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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13
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2answers
2k views

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 ...
7
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1answer
999 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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2answers
632 views

Are phylogenetic tree construction algorithms any different than general clustering algorithms?

Are phylogenetic tree construction algorithms any different from clustering algorhithms? I suspect the answer is no. Of course phylogenetic tree construction uses biological knowledge, e.g special ...
6
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2answers
167 views

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 ...
5
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1answer
74 views

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 ...
5
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1answer
158 views

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 ...
4
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2answers
29k views

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 ...
4
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2answers
1k views

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? ...
4
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1answer
1k views

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 ...
4
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1answer
161 views

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 ...
4
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2answers
2k views

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 ...
4
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1answer
477 views

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 ...
3
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1answer
637 views

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 (...
3
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1answer
1k views

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 ...
3
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1answer
170 views

sva for RNA-Seq data without known phenotype

I have been working on RNA-Seq data from two different cohorts, and they show very strong batch effect (~35% variance explained by 1st component in PCA). Since I am trying to do a class discovery from ...
3
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0answers
60 views

How are the values of prop.part() and prop.clades() calculated?

Consider the following dataset: ...
2
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4answers
104 views

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 ...
2
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2answers
125 views

Using multidimensional scaling to visualize protein sequences by functionality

I have a multiple sequence alignment (MSA) of protein sequences, with which I have performed multidimensional scaling to visualize their clustering. Using R, I used the ...
2
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3answers
125 views

In Seurat, how can I export cluster IDs to csv files

I am doing scRNAseq analysis with Seurat. I clustered the cells using the FindClusters() function. What I want to do is to export information about which cells belong to which clusters to a CSV file. ...
2
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1answer
109 views

How do I plot clusters based on DNA sequence alignment?

I have a group of about 1050 sequences that have been aligned using blastn. I am now trying to create a cluster plot of the sequences in order to identify similar sequences, something like this: ...
2
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2answers
53 views

How do I install hammock?

I'm working with phage peptides libraries. Currently I'm analysing a massive data set from phage selection, NGS readout, preprocessed already (fasta file). I want to analyse the sequences to cluster ...
2
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2answers
57 views

Tools or softwares for clustering evaluation

I am using a few clustering algorithms as well as my own tool for protein sequences. Also, I have benchmarked clustering results (i.e. ground truth) to compare with the results. Is there any tool/...
2
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2answers
119 views

Find most similar genes to a set of genes of interest in time series RNA-seq data

I have gene expression data (RNA-seq) for 30 different time points (from 0 to 60 min each 2 min). I have a set of 8 genes that behave similarly (although not identically) and I want to find the top X ...
2
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2answers
483 views

Interpretation of hierarchical clustering with bootstrapping

I have data that includes 'cases' and 'controls' and have carried out hierarchical clustering. I used the pvclust package in R to bootstrap the results and ...
2
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2answers
249 views

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 ...
2
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1answer
95 views

How I know which gene is a good predictor in this neural network or not?

I have 25 highly differentially expressed genes among and patients to chemotherapy. I have made a neural network of these genes. The accuracy of the model is 0.73 ...
2
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2answers
71 views

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 ...
2
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0answers
65 views

How to extract clusters from a phylogenetic tree?

I am using Biopython Phylo and RDkit Cluster to obtain a UPGMA tree from a distance matrix of 5k x 5k entries. How can I extract clustered entry names given a number of clusters? For example, Bio....
2
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0answers
75 views

Clustering issue about overlapping CD4, CD8, and Foxp3 genes in mouse tumor models

bioinformatics scientists. I hope your work goes smoothly well and be safe. I'm stuck in trouble at the step of clustering. Briefly, I downloaded fastq files from a published study (https://www.ncbi....
2
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0answers
111 views

vst() from DESeq2 vs voom() from limma

I have used both to transform my leukaemia RNA-Seq data for subsequent hierarchical clustering. The result is quite different. Some subtypes of leukaemia only form a cluster (or at least sit closer) ...
2
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0answers
416 views

Understanding BuildClusterTree of Seurat

I am trying to understand how to use BuildClusterTree of Seurat to understand the relationship between clusters. Being from neither a bioinformatics or statistical ...
1
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1answer
359 views

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 ...
1
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2answers
45 views

How to split a Seurat cluster in several subclusters?

I've analyzed my scRNA-seq data and have a couple of Seurat clusters that show more than one cell type in each cluster. (for example, cluster 9 shows both NK and CD4 cells) How can I split a cluster ...
1
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1answer
58 views

Seurat clustering Methods-resolution parameter explanation

I am learning the Seurat algorithms to cluster the scRNA-seq datasets. I found this explanation, but am confused. Can someone explain it to me, "The FindClusters function implements the procedure,...
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1answer
39 views

Find selective markers for one cluster automatically

I detected all markers for each cluster and checked 20 top markers for my clusters one by one. Is there any way that I figure out the selective markers automatically from all the clusters? For ...
1
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1answer
4k views

Changing active.ident in Seurat

Im trying to change the active.ident to another column in metadata but this error keeps popping up! I recently upgraded to R version 4.0.2 from 3.6.1 The older version was working but the new one isn'...
1
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1answer
402 views

Hierarchical clustering for outlier detection - single cell RNASeq & WGCNA

I wish to conduct WGCNA on a single cell RNASeq dataset and, when choosing the optimal beta parameter after running pickSoftThreshold am presented with a rather ...
1
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2answers
639 views

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 ...
1
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2answers
77 views

Positive marker and negative marker in scRNA-seq datasets

I am learning about the marker genes and clustering by Seurat in scRNA-seq datasets. However, I am confused about the term positive marker and negative marker. What I understand is the marker genes of ...
1
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1answer
30 views

Metagenomics: Identifying most common sequences

I am working on a project and used the following command: ...
1
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1answer
46 views

data visualization RNAseq : scaling data for PCA and cluster dendogram

I have count data from a RNAseq experiment (2 samples are from normal cells and 3 samples are cells with a disease), and the data is already standardized by trimmed mean of M values (TMM). I want to ...
1
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1answer
30 views

classifying samples by TCGA signature

I have some RNA-seq samples from multiple glioblastoma tumours that I'm now trying to classify according to a specific gene signature (from Verhaak et al., 2010) using R. The gene signature is ...
1
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1answer
77 views

How to identify latent variables in single-cell RNA-Seq data

I have a single-cell RNASeq sample, in which I'd like to identify latent variables (e.g. response to stress) that I think might be affecting the clustering. The approach I was planning to use is to ...
1
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3answers
92 views

K means clustering, would PCA be a better option?

I have the data below. I need to use a clustering method to classify them and into categories of "Heterozygotote, Allele 1, Allele 2 and No Call. The values in RFU1 and RFU2 are used to determine the ...
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0answers
22 views

NMF - Subscript out of bounds

I've calculated the cophenetic coefficients for the NMF of gene expression data, but is giving error when performing the clustering information step as given below: ...
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0answers
14 views

General Question: Statistical Alternatives to Oncoprint

I am a computational genomics student who has recently joined a research lab as an RA. We often work with oncoprints (comuts/heatmaps), and we visualize molecular signatures by reorganizing the comut. ...
1
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1answer
73 views

Clustering with Seurat

My data consists of two groups control and stim. I'm concerned that my clustering in the stim group is dominated by the unregulated genes. I can remove these genes and recluster but is there a way to ...
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0answers
20 views

How to use CD-HIT to filter protein sequences dataset by certain similarity threshold?

I am looking at using CD-HIT to efficiently filter my protein sequences dataset by a similarity threshold of 70% (cut-off). More precisely, what I want to achieve is that for all the remaining ...
1
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0answers
43 views

Clusters in scRNA of Glioblastoma

There is a scRNA dataset on Glioblastoma from 10xgenomics. Unfortunately, there seems to be no research paper related to that data. Question 0 : May be there is paper ? How to find it ? I am not ...
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0answers
20 views

What is the best approach to classify a patient cohort by the expression (low, int, high) of a single gene of interest?

I am working with a dataset of nearly 100 patients. I performed Salmon quantification with genecodeV34 and imported the results with tximeta. I normalised the TPM salmon output with TPM (using edgeR, ...