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Showing top results for tag: clustering • reset
0
votes
1
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152
views
How to show relabel sub cluster on the original cluster in Seurat
scRNA-seq seurat cluster clustering
updated 16 hours ago by ▴ 580 • written 2 days ago by • 0
0
votes
1
reply
138
views
Identification of cell types/groups in single-cell data
cell single type clustering
updated 5 days ago by ▴ 90 • written 5 days ago by ▴ 10
1
vote
1
reply
143
views
How to add metadata to dendrogram of hierarchical clustering in R
metadata Hierarchical clustering
updated 9 days ago by ★ 1.9k • written 10 days ago by • 0
4
votes
2
replies
175
views
Clustering resolution for scRNA-seq
clustering single-cell
updated 12 days ago by ★ 1.3k • written 13 days ago by • 0
0
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0
replies
120
views
Neighboring index between clusters on a map
connectivity clustering
18 days ago by thejustpark ▴ 80
0
votes
0
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81
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Is it okay to cluster rows and columns with a different linkage?
Clustering R
updated 26 days ago by 54k • written 26 days ago by • 0
0
votes
2
replies
192
views
Experience with Cytobank
Clustering Cytobank FlowSOM
5 weeks ago by morten.hansen.01 • 0
1
vote
1
reply
142
views
%% error in Rstudio
rstudio ERROR seurat clustering
updated 6 weeks ago by ▴ 290 • written 6 weeks ago by • 0
3
votes
1
reply
167
views
Is reclustering of a cluster obtained from hierarchical clustering "allowed"?
analysis cluster hierarchical clustering
updated 7 weeks ago by ★ 2.5k • written 7 weeks ago by ▴ 10
0
votes
2
replies
417
views
individual-level allele frequencies
allele frequencies clustering plink
updated 7 weeks ago by 8.4k • written 13 months ago by ▴ 160
0
votes
1
reply
140
views
Retrieving Clusters from Clustermatrix, obtained with Hierarchical Clustering
seaborn python Hierarchical clustering
updated 7 weeks ago by ▴ 250 • written 8 weeks ago by ▴ 10
3
votes
1
reply
182
views
usearch11 cluster_fast option
usearch proteins clustering
updated 11 weeks ago by 107k • written 11 weeks ago by ▴ 10
3
votes
5
replies
303
views
Opposing expression profiles in the same WGCNA module
clustering WGCNA
11 weeks ago by cfourps ▴ 10
0
votes
0
replies
95
views
How was hierarchical clustering established for mRNA expression data?
clustering mRNA expression
12 weeks ago by ceruleanivy ▴ 30
4
votes
4
replies
388
views
distance matrix as input in R clustering functions ?
k-medioids-genetic-distances-mash R Clustering
updated 3 months ago by 25k • written 3 months ago by ▴ 30
0
votes
0
replies
95
views
Differentiating alleles from paralogs in comparison of transcriptomes within species
clustering transcriptome paralog trinity assembly
3 months ago by jfaberha ▴ 10
2
votes
2
replies
289
views
Why clusters look different in single nuclear RNA Seq.
snRNA clustering seurat
updated 4 months ago by 77k • written 4 months ago by ▴ 10
2
votes
1
reply
414
views
how to define open-pangenome?
python fasta genome dna clustering
updated 4 months ago by ▴ 20 • written 6 months ago by ▴ 50
0
votes
1
reply
183
views
Hierarchical clustering using GISTIC 2.0 result
clustering CNV hierarchical GISTIC CNA
updated 4 months ago by ★ 2.5k • written 4 months ago by ▴ 10
0
votes
0
replies
152
views
Supervised clustering from gene expression (fold change) data
clustering expression supervised
4 months ago by nerea.bilbao • 0
1
vote
1
reply
155
views
RMSD clustering
Clustering
updated 4 months ago by ★ 13k • written 4 months ago by • 0
0
votes
2
replies
208
views
Clustering 10X scRNA data based on selected markers
clustering scRNA seurat umap pca
4 months ago by A • 0
24
votes
6
replies
3.7k
views
Tutorial: A simple tutorial for a complex ComplexHeatmap
complexheatmap clustering arthritis pam Tutorial
4 weeks ago by Kevin Blighe 77k
6
votes
3
replies
3.3k
views
Tool: Clustering of short peptide sequences
peptide clustering phage display Tool
updated 5 months ago by • 0 • written 6.0 years ago by ▴ 410
7
votes
12
replies
1.1k
views
RNAseq data analysis of pooled data
DESeq2 mapping featurecounts clustering RNA-Seq
updated 5 months ago by ★ 2.3k • written 5 months ago by ▴ 20
4
votes
3
replies
595
views
Hierarchical Clustering of GO terms
Clustering GO similarity Ontology
updated 5 months ago by 77k • written 5 months ago by ▴ 160
0
votes
0
replies
237
views
News: 3-day ONLINE TRAINING - NEXTFLOW
pipeline programming workflow cloud clustering
updated 6 months ago by 107k • written 6 months ago by ★ 2.0k
3
votes
2
replies
820
views
Pheatmap/Complexheatmap: making a continuous color scale with NAs
clustering pathways complexheatmap pheatmap
6 months ago by Ridha ▴ 50
0
votes
7
replies
766
views
Cannot resize rowlabels in aheatmap
clustering aheatmap R
updated 6 months ago by 5.4k • written 6 months ago by • 0
5
votes
4
replies
840
views
Interpretation of Principal component analysis
clustering
updated 6 months ago by ★ 13k • written 6 months ago by • 0
1
vote
2
replies
376
views
Clustering two different RNA-seq timeseries results to identify shared/opposite gene patterns?
RNA-seq trajectories timeseries clustering
5 months ago by kelen ▴ 170
0
votes
0
replies
199
views
Identify cell type from bulk RNA sequencing data
sequencing type clustering r
6 months ago by minoo ▴ 10
0
votes
0
replies
259
views
Does anyone succeded clustering TCGA data?
RNA-Seq TCGA clustering
updated 6 months ago by 20 • written 7 months ago by • 0
1
vote
1
reply
289
views
determine the robustness of single-cell clusters
clustering RNA-Seq rna-seq R Seurat
updated 7 months ago by ▴ 290 • written 7 months ago by • 0
0
votes
0
replies
238
views
Cluster Stability Assesment
rna-seq Seurat clustering R
7 months ago by Maria17 • 0
3
votes
5
replies
394
views
Clustering sequences with low identity
clustering sequences
updated 7 months ago by ★ 13k • written 7 months ago by ▴ 820
1
vote
3
replies
311
views
How to run nucmer without reference? (viruses metagenomics)
assembly clustering metagenomics virus nucmer
updated 7 months ago by ★ 3.1k • written 7 months ago by ▴ 150
3
votes
5
replies
712
views
Is my WGCNA soft threshold (power) too low?
wgcna RNA-Seq clustering network
7 months ago by jfaberha ▴ 10
0
votes
0
replies
355
views
Using ATACseq CPM for clustering samples
ATAC-seq normalization clustering
8 months ago by barati • 0
6
votes
5
replies
526
views
CD-HIT: representative sequence vs consensus sequence
CD-HIT clustering
8 months ago by rob_DNA ▴ 10
0
votes
0
replies
270
views
Cluster sequences in a network by their editing distance - in R
R network analysis clustering editing distance
8 months ago by fendermannn • 0
0
votes
1
reply
316
views
How to select the number of clusters once I have the HCL (average linkeage) tree
hierarchical clustering gene co-expression
9 months ago by sofiablancoglez • 0
1
vote
1
reply
813
views
Which tool for clustering (sub-networking) of protein-protein interaction networks based on the Gene Ontology Biological Process of proteins?
cytoscape clustering Gene Ontology sub-network
updated 9 months ago by ▴ 450 • written 9 months ago by ▴ 70
2
votes
11
replies
7.4k
views
7 follow
CD-HIT Clustering output
CD-HIT Clustering
updated 9 months ago by ▴ 70 • written 7.2 years ago by • 0
0
votes
0
replies
400
views
Analyze RPPA cancer data in R for clustering patients and differential protein expression
RPPA RPPanalyzer R clustering DE
10 months ago by svlachavas ▴ 750
3
votes
3
replies
323
views
Clustering similiar genes from many genomes
Python genome pangenomics clustering
updated 10 months ago by 19k • written 10 months ago by • 0
0
votes
4
replies
353
views
identification of rare cell population in Sc-RNA sequencing
rna-seq R clustering rare population seurat
10 months ago by Maria17 • 0
1
vote
2
replies
430
views
How to do unsupervised clustering of RNA-Seq data
RNA-Seq clustering next-gen
10 months ago by Kumar ▴ 120
2
votes
1
reply
511
views
Correlating metadata with expression based k-means cluster (in R)
R k-means clustering
updated 10 months ago by ★ 1.3k • written 13 months ago by ▴ 270
1
vote
2
replies
481
views
optimal number of clusters from distance matrix input
clustering R
updated 11 months ago by 77k • written 11 months ago by ▴ 130
50 results • Page 1 of 1
Recent Votes
Answer: How can I extract upstream regions in fasta for all blastx hits locally performe
C: What Are The Most Common Stupid Mistakes In Bioinformatics?
Comment: Beginner problem: installed python3.7.12 but py_available() return FALSE
A: Automatic Outlier Detection for RNA-seq data
A: ATAC-seq sample normalization (quantil normalization)
C: Help to analyze DEseq-MA-Plot.
A: Optimize bwa mem in parallel on a SLURM cluster
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Recent Replies
Comment: Automatic Outlier Detection for RNA-seq data by Kevin Blighe 77k
There is actually, well, a sort of citation off the top of my head. Please see the PLINK documentation (section '*Outlier detection diagnos…
Answer: Batch effects by swbarnes2 11k
It's always safest to get raw data and normalize it yourself. If one dataset is control, and the other is not, there is no magic way to …
Comment: GREP from multiFasta file and keep headers by Pierre Lindenbaum 138k
your command line with `grep` **implies** that each record in your fasta file takes only two line (?). One line for the header, and one lin…
Answer: In what way should cellranger count be performed , when there are multiple runs by swbarnes2 11k
If you did **one** library prep and ran that one library prep multiple times, it is probably easiest to combine the fastqs (make sure to gi…
Comment: Splice aware vs splice unaware aligners? by swbarnes2 11k
I think for time's sake a not-splice aware aligner isn't going to search horribly far away for the other half of a read, while a splice-awa…
Comment: Beginner problem: installed python3.7.12 but py_available() return FALSE by Sashu • 0
Anyway, thanks your reply!
Comment: Automatic Outlier Detection for RNA-seq data by simplitia ▴ 60
@kevin thank is a great answer. We are having the same issue with outliers. With the 2nd part using > 3 SD; do you have a reference for …
Comment: How to use MACS2 output for DESEQ2 differential analysis during ATAC-seq? How to by Papyrus ★ 1.3k
Take a look at the [DiffBind][1] R package (which internally uses `DESeq2`, or `edgeR`), the tutorial [vignette][2] is quite extensive. …
Comment: Beginner problem: installed python3.7.12 but py_available() return FALSE by Sashu • 0
I forget to tell that I have followed the error message but this problem still existed...
Comment: Beginner problem: installed python3.7.12 but py_available() return FALSE by jared.andrews07 ★ 11k
Follow the error message. Allow reticulate to handle the python environment itself.
Comment: How to perform DE anaysis on a data set in which biological replicates have high by Gisele • 0
Thank you! This is my next step to try to understand what is the best choice.
Comment: Error message running GeMoMa by Dardo • 0
can you solve this problem? this is my problem too
Comment: How to download BLAST+ on Centos (6) by Nelo • 0
okie Tnkq
Comment: Need help to remove NA values from data frame by ponganta ▴ 490
Agreed, especially regarding `dplyr::rename()`. I didn't think about that. Regarding these two functions, there are oftentimes namespace …
Comment: blast culling_limit option behavior by joe.westley • 0
Hi GenoMax, sorry for the late response. Yes I am looking to only keep one hit. I am not sure I follow the idea that all the reported hit…
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