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Questions tagged [clustering]

Clustering is the task of grouping a set of objects in such a way that objects in the same group (called a cluster) are more similar (in some sense) to each other than to those in other groups (clusters).

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Can I get the graph generated by cellranger

I’ve run the cellranger analysis pipeline on single cell RNASeq datasets. I can import the matrix and graph-based clusters into R. Doing this I can optimise the dimension reduction and plot cells with ...
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How to create a dendrogram of clusters and reconstruct phylogenetic relationship

I'm working with a Daphnia data set looking at the 16s gene pulled from the BOLD database. So far I did a multiple sequence alignment and attempted to cluster and plot a dendrogram: ...
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Comparing between different set of clusters produced from the same network

I have a set of eight gene clusters which I obtained from clustering a network. However, I had to update the genes in the network at a later stage which lead to certain deletions (genes not present in ...
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Using external list of PCs for clustering

I am going to use principal components (PCs) comes from calcPCA function in URD program for clustering my cells in Seurat; So ...
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Seurat for clustering bulk RNA-seq?

Is it ever ok to use Seurat for clustering bulk samples? I am looking at FPKM data from ~750 bulk RNA-seq samples generated using Cufflinks. As suggested for FPKM ...
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Check if a set of genes fall more on a specific cluster than other clusters

I have a network which I clustered into 11 smaller clusters. I have a set of genes and I would like to check if statistically significant number of these genes fall on any specific cluster. One method ...
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Non-redundant set of indices for AAindex?

AAindex has 566 indices with real values for each of the 20 amino acids mostly from wetlab measurements. Many of these values are highly correlated, and thus do not make good features for ...
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How to combine multiple kernels of large sample datasets?

I have multiple large sample datasets in matrix format (each has 15000 rows and 5-50 columns) corresponding to different experiments. Each matrix contains the same number of samples(rows) but the ...
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RNA-Seq: clustering/treatment of genes with low expression

I have some RNA-Seq data from leukaemia patients. I want to do unsupervised clustering on them with some other published leukaemia RNA-Seq data and see how they cluster. There are a few problems I ...
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Quality checking benchmarks for clustering

I'm currently working with several RNAseq datasets from the ENCODE database. My approach to assessing the quality of the data, i.e, reproducibility is by automating the assessment of expression ...
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case/control phenotype prediction - population stratification with R

I'm struggling these last days on a case/control phenotype prediction problem based on genotype (individual x SNPs with more than 10k individuals and approx 18k SNPs encoded as 0,1,2). Thanks to PCA ...
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Omics data: How to interpret heatmap and dendrogram output?

How to interpret heat map and dendrogram output for biological data (omics) in words (when writing results and discussion)? What should I consider (statistics behind?) and what is the best approach? ...
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How to scale the size of heat map and row names font size?

I have an expression data matrix (120X15; 15 samples and 120 genes), my heatmap looks blurred and raw names (gene names) looks very small and can not read. How can I improve my scripts? Here is the ...
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Is removing samples based on clustering for downstream analysis a right choice?

I'm using TCGA Lung cancer data. I'm interested in doing differential analysis between Lung vs Normal. Before DEA, to check the distance between each pair of samples I plotted an MDS plot: In this, I ...
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How to decide number of neighbors and resolution for Louvain clustering

I am using Louvain clustering (1,2) to cluster cells in scRNAseq data, as implemented by scanpy. One of the parameter required for this kind of clustering is the number of neighbors used to construct ...
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What could be the reason for the samples not clustering?

I'm performing RNA-seq analysis. I have used Hisat2 for aligning reads to the genome and stringtie for quantification and extracted read count information directly from the files generated by ...
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1answer
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Evaluate clusters of individuals by using their sequence data

For a dataset of several hundred individuals, I applied a hierarchical clustering to generate clusters based on a functional trait that sets them apart. My task is now to evaluate if these clusters ...
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How can I calculate and compare intra-cluster correlation for each GO term and pathway?

How can I calculate and compare intra-cluster correlation for each GO term and pathway? I want for all the genes, which belong to the same GO-term, calculate a similarity score. Each GO term can be ...
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factoextra: Error in if (xlab == “x”) xlab <- “x value” : argument is of length zero

I just followed the tutorial trying to do clustering on my own data, but I can't visualize it because fviz_cluster function is giving me an error: Error in if (...
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Find Patterns in Cluster

I have a heatmap and I would like to find some rectangles. I have already used clustermap. But here, I can not calculate these rectangles. The order of the data should not be changed. This Code is ...
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Getting hierarchy of cell populations with Drop-seq data

I plan on collecting some drop-seq data from brain tissue (from mice and humans). Using only the 75-85% of genes that have 1:1 orthology between mice and humans, I'd like to cluster the cells by ...
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How to obtain clusters of hierarchical heatmap when using Python?

Is there a good way of obtaining the labels (e.g. genes) within individual clusters that haven been clustered hierarchically in Python (preferentially, but not necessarily, by seaborn)? I found these ...
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1answer
358 views

Using the t-SNE algorithm on microarray data + an error bonus

I'm trying to use the t-SNE algorithm on some microarrays data. More specifically my data frame has 18600 columns with genes (features) and 72 rows with conditions with replicates ( 10xWt , 10xTg , ...
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1answer
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Should the cell sorting marker genes be excluded during clustering?

We sort different populations of blood cells using a number of fluorescent flow cytometry markers and then sequence RNA. We want to see what the transcriptome tells us about the similarity and ...
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validating identified sub-populations of cells in scRNA-seq

In the analyses of single-cell RNA-seq data there are different unsupervised approaches to identify putative subpopulations (e.g. as available with Suerat or SCDE packages). Is there a good way of ...