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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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Confidence intervals around Q-matrix values from multiple STRUCTURE runs

Context: I've run STRUCTURE on a set of 84 individuals (RADseq data) for a range of K values (2--7). I've specified 20 replicate STRUCTURE runs per K value, and these were passed to CLUMPAK to ...
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Done miRNA sequencing from animal tissue & have 1 control sample in duplicates 1 treatment group as test. In PCA plot clustering is not there

I have done miRNA sequencing from animal tissue and have control sample in duplicates . Like wise one treatment group as test. In PCA plot clustering is not there. There is very randomness. Is it ...
M Javed's user avatar
4 votes
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split fastq file containing a sequence block at different locations

I have some fastq files (obtained from nanopore sequencing) that contain reads that can be of either of these 5 forms: a known CDS with 3'UTR: ...
jetpacks_reno's user avatar
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2 answers
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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 ...
GIONII's user avatar
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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'...
Rainman's user avatar
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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 ...
rimo's user avatar
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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 ...
Xin Xu's user avatar
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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 ...
brownsloth's user avatar
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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 ...
Henry Gong's user avatar
2 votes
1 answer
54 views

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 ...
joshua213p's user avatar
2 votes
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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 (...
joshua213p's user avatar
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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 ...
719016's user avatar
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1 answer
126 views

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 ...
Apple Ball's user avatar
3 votes
2 answers
162 views

hierarchical clustering of kmers and their counts

I have a list of kmers and their frequencies broken down like this: ...
rimo's user avatar
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1 answer
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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+ ...
Wang Ming's user avatar
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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 ...
venkatesh war's user avatar
3 votes
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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 ...
user3523406's user avatar
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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 ...
burger's user avatar
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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 ...
Marco's user avatar
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1 answer
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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-...
r-newbie's user avatar
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1 answer
230 views

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): ...
nomad culture's user avatar
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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 ...
Lara's user avatar
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2 answers
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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 ...
ShaniS's user avatar
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3 answers
4k 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 ...
Shani's user avatar
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2 votes
3 answers
3k 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. ...
Apppii092's user avatar
1 vote
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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: ...
Kartika's user avatar
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1 answer
271 views

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: ...
Kartika's user avatar
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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. ...
dunkindonts's user avatar
2 votes
1 answer
770 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,...
MK Huda's user avatar
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662 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 ...
MK Huda's user avatar
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1 answer
346 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 ...
Sadaf Fazeli's user avatar
2 votes
1 answer
646 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: ...
Widget's user avatar
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2 votes
1 answer
329 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 ...
Bak's user avatar
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2 votes
2 answers
107 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 ...
icrf's user avatar
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1 vote
0 answers
79 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 ...
Frix's user avatar
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0 votes
1 answer
34 views

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 ...
gcorso's user avatar
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1 answer
367 views

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 ...
Anonymous Scientist's user avatar
1 vote
0 answers
51 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 ...
Alexander Chervov's user avatar
2 votes
1 answer
440 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 the taxa names within a given clade(s)? For example, Bio.Phylo can ...
Nurlybek Amangeldiuly's user avatar
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1 answer
31 views

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 ...
user98059's user avatar
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1 vote
1 answer
48 views

Metagenomics: Identifying most common sequences

I am working on a project and used the following command: ...
DumbledoreTheGrey's user avatar
0 votes
1 answer
876 views

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 ...
cer's user avatar
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1 vote
1 answer
194 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 ...
Mee's user avatar
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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 ...
Paria's user avatar
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2 votes
1 answer
20k 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'...
Najeha Mohamed's user avatar
1 vote
3 answers
2k views

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 ...
nmp116's user avatar
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0 votes
1 answer
5k views

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. ...
Najeha Mohamed's user avatar
1 vote
1 answer
63 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 ...
gb0413's user avatar
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2 votes
0 answers
154 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....
raiora's user avatar
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