Showing : Clustering • reset
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Expected memory usage for analyzing large single-cell seq datasets (> 450,000 cells)?
BigData Clustering memory SingleCellExperiment edgeR
updated 5 months ago by ★ 28k • written 5 months ago by • 0
2
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3
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770
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"could not find function "readTSGE" in package ctsGE" Error occurs when trying to follow ctsGE package instructions.
GeneExpression Clustering ctsGE
11 months ago jbgnielson • 0
0
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3
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893
views
Clustering coefficient of synteny network
Network syntenet Clustering coefficient
19 months ago • updated 18 months ago Alexandros • 0
0
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2
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1.2k
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Scaling and normalization by deconvolution of SMART-Seq 2 data
scran Clustering SingleCell Normalization
22 months ago Assa Yeroslaviz ★ 1.5k
0
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0
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644
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maSigPro visualizing individually each plot from each cluster
plot maSigPro Clustering
2.4 years ago oseias.rf.junior • 0
0
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1
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1.1k
views
WGCNA - Network construction and module detection
gene Clustering wgcna flashclust
updated 2.4 years ago by ▴ 50 • written 2.4 years ago by ▴ 20
0
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1
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821
views
DeSeq Strategies for run to run Replication
DESeq2 Normalization Clustering replicate
updated 2.4 years ago by 43k • written 2.4 years ago by • 0
4
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3
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2.2k
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SingleCellExperiment: Edit cluster IDs in colLabels
scran Clustering SingleCellExperiment annotate cluster
updated 2.5 years ago by 67k • written 2.5 years ago by ▴ 10
2
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2
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1.6k
views
How to judge DEG analysis of these samples could be done by using limma::voom
limma Clustering voom RNA-Seq
2.5 years ago Yang Shi ▴ 10
0
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0
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1.0k
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The gene clusters from the WGCNA dendrogram output are not in order
Clustering WGCNA
2.7 years ago chiwut.wong • 0
0
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0
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979
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Only 1 gene/ feature is present in module after WGCNA analysis
RNASeq Clustering cluster WGCNA
2.8 years ago chiwut.wong • 0
0
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1
reply
766
views
Error running hierClust
hierClust R SNPs clustering
updated 2.8 years ago by 67k • written 2.8 years ago by • 0
0
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0
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1.1k
views
ConsensusClusterPlus: annotate a class to the heatmap
Clustering ConsensusClusterPlus
3.4 years ago Gian ▴ 30
3
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2
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2.8k
views
Clustering differentially expressed genes in response to multiple treatments (using edgeR)
edger complexheatmap R clustering
updated 4.7 years ago by 52k • written 4.7 years ago by • 0
0
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4
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1.8k
views
coseq plotting error: no method for coercing this S4 class to a vector
coseq RNAseq clustering
updated 5.0 years ago by ▴ 80 • written 5.0 years ago by ▴ 40
0
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1
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2.2k
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Evaluating HCPC clusters from FactoMineR using cluster.stats from fpc library
clustering r fpc FactoMineR
5.5 years ago anahochmanova • 0
0
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3
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1.1k
views
How to find number of patients (percentage of given population) having high expression of gene A in given microarray data ?
microarray r clustering high expressed genes
updated 5.7 years ago by 67k • written 5.7 years ago by • 0
1
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6
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2.0k
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edgeR removing batch effect before using expression data for clustering
edger r batcheffect clustering removeBatchEffect
updated 5.7 years ago by 67k • written 5.7 years ago by ▴ 120
0
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1
reply
1.5k
views
Consensus Cluster Plus pre-computed distance matrix
consensusclusterplus distance clustering
updated 5.8 years ago by ▴ 420 • written 5.8 years ago by • 0
1
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2
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1.7k
views
Dunn Index for Clusters from scRNA-Seq
scRNA-Seq clustering scater scran dunn index
updated 5.9 years ago by ★ 28k • written 5.9 years ago by ▴ 60
2
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4
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2.9k
views
Silhouette Plots for Clustering Quality (Multiple Algorithm)
scRNA-Seq RNA-Seq Clustering Silhouette Plot
updated 6.0 years ago by ★ 28k • written 6.0 years ago by ▴ 60
2
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6
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2.0k
views
Change the number of clusters with scater
scater scran scrnaseq clustering
updated 6.2 years ago by ★ 28k • written 6.2 years ago by ▴ 20
0
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3
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1.4k
views
Coverage profile comparison
Targeted sequencing correlation coverage euclid clustering
6.3 years ago faramer86 • 0
3
votes
3
replies
1.3k
views
how to plot trends for differentialy expressed genes from normalized count matrix (EdgeR)
edger clustering visualization
updated 6.3 years ago by 67k • written 6.3 years ago by ▴ 10
0
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0
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780
views
DESeq aligned with HOPACH for clustering
clustering
6.5 years ago ss • 0
7
votes
6
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6.6k
views
scaling data for clustering heat map
edger heatmap clustering differential gene expression rnaseq
updated 6.7 years ago by 52k • written 6.7 years ago by ▴ 60
0
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4
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1.8k
views
Why SPADE package has been removed from bioconductor?
spade release remove clustering
updated 6.7 years ago by 67k • written 6.7 years ago by • 0
0
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1
reply
1.2k
views
Global Trend Analysis using results from EdgeR
EdgeR clustering differential gene expression consensusclusterplus kmeans
updated 6.8 years ago by ★ 28k • written 6.8 years ago by • 0
0
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0
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1.3k
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Add samples labels with ConsensusClusterPlus
consensusclusterplus microarray clustering
6.8 years ago aagata.szymanek • 0
1
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0
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1.6k
views
Job: UK/EU funded PhD Studentship: Detecting novel subtypes of cancer using data science and machine learning
PhD clustering cancer Job
7.1 years ago • updated 6.9 years ago Daniel Brewer ▴ 100
1
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3
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1.5k
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Clustering of samples based on specific gene sets
microarray differential gene expression gene set analysis clustering
6.9 years ago cherlyn.t • 0
0
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1
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1.2k
views
ConsensusClusterPlus without figures
clustering
updated 10 months ago by • 0 • written 7.2 years ago by • 0
0
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4
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1.6k
views
Gene clusters based on gene expression across samples
kmeans gene expression clustering
7.3 years ago • updated 7.2 years ago Jane Merlevede ▴ 90
0
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2
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2.3k
views
How to use RUVSeq in clustering problems?
ruvseq rna-seq clustering
updated 7.3 years ago by ▴ 980 • written 7.3 years ago by ▴ 50
0
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5
replies
3.1k
views
Choosing genes for clustering
limma clustering differential gene expression hierarchical clustering feature selection
7.4 years ago • updated 7.3 years ago lirongrossmann ▴ 80
1
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3
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1.8k
views
Selecting genes that best separate between two groups
limma genefilter ttest clustering TPM
7.4 years ago lirongrossmann ▴ 80
11
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8
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12k
views
Limma and batch effect
limma differential gene expression clustering removebatcheffect
updated 7.4 years ago by 52k • written 7.4 years ago by ▴ 80
0
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2
replies
5.0k
views
When is centering and scaling needed before doing hierarchical clustering?
clustering hierarchical clustering
written 7.5 years ago by ▴ 20
0
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1
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2.2k
views
Observation/case weighting in cluster analysis in R
hclust hierarchical clustering clustering weight
updated 7.5 years ago by ★ 28k • written 7.5 years ago by • 0
6
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2
replies
5.9k
views
Cell type specific cell markers for Seurat based analysis.
single cell seurat clustering
updated 7.5 years ago by ▴ 40 • written 7.5 years ago by ▴ 20
1
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4
replies
1.7k
views
OrgDb for Tetrahymena thermophila
annotation clustering
updated 7.7 years ago by ★ 4.1k • written 7.7 years ago by • 0
1
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1
reply
7.1k
views
WGCNA: Different Detect Cut Heights Across Multiple Blocks
wgcna clustering gene expression
updated 7.8 years ago by ★ 3.0k • written 7.8 years ago by ▴ 10
3
votes
1
reply
11k
views
Error using function NbClust regarding multiple values in the argument "index" of package NbClust for getting the optimal number of clusters of a dat…
NbClust clustering looping list object function creation
updated 7.8 years ago by ▴ 20 • written 9.4 years ago by ▴ 840
1
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1
reply
2.7k
views
ConsensusClusterPlus matrix error
bioconductor clustering consensusclusterplus
8.0 years ago kyn ▴ 10
0
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5
replies
3.0k
views
Questions on using clusterProfiler
clustering clusterprofiler
8.3 years ago zhangducsu • 0
0
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1
reply
1.9k
views
Question about seed in ConsensusClusterPlus, can't repeat the result
bioconductor consensusclusterplus clustering
8.3 years ago afraTW • 0
0
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3
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2.4k
views
maSigPro genes from clusters
masigpro clustering
updated 8 months ago by • 0 • written 8.6 years ago by • 0
0
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0
replies
1.4k
views
Running Mclust package in R, using maximum a posteriori (MAP)
r mclust clustering
8.6 years ago mabdulsa • 0
0
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3
replies
2.7k
views
Prior Control with Mclust package
R mclust clustering
updated 8.7 years ago by ▴ 510 • written 8.7 years ago by • 0
2
votes
6
replies
3.4k
views
Clustering and bootstrapping of RNASeq samples
clustering pvclust vsd edgeR rnaseq
written 8.7 years ago by ▴ 90
50 results • Page 1 of 1
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Comment: How to visualize these pathways using pathview by Guido Hooiveld ★ 4.1k
FYI: a similar, if not identical issue has been reported before (`pathview` has problems visualizing some pathways, but not all). You likel…
Comment: Why select top highly expressed genes based on normalized counts, but then plot by Quang NN ▴ 10
I see. Thank you ATpoint!
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by Prakash Sah • 0
Thanks James!
Comment: Why select top highly expressed genes based on normalized counts, but then plot by ATpoint ★ 4.6k
I think I explained what the differences between approach 1 and 2 is in my answer. I assume that the tutorial uses vst because it is varian…
Comment: Why select top highly expressed genes based on normalized counts, but then plot by Quang NN ▴ 10
Thank you ATpoint for your responses. I am a bit confused because the difference between the two approaches is the selection of the genes…
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Bioconductor Course, Kenya 2025: Applications Open!
Comment: can't install tscR
Answer: Csaw normalization strategies - general inquiry
A: DESeq2 interaction term
Comment: Recount3 data correspond to TCGA data
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