User: singcell

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singcell0
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Posts by singcell

<prev • 12 results • page 1 of 2 • next >
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Comment: C: Cluster sub-set analysis using Seurat
... Thank you for your reply. I have got integrated Seurat object containing KO and WT samples. Can I still use `subset()` function? Can I still differentiate between WT and KO samples during downstream analysis after subsetting. ...
written 22 days ago by singcell0
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8 follow
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Cluster sub-set analysis using Seurat
... I am trying to dig deeper into my Seurat single-cell data analysis. If I want to further sub-cluster a big cluster then what would be the best way to do it: 1) Decreasing the resolution at `FindClusters` stage or 2) extracting the individual cell index and re-clustering and then further analysis ...
single-cell seurat written 23 days ago by singcell0 • updated 23 days ago by igor11k
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Comment: C: Deterimining overall number of differentially expressed genes between WT and KO
... Thank you for suggestion. I am new to this website. How can I convert my response from answer to comment? ...
written 28 days ago by singcell0
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Answer: A: Deterimining overall number of differentially expressed genes between WT and KO
... @jomo018 Thank you for your help. It worked however, I am seeing the FC other way round. When I run `Idents(seurat_obj)` I see multiple levels or clusters. I am wondering how `Idents(seurat_obj) <- seurat_obj$stim`is able to assign cells to correct idents or KO or WT. ...
written 4 weeks ago by singcell0
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Comment: C: Deterimining overall number of differentially expressed genes between WT and KO
... @jomo018 way worked. Thank you for your help, anyway. ...
written 4 weeks ago by singcell0
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Comment: C: Deterimining overall number of differentially expressed genes between WT and KO
... @jomo018 way worked. Thank you for your help, anyway. ...
written 4 weeks ago by singcell0
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Deterimining overall number of differentially expressed genes between WT and KO samples
... I am comparing differentially expressed genes (DEGs) between WT and KO samples. If I want to compare DEGs between conditions in a particular cluster I use `FindMarkers` function of Seurat tool by indicating ident.1 and ident.2. However if I wanted to compare overall DEGs between WT and KO samples a ...
scrna-seq findmarkers seurat deg written 4 weeks ago by singcell0
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Comment: C: EdgeR for single cell differential expression analysis
... Hello, Helpful post. I have a question hopefully you can help. I am comparing differentially expressed genes (DEGs) between WT and KO. When I want to compare DEGs between conditions specific to particular cluster I use `Findcluster` function of Seurat tool. Now I wanted to compare overall DEGs bet ...
written 4 weeks ago by singcell0
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Is it possible to determine if cells are clustered by samples and not by cell types?
... I am analyzing single-cell RNA-Seq data from 10x platform using Seurat. I have couple of questions: 1) Is it possible to determine if cells are clustered by samples and not by cell types. Which tool can I use for this analysis? 2) If there is any simple tool available to remove this effect. Than ...
single-cell rna-seq seurat sample variation written 5 weeks ago by singcell0 • updated 20 days ago by Biostar ♦♦ 20
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Calculating in SEURAT, list of highly dysregulated genes across conditions in a particular cluster.
... I am trying to integrate two datasets from different conditions using Seurat vignette "Integrating stimulated vs. control PBMC datasets" #3.1 I wanted to Identify highly dys-regulated genes or highlighting genes that exhibit dramatic responses across conditions in a particular cluster. For example, ...
stimulated vs control pbmcs rna-seq seurat written 3 months ago by singcell0

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