How label Group list after integratin scRNA-seq and scATAC-seq data

[IqRaZaFaR16]

Hello everyOne i have a question related to created Group list after integrating scRNA-seq data with scATAC-seq data we have identify totaly 6 clusters from both scRNA and scATAC-seq
whats the logic behind this to generate group list

should i consider number of cells compared with scRNA-seq and scATAC-seq

# Define the groupList based on the clusters and developmental stages
groupList <- SimpleList(
    G1 = SimpleList(
        ATAC = Merged.proj2.SPG$cellNames[
            Merged.proj2.SPG$Clusters %in% c("C4")  
        ],
        RNA = colnames(SPG.seRNA)[
            SPG.seRNA$idents.rename2 %in% c("G1") 
        ]
    ),
    preL = SimpleList(
        ATAC = Merged.proj2.SPc$cellNames[
            Merged.proj2.SPc$Clusters %in% c("C3")  
        ],
        RNA = colnames(SPc.seRNA)[
            SPc.seRNA$idents.rename2 %in% c("preL") 
        ]
    ),
    ePL = SimpleList(
        ATAC = Merged.proj2.SPc$cellNames[
            Merged.proj2.SPc$Clusters %in% c("C5")  
        ],
        RNA = colnames(SPc.seRNA)[
            SPc.seRNA$idents.rename2 %in% c("ePL")
        ]
    ),
    IPL = SimpleList(
        ATAC = Merged.proj2.SPc$cellNames[
            Merged.proj2.SPc$Clusters %in% c("C2")  
        ],
        RNA = colnames(SPc.seRNA)[
            SPc.seRNA$idents.rename2 %in% c("IPL")
        ]
    )
    mPL = SimpleList(
        ATAC = Merged.proj2.SPc$cellNames[
            Merged.proj2.SPc$Clusters %in% c("C6")  
        ],
        RNA = colnames(SPc.seRNA)[
            SPc.seRNA$idents.rename2 %in% c("mPL")
        ]
    ),
    L = SimpleList(
        ATAC = Merged.proj2.SPc$cellNames[
            Merged.proj2.SPc$Clusters %in% c("C1")  
        ],
        RNA = colnames(SPc.seRNA)[
            SPc.seRNA$idents.rename2 %in% c("L")
        ]
    ),)

[immanuelazn]

Hi @IqRaZaFaR16! Thanks for using ArchR! Please make sure that your post belongs in the Issues section. Only bugs and error reports belong in the Issues section. Usage questions and feature requests should be posted in the Discussions section, not in Issues.

If you are getting an error, it is likely due to something specific to your dataset, usage, or computational environment, all of which are extremely challenging to troubleshoot. As such, we require reproducible examples (preferably using the tutorial dataset) from users who want assistance. If you cannot reproduce your error, we will not be able to help.
Before going through the work of making a reproducible example, search the previous Issues, Discussions, function definitions, or the ArchR manual and you will likely find the answers you are looking for.
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In addition to a reproducible example, you must do the following things before we help you, unless your original post already contained this information:
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[IqRaZaFaR16]

could you please respond on my issue 04/07/2025 10:52:28 "Immanuel Abdi" ***@***.***> wrote: Hi @IqRaZaFaR16! Thanks for using ArchR! Please make sure that your post belongs in the Issues section. Only bugs and error reports belong in the Issues section. Usage questions and feature requests should be posted in the Discussions section, not in Issues. If you are getting an error, it is likely due to something specific to your dataset, usage, or computational environment, all of which are extremely challenging to troubleshoot. As such, we require reproducible examples (preferably using the tutorial dataset) from users who want assistance. If you cannot reproduce your error, we will not be able to help. Before going through the work of making a reproducible example, search the previous Issues, Discussions, function definitions, or the ArchR manual and you will likely find the answers you are looking for. If your post does not contain a reproducible example, it is unlikely to receive a response. In addition to a reproducible example, you must do the following things before we help you, unless your original post already contained this information: 1. If you've encountered an error, have you already searched previous Issues to make sure that this hasn't already been solved? 2. Did you post your log file? If not, add it now. 3. Remove any screenshots that contain text and instead copy and paste the text using markdown's codeblock syntax (three consecutive backticks). You can do this by editing your original post. — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.Message ID: ***@***.***> immanuelazn left a comment (GreenleafLab/ArchR#2292) Hi @IqRaZaFaR16! Thanks for using ArchR! Please make sure that your post belongs in the Issues section. Only bugs and error reports belong in the Issues section. Usage questions and feature requests should be posted in the Discussions section, not in Issues. If you are getting an error, it is likely due to something specific to your dataset, usage, or computational environment, all of which are extremely challenging to troubleshoot. As such, we require reproducible examples (preferably using the tutorial dataset) from users who want assistance. If you cannot reproduce your error, we will not be able to help. Before going through the work of making a reproducible example, search the previous Issues, Discussions, function definitions, or the ArchR manual and you will likely find the answers you are looking for. If your post does not contain a reproducible example, it is unlikely to receive a response. In addition to a reproducible example, you must do the following things before we help you, unless your original post already contained this information: 1. If you've encountered an error, have you already searched previous Issues to make sure that this hasn't already been solved? 2. Did you post your log file? If not, add it now. 3. Remove any screenshots that contain text and instead copy and paste the text using markdown's codeblock syntax (three consecutive backticks). You can do this by editing your original post. — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.Message ID: ***@***.***>

[IqRaZaFaR16]

I am currently using ArchR to analyze scATAC-seq and scRNA-seq data. In the tutorial, it is mentioned that a group list is generated by assigning clusters from the scATAC-seq data and cell type labels from the scRNA-seq data. Could you please clarify the basis on which these clusters from scATAC-seq data and cell type labels from scRNA-seq are assigned to generate the group list?