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).
83
questions
2
votes
1
answer
57
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 ...
- 21
3
votes
2
answers
56
views
hierarchical clustering of kmers and their counts
I have a list of kmers and their frequencies broken down like this:
...
- 494
2
votes
1
answer
34
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+ ...
- 101
2
votes
1
answer
28
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 ...
3
votes
1
answer
226
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 ...
- 265
1
vote
1
answer
68
views
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 ...
- 2,139
1
vote
0
answers
100
views
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 ...
- 141
1
vote
1
answer
67
views
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-...
- 11
2
votes
1
answer
129
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 ...
- 836
2
votes
0
answers
33
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):
...
0
votes
0
answers
26
views
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 ...
- 101
1
vote
2
answers
428
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 ...
- 51
2
votes
2
answers
2k
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 ...
- 21
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.
...
- 27
1
vote
0
answers
31
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:
...
- 11
0
votes
1
answer
182
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:
...
- 11
1
vote
0
answers
16
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. ...
- 11
2
votes
1
answer
444
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,...
- 163
1
vote
2
answers
387
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 ...
- 163
1
vote
1
answer
135
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 ...
- 23
2
votes
1
answer
373
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:
...
- 23
2
votes
1
answer
270
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 ...
- 21
2
votes
2
answers
87
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 ...
- 21
1
vote
0
answers
63
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 ...
- 11
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 ...
- 149
0
votes
1
answer
268
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 ...
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 ...
2
votes
1
answer
266
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 ...
0
votes
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 ...
- 347
1
vote
1
answer
41
views
Metagenomics: Identifying most common sequences
I am working on a project and used the following command:
...
0
votes
1
answer
582
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 ...
- 105
1
vote
1
answer
132
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 ...
- 71
0
votes
0
answers
83
views
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 ...
- 1
2
votes
1
answer
13k
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
vote
3
answers
1k
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 ...
- 11
0
votes
1
answer
4k
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.
...
1
vote
1
answer
47
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 ...
- 21
2
votes
0
answers
115
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....
- 77
0
votes
1
answer
74
views
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 ...
- 159
1
vote
0
answers
273
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) ...
- 105
2
votes
0
answers
672
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 ...
- 193
1
vote
1
answer
103
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 ...
- 1,773
2
votes
2
answers
61
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/...
- 195
1
vote
1
answer
48
views
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 ...
- 35
1
vote
3
answers
123
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 ...
0
votes
1
answer
423
views
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 ...
- 1
0
votes
1
answer
553
views
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 ...
- 35
0
votes
2
answers
183
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 ...
2
votes
2
answers
151
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 ...
- 1,022
1
vote
0
answers
142
views
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 ...
- 516