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xgaoo / ClusterMap

ClusterMap is an R package to analyze and compare two or more single cell expression datasets.
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Exporting differential expressed genes after simple run #15

Open typatt50 opened 4 years ago

typatt50 commented 4 years ago

Is there a way to export the list of genes that are differential between (Specific to) clusters after a simple run, without the raw RDS file? I unfortunately don’t have access to the raw data currently, and would like to be able to assign candidate genes to each of the new clusters

xgaoo commented 4 years ago

Could you explain what kind of data you have? Seurat can call differential genes if you have the gene expression table. If you don't have, I'm not sure how you run the ClusterMap.     ------------------ Original ------------------ From:  "typatt50"<notifications@github.com>; Date:  Fri, Jul 31, 2020 05:54 AM To:  "xgaoo/ClusterMap"<ClusterMap@noreply.github.com>; Cc:  "Subscribed"<subscribed@noreply.github.com>; Subject:  [xgaoo/ClusterMap] Exporting differential expressed genes after simple run (#15)

 

Is there a way to export the list of genes that are differential between (Specific to) clusters after a simple run, without the raw RDS file? I unfortunately don’t have access to the raw data currently, and would like to be able to assign candidate genes to each of the new clusters

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typatt50 commented 4 years ago

Could you explain what kind of data you have? Seurat can call differential genes if you have the gene expression table. If you don't have, I'm not sure how you run the ClusterMap.     ------------------ Original ------------------ From:  "typatt50"<notifications@github.com>; Date:  Fri, Jul 31, 2020 05:54 AM To:  "xgaoo/ClusterMap"<ClusterMap@noreply.github.com>; Cc:  "Subscribed"<subscribed@noreply.github.com>; Subject:  [xgaoo/ClusterMap] Exporting differential expressed genes after simple run (#15)

 

Is there a way to export the list of genes that are differential between (Specific to) clusters after a simple run, without the raw RDS file? I unfortunately don’t have access to the raw data currently, and would like to be able to assign candidate genes to each of the new clusters

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I am currently trying to apply this tool to several human samples to compare clusters so I can map subgroups across samples. I only currently have access to the output file of Seurat "FindAllMarkers" and not the raw matrix unfortunately. I was able to do a simple run with ClusterMap with these output files to put individual clusters into subgroups, however I would like to somehow get an output of Marker genes of new subgroups I generated. Does ClusterMap have this capability? Thank you very much for the help.