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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Is it possible to cluster a sc-RNAseq expression matrix with weighting or embedding?

I have an RNAseq mouse retina gene expression matrix(24659,49300) to cluster effectively. Here is a sample(7,4): ...
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Can I use a benchmark to choose a clustering or module detection method for a gene dataset?

The paper A comprehensive evaluation of module detection methods for gene expression data says that: "We first want to provide an overview of the characteristics and performance of current module ...
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Assigning subcluster idents to original object

I have a scRNA-seq Seurat object I've analyzed, and I noticed that for some of the clusters, there's more than one cell type. I've created a subset which and run FindClusters again to label the cell ...
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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 ...
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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. ...
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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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NMF clustering not giving results

I'm trying to run the Non-Negative Matrix Factorization(NMF) for my Gene Expression dataset which was originally in matrix form. But it throws errors as given below: ...
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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. ...
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Functional similarity between 2 genes based on GO-tags

I need to evaluate the functional similarity or closeness of pairs of genes from Gene Ontology (GO) tags, and it is important that this similarity is not determined through sequence-similarity. I ...
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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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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 ...
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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 ...
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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: ...
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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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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 ...
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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 ...
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Dataset showing evolution of gene

As a way to exemplify how the hierarchical clustering of particular DNA sequences can be used to derive phylogenetic trees, I'm looking for a (even very small) dataset of the same genes (or other ...
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Clustering RNAseq fold-change data

I have a dataset that looks something like this Treatment1 Treatment 2 Control Sample1 3.23. 0.87. 1 Sample2 1.71. 1. 1 Sample3 2.88. 5.65 1 Sample4 0.77. 1.34 1 The numbers describe a fold ...
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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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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....
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Picking number of samples for clustering [closed]

I have expression data for 100 samples and clinical data for 50 among them. I want to carryout k-means clustering using expression data and then do a survival analysis (Kaplan-Meier analysis) using ...
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Metagenomics: Identifying most common sequences

I am working on a project and used the following command: ...
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Calculating average mito.percentage for each cluster (seurat)

I have a tricky data set with cells that will have a higher percent of mitochondria genes than "typical" data sets. I would like to look at the mito percentage in each cluster without any ...
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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 ...
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which marker identifications method is recommended when single-nuclei RNA seq datasets are integrated across regions

I'm analyzing Sn-RNA seq datasets which include different brain regions and spinal cord in patients and normal controls. I would have different comparison within and between individuals. I've got a ...
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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, ...
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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'...
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3 answers
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RNAseq biological replicates not clustering in PCA plots

I have RNAseq data from 4 samples with 3 biological replicates per sample. I am currently trying to do the differential expression analysis with DESeq2 but the biological replicates will not cluster ...
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How to add cluster name to metadata in Seurat?

I'm working on a Seurat object and want to name the clusters according to 2 values alone (yes/no). So I want to add a new column to metadata and annotate the clusters (UMAP) with it. ...
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1 vote
1 answer
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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 ...
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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....
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about the normalization of RNAseq data for calculating distance for unsupervised learning

I have been working on clustering using RNAseq data. To compute distance, what kinds of normalization is optimal? Can we use normalization using relative log normalization? I understand this should ...
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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) ...
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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 ...
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1 vote
1 answer
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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 ...
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2 votes
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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/...
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choosing a good representative genome subset

I'm trying to build a genomic database for DNA alignments. I started with NCBI accessions, but the data is very multiplicative, so I want to use subset of [max] N different strains for each specie. my ...
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1 vote
3 answers
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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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Clustering information saved in Seurat object

Seurat V2 had a option to find clustering information saved in object: PrintFindClustersParams(object = pbmc). How can I get the same clustering parameters from objects in Seurat3? Do I need to ...
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how to interpret of "pvclust" dendrogram and finding height for cutting dendrogram?

I study on RNA-seq expression dataset about one cancer in TCGA. I downloaded FPKM dataset and removed batch effect by ComBat() function. Now, I used pvclust for ...
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What kind of analysis is practically done on GSE data files?

I have a GSE data file in csv file format containing fields such as: ID, adj.P.Val, P.Value, t, B, logFC, Gene.symbol, Gene.title. In which adj.P.Val, P.Value, t, B, logFC fields being numeric. What ...
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2 votes
2 answers
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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 ...
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Error using bseqsc

I will be very grateful for any hint on how to overcome the error. I wish to deconvolve my bulk RNA seq data obtained from the lungs of mice using single cell RNA seq data. For practice, I am ...
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Clustering using cellranger

Is it possible to run cell ranger clustering using only a gene x cell matrix? Cellranger reanalyze performs clustering but requires a hd5f file. I don't want to run the whole pipeline (including ...
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1 answer
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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 ...
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Cluster is split in 2-3 locations on tsne plot - Suerat

I am running a single cell dataset (count data - exon) through Seurat. After running tsne I see a cluster (13) split in 3 different locations on the plot. Here are the commands I am running: ...
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2 votes
2 answers
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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 ...
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How to write the subclusters in file?

I have constructed a gene co-expression network from RNA-seq data. The network file is in edge list format of memory around 1gb which was created by calculating Pearson correlation of each gene pairs ...
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6 votes
2 answers
711 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 ...
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GBS: clustering of PCoA axes with R package mclust to describe identity by missingness

I have a SNP dataset with 56 populations and 430 samples that was produced by GBS sequencing. I need to identify groups of samples that have similar patterns of genotype missingness, since there is ...
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