Showing : Clustering • reset
2
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"could not find function "readTSGE" in package ctsGE" Error occurs when trying to follow ctsGE package instructions.
GeneExpression Clustering ctsGE
9 weeks ago jbgnielson • 0
0
votes
3
replies
572
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Clustering coefficient of synteny network
Network syntenet Clustering coefficient
10 months ago • updated 9 months ago Alexandros • 0
0
votes
2
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710
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Scaling and normalization by deconvolution of SMART-Seq 2 data
scran Clustering SingleCell Normalization
13 months ago Assa Yeroslaviz ★ 1.5k
0
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0
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435
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maSigPro visualizing individually each plot from each cluster
plot maSigPro Clustering
20 months ago oseias.rf.junior • 0
0
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1
reply
822
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WGCNA - Network construction and module detection
gene Clustering wgcna flashclust
updated 20 months ago by ▴ 50 • written 20 months ago by ▴ 20
0
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1
reply
636
views
DeSeq Strategies for run to run Replication
DESeq2 Normalization Clustering replicate
updated 20 months ago by 41k • written 20 months ago by • 0
4
votes
3
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1.5k
views
SingleCellExperiment: Edit cluster IDs in colLabels
scran Clustering SingleCellExperiment annotate cluster
updated 21 months ago by 65k • written 21 months ago by ▴ 10
2
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2
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1.2k
views
How to judge DEG analysis of these samples could be done by using limma::voom
limma Clustering voom RNA-Seq
21 months ago Yang Shi ▴ 10
0
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0
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758
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The gene clusters from the WGCNA dendrogram output are not in order
Clustering WGCNA
2.0 years ago chiwut.wong • 0
0
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0
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766
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Only 1 gene/ feature is present in module after WGCNA analysis
RNASeq Clustering cluster WGCNA
2.0 years ago chiwut.wong • 0
0
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1
reply
602
views
Error running hierClust
hierClust R SNPs clustering
updated 2.1 years ago by 65k • written 2.1 years ago by • 0
0
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0
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834
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ConsensusClusterPlus: annotate a class to the heatmap
Clustering ConsensusClusterPlus
2.7 years ago Gian ▴ 30
3
votes
2
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2.1k
views
Clustering differentially expressed genes in response to multiple treatments (using edgeR)
edger complexheatmap R clustering
updated 4.0 years ago by 50k • written 4.0 years ago by • 0
0
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4
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1.4k
views
coseq plotting error: no method for coercing this S4 class to a vector
coseq RNAseq clustering
updated 4.3 years ago by ▴ 80 • written 4.3 years ago by ▴ 30
0
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1
reply
1.9k
views
Evaluating HCPC clusters from FactoMineR using cluster.stats from fpc library
clustering r fpc FactoMineR
4.8 years ago anahochmanova • 0
0
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3
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935
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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 4.9 years ago by 65k • written 4.9 years ago by • 0
1
vote
6
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1.6k
views
edgeR removing batch effect before using expression data for clustering
edger r batcheffect clustering removeBatchEffect
updated 5.0 years ago by 65k • written 5.0 years ago by ▴ 110
0
votes
1
reply
1.2k
views
Consensus Cluster Plus pre-computed distance matrix
consensusclusterplus distance clustering
updated 5.1 years ago by ▴ 420 • written 5.1 years ago by • 0
1
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2
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1.4k
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Dunn Index for Clusters from scRNA-Seq
scRNA-Seq clustering scater scran dunn index
updated 5.1 years ago by ★ 28k • written 5.2 years ago by ▴ 50
2
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4
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2.3k
views
Silhouette Plots for Clustering Quality (Multiple Algorithm)
scRNA-Seq RNA-Seq Clustering Silhouette Plot
updated 5.2 years ago by ★ 28k • written 5.2 years ago by ▴ 50
2
votes
6
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1.7k
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Change the number of clusters with scater
scater scran scrnaseq clustering
updated 5.5 years ago by ★ 28k • written 5.5 years ago by ▴ 20
0
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3
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1.2k
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Coverage profile comparison
Targeted sequencing correlation coverage euclid clustering
5.5 years ago faramer86 • 0
3
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3
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1.1k
views
how to plot trends for differentialy expressed genes from normalized count matrix (EdgeR)
edger clustering visualization
updated 5.6 years ago by 65k • written 5.6 years ago by ▴ 10
0
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0
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665
views
DESeq aligned with HOPACH for clustering
clustering
5.8 years ago ss • 0
7
votes
6
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5.7k
views
scaling data for clustering heat map
edger heatmap clustering differential gene expression rnaseq
updated 5.9 years ago by 50k • written 5.9 years ago by ▴ 60
0
votes
4
replies
1.6k
views
Why SPADE package has been removed from bioconductor?
spade release remove clustering
updated 6.0 years ago by 65k • written 6.0 years ago by • 0
0
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1
reply
993
views
Global Trend Analysis using results from EdgeR
EdgeR clustering differential gene expression consensusclusterplus kmeans
updated 6.0 years ago by ★ 28k • written 6.0 years ago by • 0
0
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0
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1.1k
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Add samples labels with ConsensusClusterPlus
consensusclusterplus microarray clustering
6.1 years ago aagata.szymanek • 0
1
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0
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1.4k
views
Job: UK/EU funded PhD Studentship: Detecting novel subtypes of cancer using data science and machine learning
PhD clustering cancer Job
6.4 years ago • updated 6.1 years ago Daniel Brewer ▴ 100
1
vote
3
replies
1.2k
views
Clustering of samples based on specific gene sets
microarray differential gene expression gene set analysis clustering
6.2 years ago cherlyn.t • 0
0
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1
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977
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ConsensusClusterPlus without figures
clustering
updated 8 weeks ago by • 0 • written 6.5 years ago by • 0
0
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4
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1.3k
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Gene clusters based on gene expression across samples
kmeans gene expression clustering
6.5 years ago Jane Merlevede ▴ 90
0
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2
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2.0k
views
How to use RUVSeq in clustering problems?
ruvseq rna-seq clustering
updated 6.6 years ago by ▴ 950 • written 6.6 years ago by ▴ 50
0
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5
replies
2.5k
views
Choosing genes for clustering
limma clustering differential gene expression hierarchical clustering feature selection
6.6 years ago lirongrossmann ▴ 80
1
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3
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1.5k
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Selecting genes that best separate between two groups
limma genefilter ttest clustering TPM
6.6 years ago lirongrossmann ▴ 80
11
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8
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10k
views
Limma and batch effect
limma differential gene expression clustering removebatcheffect
updated 6.6 years ago by 50k • written 6.6 years ago by ▴ 80
0
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2
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4.6k
views
When is centering and scaling needed before doing hierarchical clustering?
clustering hierarchical clustering
written 6.7 years ago by ▴ 20
0
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1
reply
1.9k
views
Observation/case weighting in cluster analysis in R
hclust hierarchical clustering clustering weight
updated 6.8 years ago by ★ 28k • written 6.8 years ago by • 0
6
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2
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5.3k
views
Cell type specific cell markers for Seurat based analysis.
single cell seurat clustering
updated 6.8 years ago by ▴ 40 • written 6.8 years ago by ▴ 20
1
vote
4
replies
1.4k
views
OrgDb for Tetrahymena thermophila
annotation clustering
updated 6.9 years ago by ★ 3.9k • written 6.9 years ago by • 0
1
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1
reply
6.2k
views
WGCNA: Different Detect Cut Heights Across Multiple Blocks
wgcna clustering gene expression
updated 7.1 years ago by ★ 3.0k • written 7.1 years ago by ▴ 10
3
votes
1
reply
9.7k
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 7.1 years ago by ▴ 20 • written 8.6 years ago by ▴ 830
1
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2
replies
2.2k
views
How to adjust the parameters of WGCNA
WGCNA RNA-seq co-expression network module clustering
updated 7.2 years ago by ★ 3.0k • written 7.2 years ago by • 0
1
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1
reply
2.3k
views
ConsensusClusterPlus matrix error
bioconductor clustering consensusclusterplus
7.2 years ago kyn ▴ 10
0
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5
replies
2.6k
views
Questions on using clusterProfiler
clustering clusterprofiler
7.6 years ago zhangducsu • 0
0
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1
reply
1.6k
views
Question about seed in ConsensusClusterPlus, can't repeat the result
bioconductor consensusclusterplus clustering
7.6 years ago afraTW • 0
0
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2
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2.0k
views
maSigPro genes from clusters
masigpro clustering
updated 7.8 years ago by ▴ 90 • written 7.9 years ago by • 0
0
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0
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1.2k
views
Running Mclust package in R, using maximum a posteriori (MAP)
r mclust clustering
7.9 years ago mabdulsa • 0
0
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3
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2.3k
views
Prior Control with Mclust package
R mclust clustering
updated 7.9 years ago by ▴ 510 • written 7.9 years ago by • 0
2
votes
6
replies
3.0k
views
Clustering and bootstrapping of RNASeq samples
clustering pvclust vsd edgeR rnaseq
written 7.9 years ago by ▴ 90
50 results • Page 1 of 1
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Replies
Comment: Deseq2 and Normalization of RNA sequencing data by kcarey • 0
Noise in terms of expression...to make sure that the information reported is not due to artifacts and actually expression. When I had FPKM …
Answer: NEED FOR NESSASORY HELP by Gordon Smyth 50k
Is this quesion related to your earlier question? https://support.bioconductor.org/p/9157127/ If you've already done an edgeR analysis, yo…
Answer: Gene-by-sample covariates in limma by Gordon Smyth 50k
Your first method would be valid if, instead of taking ratios, you instead used the differences between the log-transformed 13C and 12C int…
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p- by Gordon Smyth 50k
You have discovered something that I have pointed out many times on this forum. fgsea does not implement the classic GSEA method published …
Comment: Once again a "Model matrix not full rank" by James W. MacDonald 65k
In that case both time and treatment are identical things, so choose one and go with it.
Votes
Bioconductor 3.19 is Released!
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
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