/spatial transcriptomics data
5 stars 0 forks source link

Human dorsolateral prefrontal cortex data #1

Closed WUZHExl closed 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.

feiyoung commented 2 years ago

Thank you for your attention to DR-SC. We preprocessed the raw data as follows. First, we used SPARK (https://github.com/xzhoulab/SPARK/) to choose the top 2000 spatially variable genes. Then, Log-normalization was performed on the selected gene-spot matrix, which was implemented by using the R function NormalizeData in the Seurat package. Finally, we input the normlized matrix as well as spatial coordinates into DR.SC core function.

In DR.SC package, we provide a high-level function to implement DR-SC, named DR.SC. User only require to create a proper Seurat object to input it to the DR.SC function. You can refer to the vignettes for more details: https://feiyoung.github.io/DR.SC/articles/DR.SC.DLPFC.html

WUZHExl commented 2 years ago

Thank you for your help, Professor Liu.

------------------ 原始邮件 ------------------ 发件人: "feiyoung/DR.SC" @.>; 发送时间: 2022年7月31日(星期天) 晚上10:02 @.>; @.**@.>; 主题: Re: [feiyoung/DR.SC] Human dorsolateral prefrontal cortex data (Issue #1)

Thank you for your attention to DR-SC. We preprocessed the raw data as follows. First, we used SPARK (https://github.com/xzhoulab/SPARK/) to choose the top 2000 spatially variable genes. Then, Log-normalization was performed on the selected gene-spot matrix, which was implemented by using the R function NormalizeData in the Seurat package. Finally, we input the normlized matrix as well as spatial coordinates into DR.SC core function.

In DR.SC package, we provide a high-level function to implement DR-SC, named DR.SC. User only require to create a proper Seurat object to input it to the DR.SC function. You can refer to the vignettes for more details: https://feiyoung.github.io/DR.SC/articles/DR.SC.HCC1.html

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: @.***>

feiyoung commented 2 years ago

You are wellcome. In addition, the DLPFC data used in our paper are uploaded; Please see https://github.com/feiyoung/DR-SC.Analysis/tree/main/data/DLPFC_data.

WUZHExl commented 2 years ago

Hello, when I run visium_human_dorsolateral_prefrontal_cortex.R, in ij <-find_neighbors(sce, platform="Visium")has an error. Error in rownames<-(*tmp*, value = value[[2]]) : invalid rownames length What is the cause?

feiyoung commented 2 years ago

Hello, when I run visium_human_dorsolateral_prefrontal_cortex.R, in ij <-find_neighbors(sce, platform="Visium")has an error. Error in rownames<-(*tmp*, value = value[[2]]) : invalid rownames length What is the cause?

find_neighbors function has been updated that only support matrix object rather than complex singleCellExperiment object input. You can change: ij <- find_neighbors(sce, platform="Visium") to : ij <- find_neighbors(pos, platform="Visium"). Hope this can help you!

WUZHExl commented 2 years ago

Thank you very much for sharing the data with me.It help me a lot.

------------------ 原始邮件 ------------------ 发件人: "feiyoung/DR.SC" @.>; 发送时间: 2022年7月31日(星期天) 晚上10:38 @.>; @.**@.>; 主题: Re: [feiyoung/DR.SC] Human dorsolateral prefrontal cortex data (Issue #1)

You are wellcome. In addition, the DLPFC data used in our paper are uploaded; Please see https://github.com/feiyoung/DR-SC.Analysis/tree/main/data/DLPFC_data.

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: @.***>