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Showing top results for tag: clustering • reset
0
votes
0
replies
71
views
How to show relabel sub cluster on the original cluster in Seurat
scRNA-seq seurat cluster clustering
1 day ago by bt20022 • 0
0
votes
1
reply
135
views
Identification of cell types/groups in single-cell data
cell single type clustering
updated 3 days ago by ▴ 80 • written 3 days ago by ▴ 10
1
vote
1
reply
141
views
How to add metadata to dendrogram of hierarchical clustering in R
metadata Hierarchical clustering
updated 8 days ago by ★ 1.9k • written 8 days ago by • 0
4
votes
2
replies
167
views
Clustering resolution for scRNA-seq
clustering single-cell
updated 10 days ago by ★ 1.3k • written 11 days ago by • 0
0
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0
replies
120
views
Neighboring index between clusters on a map
connectivity clustering
17 days ago by thejustpark ▴ 80
0
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0
replies
79
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Is it okay to cluster rows and columns with a different linkage?
Clustering R
updated 24 days ago by 54k • written 24 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
165
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
416
views
individual-level allele frequencies
allele frequencies clustering plink
updated 7 weeks ago by 8.4k • written 12 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 7 weeks ago by ▴ 10
3
votes
1
reply
180
views
usearch11 cluster_fast option
usearch proteins clustering
updated 11 weeks ago by 107k • written 11 weeks ago by ▴ 10
3
votes
5
replies
301
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
11 weeks ago by ceruleanivy ▴ 30
4
votes
4
replies
379
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
288
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
412
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
182
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
147
views
Supervised clustering from gene expression (fold change) data
clustering expression supervised
4 months ago by nerea.bilbao • 0
1
vote
1
reply
154
views
RMSD clustering
Clustering
updated 4 months ago by ★ 13k • written 4 months ago by • 0
0
votes
2
replies
207
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
29 days 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
590
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
236
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
811
views
Pheatmap/Complexheatmap: making a continuous color scale with NAs
clustering pathways complexheatmap pheatmap
6 months ago by Ridha ▴ 50
0
votes
7
replies
762
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
831
views
Interpretation of Principal component analysis
clustering
updated 6 months ago by ★ 13k • written 6 months ago by • 0
1
vote
2
replies
375
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
198
views
Identify cell type from bulk RNA sequencing data
sequencing type clustering r
6 months ago by minoo ▴ 10
0
votes
0
replies
258
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
285
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
387
views
Clustering sequences with low identity
clustering sequences
updated 7 months ago by ★ 13k • written 7 months ago by ▴ 820
1
vote
3
replies
309
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
703
views
Is my WGCNA soft threshold (power) too low?
wgcna RNA-Seq clustering network
7 months ago by jfaberha ▴ 10
0
votes
0
replies
354
views
Using ATACseq CPM for clustering samples
ATAC-seq normalization clustering
8 months ago by barati • 0
6
votes
5
replies
524
views
CD-HIT: representative sequence vs consensus sequence
CD-HIT clustering
8 months ago by rob_DNA ▴ 10
0
votes
0
replies
269
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
314
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
811
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 7.1 years ago by • 0
0
votes
0
replies
398
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
351
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
425
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
508
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
479
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
Comment: Misuse of RPKM or TPM normalization when comparing across samples and sequencing
Misuse of RPKM or TPM normalization when comparing across samples and sequencing protocols
Answer: Misuse of RPKM or TPM normalization when comparing across samples and sequencing
A: How Do You Justify Your Rna-Seq Expression Threshold (Fpkm/Rpkm) ?
Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
Comment: Workshop for population genomics
Comment: ATAC-seq sample normalization
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Recent Replies
Comment: Problem loading my multifasta by GenoMax 107k
> Invalid msa or the file does not exist! Looks like the program needs a multiple sequence alignment (MSA) file NOT a simple multi-fasta f…
Comment: Misuse of RPKM or TPM normalization when comparing across samples and sequencing by Gordon Smyth ★ 3.4k
There is another subtlety here to do with correction for gene length in the RPKM and TPM measures. Log-counts-per-million performs quite re…
Answer: Create genome-unique intervals from overlapping records in a bed file by Alex Reynolds 33k
You could use [BEDOPS][1] `bedops --partition` to easily calculate disjoint elements from a set of overlapping elements. Then you could pas…
Answer: What is the Sleuth intercept and how can Sleuth be used when you have >2 treatme by bkleiboeker ▴ 20
https://github.com/pachterlab/sleuth/issues/156
Comment: filtering and converting data frame to table by Papyrus ★ 1.3k
If the string before the "." is always the same, you can do `substr(dataframe$gene_name,5,999)`, or `gsub("AMP.","",dataframe$gene_name)`. …
Answer: Workshop for population genomics by pabe • 0
I highly recommend http://popgen.dk/popgen21/ They provide an annual summer course so keep an eye out for 2022. In the meantime, here a…
Comment: Whole genome coverage plot by ATpoint 54k
He says > No, do not align to masked genome for any purpose. Filter out the reads mapped to the masked region after whole-genome alignment…
Comment: Whole genome coverage plot by cmdcolin ★ 1.6k
i was skeptical of this but here is lh3 saying so also https://www.biostars.org/p/3232/#3235 :)
Comment: Workshop for population genomics by GenoMax 107k
There may be one in 2022. They seem to hold them every other year. This link is the for the last one: https://evomics.org/2020-workshop-on-…
Comment: Tools or Method for batch analysis of Paired end WES data in a queue way. by Jeremy Leipzig 20k
those tools definitely work in a breadth-first manner as you wanted
Answer: ROC_AUC curve for performance of a classification by Kevin Blighe 77k
> I want clarify on this point, is it possible to get AUC 100% It is possible but not credible. This can occur when the model is 'overfi…
Comment: IMPUTE2 -merge_ref_panels by Kevin Blighe 77k
If there are no warnings or errors, and the program indicates that the command was successful, then there should be output files with prefi…
Comment: ABOUT affymetrix genotyping console (GTC) software and TCGA CNV workflow by Kevin Blighe 77k
HI, if the copy number from GTC is 1, this equates to a log2 ratio of -1. Please see: log2(1 / 2) [1] -1 Why we use 2? - 2 is the…
Comment: bad file format in HMM file by pavelasquezv ▴ 20
It is true. Thanks a lot, Mensur. Now it is working well All the best Alex
Comment: IMPUTE2 -merge_ref_panels by raalsuwaidi ▴ 10
there is no error or warning, but in the summary file the last entry is as follows: --------- Run log --------- RESETTING PARAMETERS FO…
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