Showing : Clustering • reset
1
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518
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Expected memory usage for analyzing large single-cell seq datasets (> 450,000 cells)?
BigData Clustering memory SingleCellExperiment edgeR
updated 12 weeks ago by ★ 28k • written 12 weeks ago by • 0
2
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3
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695
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"could not find function "readTSGE" in package ctsGE" Error occurs when trying to follow ctsGE package instructions.
GeneExpression Clustering ctsGE
8 months ago jbgnielson • 0
0
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3
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752
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Clustering coefficient of synteny network
Network syntenet Clustering coefficient
16 months ago Alexandros • 0
0
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2
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1.1k
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Scaling and normalization by deconvolution of SMART-Seq 2 data
scran Clustering SingleCell Normalization
19 months ago Assa Yeroslaviz ★ 1.5k
0
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0
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595
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maSigPro visualizing individually each plot from each cluster
plot maSigPro Clustering
2.2 years ago oseias.rf.junior • 0
0
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1
reply
1.1k
views
WGCNA - Network construction and module detection
gene Clustering wgcna flashclust
updated 2.2 years ago by ▴ 50 • written 2.2 years ago by ▴ 20
0
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1
reply
779
views
DeSeq Strategies for run to run Replication
DESeq2 Normalization Clustering replicate
updated 2.2 years ago by 42k • written 2.2 years ago by • 0
4
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3
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1.9k
views
SingleCellExperiment: Edit cluster IDs in colLabels
scran Clustering SingleCellExperiment annotate cluster
updated 2.3 years ago by 67k • written 2.3 years ago by ▴ 10
2
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2
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1.5k
views
How to judge DEG analysis of these samples could be done by using limma::voom
limma Clustering voom RNA-Seq
2.3 years ago Yang Shi ▴ 10
0
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0
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927
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The gene clusters from the WGCNA dendrogram output are not in order
Clustering WGCNA
2.5 years ago chiwut.wong • 0
0
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0
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923
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Only 1 gene/ feature is present in module after WGCNA analysis
RNASeq Clustering cluster WGCNA
2.6 years ago chiwut.wong • 0
0
votes
1
reply
731
views
Error running hierClust
hierClust R SNPs clustering
updated 2.6 years ago by 67k • written 2.6 years ago by • 0
0
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0
replies
1.1k
views
ConsensusClusterPlus: annotate a class to the heatmap
Clustering ConsensusClusterPlus
3.2 years ago Gian ▴ 30
3
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2
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2.5k
views
Clustering differentially expressed genes in response to multiple treatments (using edgeR)
edger complexheatmap R clustering
updated 4.5 years ago by 51k • written 4.5 years ago by • 0
0
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4
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1.7k
views
coseq plotting error: no method for coercing this S4 class to a vector
coseq RNAseq clustering
updated 4.8 years ago by ▴ 80 • written 4.8 years ago by ▴ 30
0
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1
reply
2.1k
views
Evaluating HCPC clusters from FactoMineR using cluster.stats from fpc library
clustering r fpc FactoMineR
5.3 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 5.4 years ago by 67k • written 5.4 years ago by • 0
1
vote
6
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1.9k
views
edgeR removing batch effect before using expression data for clustering
edger r batcheffect clustering removeBatchEffect
updated 5.5 years ago by 67k • written 5.5 years ago by ▴ 120
0
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1
reply
1.4k
views
Consensus Cluster Plus pre-computed distance matrix
consensusclusterplus distance clustering
updated 5.6 years ago by ▴ 420 • written 5.6 years ago by • 0
1
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2
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1.6k
views
Dunn Index for Clusters from scRNA-Seq
scRNA-Seq clustering scater scran dunn index
updated 5.7 years ago by ★ 28k • written 5.7 years ago by ▴ 60
2
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4
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2.7k
views
Silhouette Plots for Clustering Quality (Multiple Algorithm)
scRNA-Seq RNA-Seq Clustering Silhouette Plot
updated 5.8 years ago by ★ 28k • written 5.8 years ago by ▴ 60
2
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6
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2.0k
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Change the number of clusters with scater
scater scran scrnaseq clustering
updated 6.0 years ago by ★ 28k • written 6.0 years ago by ▴ 20
0
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3
replies
1.4k
views
Coverage profile comparison
Targeted sequencing correlation coverage euclid clustering
6.1 years ago faramer86 • 0
3
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3
replies
1.2k
views
how to plot trends for differentialy expressed genes from normalized count matrix (EdgeR)
edger clustering visualization
updated 6.1 years ago by 67k • written 6.1 years ago by ▴ 10
0
votes
0
replies
748
views
DESeq aligned with HOPACH for clustering
clustering
6.3 years ago ss • 0
7
votes
6
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6.3k
views
scaling data for clustering heat map
edger heatmap clustering differential gene expression rnaseq
updated 6.4 years ago by 51k • written 6.4 years ago by ▴ 60
0
votes
4
replies
1.8k
views
Why SPADE package has been removed from bioconductor?
spade release remove clustering
updated 6.5 years ago by 67k • written 6.5 years ago by • 0
0
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1
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1.1k
views
Global Trend Analysis using results from EdgeR
EdgeR clustering differential gene expression consensusclusterplus kmeans
updated 6.5 years ago by ★ 28k • written 6.5 years ago by • 0
0
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0
replies
1.2k
views
Add samples labels with ConsensusClusterPlus
consensusclusterplus microarray clustering
6.6 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
6.9 years ago • updated 6.6 years ago Daniel Brewer ▴ 100
1
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3
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1.4k
views
Clustering of samples based on specific gene sets
microarray differential gene expression gene set analysis clustering
6.7 years ago cherlyn.t • 0
0
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1
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1.1k
views
ConsensusClusterPlus without figures
clustering
updated 8 months ago by • 0 • written 7.0 years ago by • 0
0
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4
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1.5k
views
Gene clusters based on gene expression across samples
kmeans gene expression clustering
7.1 years ago • updated 7.0 years ago Jane Merlevede ▴ 90
0
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2
replies
2.2k
views
How to use RUVSeq in clustering problems?
ruvseq rna-seq clustering
updated 7.1 years ago by ▴ 980 • written 7.1 years ago by ▴ 50
0
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5
replies
2.9k
views
Choosing genes for clustering
limma clustering differential gene expression hierarchical clustering feature selection
7.2 years ago • updated 7.1 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
7.1 years ago lirongrossmann ▴ 80
11
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8
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11k
views
Limma and batch effect
limma differential gene expression clustering removebatcheffect
updated 7.2 years ago by 51k • written 7.2 years ago by ▴ 80
0
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2
replies
4.9k
views
When is centering and scaling needed before doing hierarchical clustering?
clustering hierarchical clustering
written 7.2 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 7.3 years ago by ★ 28k • written 7.3 years ago by • 0
6
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2
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5.7k
views
Cell type specific cell markers for Seurat based analysis.
single cell seurat clustering
updated 7.3 years ago by ▴ 40 • written 7.3 years ago by ▴ 20
1
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4
replies
1.6k
views
OrgDb for Tetrahymena thermophila
annotation clustering
updated 7.4 years ago by ★ 4.1k • written 7.4 years ago by • 0
1
vote
1
reply
6.9k
views
WGCNA: Different Detect Cut Heights Across Multiple Blocks
wgcna clustering gene expression
updated 7.6 years ago by ★ 3.0k • written 7.6 years ago by ▴ 10
3
votes
1
reply
10k
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 7.6 years ago by ▴ 20 • written 9.1 years ago by ▴ 830
1
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2
replies
2.5k
views
How to adjust the parameters of WGCNA
WGCNA RNA-seq co-expression network module clustering
updated 7.7 years ago by ★ 3.0k • written 7.7 years ago by • 0
1
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1
reply
2.6k
views
ConsensusClusterPlus matrix error
bioconductor clustering consensusclusterplus
7.7 years ago kyn ▴ 10
0
votes
5
replies
2.9k
views
Questions on using clusterProfiler
clustering clusterprofiler
8.1 years ago zhangducsu • 0
0
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1
reply
1.8k
views
Question about seed in ConsensusClusterPlus, can't repeat the result
bioconductor consensusclusterplus clustering
8.1 years ago afraTW • 0
0
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3
replies
2.3k
views
maSigPro genes from clusters
masigpro clustering
updated 5 months ago by • 0 • written 8.4 years ago by • 0
0
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0
replies
1.3k
views
Running Mclust package in R, using maximum a posteriori (MAP)
r mclust clustering
8.4 years ago mabdulsa • 0
0
votes
3
replies
2.6k
views
Prior Control with Mclust package
R mclust clustering
updated 8.4 years ago by ▴ 510 • written 8.4 years ago by • 0
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Comment: incomplete official symbol mitochondrial genes in org.Hs.eg.db? by Guido Hooiveld ★ 4.1k
I have contacted NCBI, and meanwhile got an an answer. See below. It turns out that the official, HGNC-approved symbols are present in the…
Comment: Question about using LRT test for time course experiments with DESeq2 by Denise • 0
Not really, we are testing some toxic compounds to identify genes that are activated in response to the toxic exposure. Genes that change o…
Comment: Combining RNAseq and microarray data using edgeR/limma-voom by Adam Marstrand • 0
Hi again, Thank you for the response! Can you expound on why it is not a good idea? I realize that the expression levels/differential expr…
Answer: Combining RNAseq and microarray data using edgeR/limma-voom by James W. MacDonald 67k
No, that's not a good idea at all. You should be doing a meta-analysis with these data rather than trying to combine like that. `GeneMeta` …
Answer: GOstats kegg analysis in wheat - help - none of the objects in the first column by James W. MacDonald 67k
Check the help page for `KEGGFrame`. Your columns are out of order.
Votes
Answer: DecideTest vs topTAGs in edgeR
Comment: DESeq Input from Salmon + tximport/tximeta
Comment: DESeq Input from Salmon + tximport/tximeta
Comment: DESeq Input from Salmon + tximport/tximeta
Answer: DESeq Input from Salmon + tximport/tximeta
Awards • All
Popular Question to Assa Yeroslaviz ★ 1.5k
Popular Question to Gordon Smyth 51k
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