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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How long should it take to cluster Uniref?
I have the Uniref90 dataset containing around 76M sequences. I have made modifications to all sequences based on a reduced amino acid alphabet.
I am trying to cluster it again at 90% identity. I am ...
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Producing just network files from BiG-SCAPE
I was wondering if anyone knows off-hand if there is a way to run BiG-SCAPE without producing the svg or html files? All I want is the networking files (which I can play with in CytoScape).
There isn'...
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Approach for alignment-free phylogenetic tree generation using kmers
I have a general question about building phylogenetic trees without alignment:
I want to build a tree using an alignment-free approach by counting kmers. I have found a lot of information in the ...
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How to obtain the KEGG mudule based on KEGG KO? (KEGG mudule enrichment)
With HUMAnN3, I got the result of the KEGG KO annotation (by humann_regroup_table:humann_regroup_table --input hmp_subset_genefamilies.tsv --groups uniref90_ko --output ...
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Is a classification tree appropriate method to use for my project?
I have about ~3000 genomes of organisms and presence (recorded as 1)/absence (recorded as 0) data of ~300 genes in them. Among 3000 genomes, we have experimental data on 20 organisms, which were ...
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scRNA: What are good dimensionality reduction/clustering parameters to get biologically plausible groupings?
I've got a moderately large set of PBMCs, over 1M cells. That means I can't easily do a grid search of dimensionality reduction/clustering parameters/methods. Some examples results I'm getting with ...
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Applying PCA or tSNE on non-numerical data
Reading through this t-sne blogpost and I'm a little unclear on how i'd use either of these algorithms here for my goals. i get it'd cluster my samples based on similarity in terms of first and second ...
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Help with finding an unsupervised learning algorithm for RNA sequence/structure pattern identification
I have a bunch of RNA sequences (and their optimal secondary structures) and their corresponding energy values (measured by mean free energy) and I'm trying to find a way to identify features (...
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Louvain/Leiden community clustering implementation in C/C++ for gene expression data
Does anybody know of a C/C++ based implementation of the Louvain or Leiden algorithms that will take gene expression looking csv input files, with the genes in columns and the samples in rows, and ...
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Mapping single cell data with annotation
Entry level Bioinformatician here.
I am trying to map my single cell data with standard annotation file or assign my Seurat cluster to cell types. I have used the singleR and celldex package to map it ...
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hierarchical clustering of kmers and their counts
I have a list of kmers and their frequencies broken down like this:
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How to identify a low proportion cell subpopulation in the single-cell RNA-seq data?
The cell subpopulation that I am interested in only accounts for around 1.2% of the total cells. I have previous FACS experiments that sort out the subpopulation from the samples (using markers CD166+ ...
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What do you use the CLANS program for?
I am reading this paper called Birth and death in the Terminal Complement pathway, doi : https://doi.org/10.1101/2022.04.21.489004 where they have performed CLANS analysis.
I understand that CLANS ...
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How to analyse Orthofinder results
I read this paper (Colletotrichum shisoi sp. nov., an anthracnose pathogen of Perilla frutescens in Japan: molecular phylogenetic, morphological and genomic evidence). We ran Orthofinder and also ...
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FlowSOM multi-step clustering
There are a few different commonly used clustering algorithms within the single-cell space, although Leiden seems to be the top choice these days. FlowSOM is a classic package for analyzing flow ...
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Clustering individuals by gene presence/absence
I have a binary matrix with individuals as row names, and gene name as column name.
So, if the gene is present in an individual, we have 1, otherwise 0.
I would like to cluster individuals based on ...
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How to get started with louvain/leiden algorithm with UMAP in R
A collegue of mine recently suggested to try the louvain algorithm for clustering multiplex cytometry data. However, implementations of louvain are kind of rare in R. To my knowledge the only stand-...
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Extracting clusters, hierarchical clustering - bulk RNASeq
I have been attempting to extract particular clusters, given by hierarchical clustering outputs from the pheatmap function (in R).
Please find the ...
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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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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 the taxa names within a given clade(s)?
For example, Bio.Phylo can ...
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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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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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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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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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