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).

Filter by
Sorted by
Tagged with
13 votes
2 answers
3k 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 ...
gc5's user avatar
  • 1,783
7 votes
1 answer
1k 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 , ...
J. Doe's user avatar
  • 575
7 votes
2 answers
1k 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 ...
Ahmed Abdullah's user avatar
6 votes
2 answers
180 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 ...
Deffiz's user avatar
  • 153
5 votes
2 answers
42k 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 ...
Kynda's user avatar
  • 95
5 votes
1 answer
113 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 ...
Peter's user avatar
  • 2,634
5 votes
1 answer
170 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 ...
Laaas's user avatar
  • 51
4 votes
2 answers
2k 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? ...
Kynda's user avatar
  • 95
4 votes
1 answer
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 ...
tsttst's user avatar
  • 153
4 votes
1 answer
241 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 ...
beginner's user avatar
  • 631
4 votes
1 answer
84 views

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
4 votes
2 answers
4k 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 ...
R-Peys's user avatar
  • 51
4 votes
1 answer
579 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 ...
Kent's user avatar
  • 105
3 votes
2 answers
129 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
  • 963
3 votes
1 answer
396 views

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
3 votes
1 answer
942 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 (...
Nikita Vlasenko's user avatar
3 votes
1 answer
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 ...
Johannes Schätzl's user avatar
3 votes
1 answer
197 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 ...
Kent's user avatar
  • 105
3 votes
0 answers
71 views

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

Consider the following dataset: ...
Namenlos's user avatar
  • 317
2 votes
4 answers
108 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 ...
Eric A Brenner's user avatar
2 votes
3 answers
2k 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
2 votes
1 answer
123 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
2 votes
2 answers
182 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 ...
Frank Henderson's user avatar
2 votes
1 answer
54 views

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
  • 101
2 votes
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
  • 21
2 votes
1 answer
709 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
  • 163
2 votes
1 answer
582 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
  • 23
2 votes
2 answers
102 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
  • 21
2 votes
1 answer
405 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
2 votes
1 answer
18k 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
2 votes
2 answers
67 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/...
SBDK8219's user avatar
  • 195
2 votes
2 answers
177 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 ...
plat's user avatar
  • 1,032
2 votes
2 answers
668 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 ...
reubenmcg's user avatar
  • 123
2 votes
2 answers
327 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 ...
Tom Kelly's user avatar
  • 873
2 votes
1 answer
25 views

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
2 votes
1 answer
42 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
1 answer
100 views

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
2 votes
1 answer
212 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 ...
h3ab74's user avatar
  • 836
2 votes
1 answer
315 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
  • 21
2 votes
1 answer
101 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 ...
Zizogolu's user avatar
  • 2,132
2 votes
2 answers
109 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 ...
user284's user avatar
  • 21
2 votes
1 answer
33 views

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
2 votes
0 answers
34 views

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
2 votes
0 answers
150 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
  • 77
2 votes
0 answers
830 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 ...
user3377241's user avatar
1 vote
1 answer
690 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 ...
Zizogolu's user avatar
  • 2,132
1 vote
2 answers
762 views

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
  • 51
1 vote
1 answer
276 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
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
  • 11
1 vote
2 answers
213 views

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 ...
Dhruv Shah's user avatar