User: hamza_karakurt

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Posts by hamza_karakurt

<prev • 23 results • page 2 of 3 • next >
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Comment: C: Modularity values of clusters and Differential Expression in scRNA-Seq
... Thank you Aaron, So basically, poorly-seperated is not useless and still can keep valuable information and among 5-6 clusters, choosing the one with the highest modularity means using the "best-seperated" one. And thank you for the information about DE analysis. Since the MNN correction does not ef ...
written 6 months ago by hamza_karakurt30
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Modularity values of clusters and Differential Expression in scRNA-Seq
... Hello everyone, I have several questions about scRNA-Seq data analysis. I am using Scater/Scran packages for analysis. As I know modularity (provided by igraph package) shows a quality measure for clustering. I used cluster_walktrap and cluster_louven algorithms after SNN and KNN graphs and found m ...
igraph scran scater scrna-seq rots written 6 months ago by hamza_karakurt30 • updated 6 months ago by Aaron Lun24k
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Enrichment Analysis with only GeneSymbols
... Hello everyone, I was looking to other posts but could not find a proper answer. I have a list of significantly changed genes and I want to do enrichment analysis with them. Is there a R/Bioconductor package that does this analysis with only GeneSymbols. Most of the packages require other informatio ...
R rna-seq gsea scrna-seq written 6 months ago by hamza_karakurt30 • updated 6 months ago by Peter Langfelder2.2k
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Comment: C: Adding labels on clusters in a t-SNE plot and changing colors
... Thank you Aaron for your answer. Basically, I can add labels on cluster with cluster coordinates in plot. This new argument will be so useful I believe. Thank you again. ...
written 7 months ago by hamza_karakurt30
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Adding labels on clusters in a t-SNE plot and changing colors
... Hello everyone, I have looked in the forum but could not find any information. I want to add labels on cluster in a t-SNE plot. I am using Scater and Scran packages for scRNA-Seq data analysis. I also want to change the color palette but could not achieve it too. I used +geom_label_repel(data$clus ...
ggplot2 rtsne scran scater scrna-seq written 7 months ago by hamza_karakurt30 • updated 7 months ago by Aaron Lun24k
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Comment: C: Silhouette Plots for Clustering Quality (Multiple Algorithm)
... Hello Aaron, Thank you for your answer. You are right I am little confused. BuildSNNGraph uses Euclidean distance but the SNN matrix is a similarity matrix I believe (that's why silhouetteplots with that matrix does not work and you added warning to tutorial "We do not use the silhouette coefficient ...
written 7 months ago by hamza_karakurt30
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Comment: C: Silhouette Plots for Clustering Quality (Multiple Algorithm)
... Thank you Aaron, This function is looking so useful. I believe the SNN matrix is a similarity matrix. I tried silhouette plots before but the results were always so bad (-1). Now I see the reason. I just have a small question. Does buildSNNGraph uses Euclidean distance or Jaccard index as a measure ...
written 7 months ago by hamza_karakurt30
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Silhouette Plots for Clustering Quality (Multiple Algorithm)
... Hello everyone, I am working on a scRNA-Seq data with multiple clustering algorithms. I want to see the quality of clustering with Silhouette plot function of "cluster" package. As I know, the function requires a distance matrix. Now my data is stored in Seurat object (can be transformed to SingleCe ...
clustering rna-seq scrna-seq silhouette plot written 7 months ago by hamza_karakurt30 • updated 7 months ago by Aaron Lun24k
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Deconvolution Method in Seurat and convert from SingleCellExperiment
... Hello everyone, I am working on scRNA-Seq data analysis. I mainly focused on Scater and Seurat. For some visual properties I (and my PI) want to use Seurat too but it only has LogNormalization. I believe it just takes the logarithm (in Seurat it is natural log not log2 I think). I want to use decon ...
rnaseq scater seurat singlecellexperiment written 9 months ago by hamza_karakurt30 • updated 9 months ago by Gordon Smyth38k
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Comment: C: Seurat to SingleCellExperiment Converting error in MAC
... Thank you so much. It worked. ...
written 10 months ago by hamza_karakurt30

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