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 8 months ago by ★ 28k • written 8 months ago by • 0
2
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3
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841
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"could not find function "readTSGE" in package ctsGE" Error occurs when trying to follow ctsGE package instructions.
GeneExpression Clustering ctsGE
13 months ago jbgnielson • 0
0
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3
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1.0k
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Clustering coefficient of synteny network
Network syntenet Clustering coefficient
21 months ago Alexandros • 0
0
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2
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1.3k
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Scaling and normalization by deconvolution of SMART-Seq 2 data
scran Clustering SingleCell Normalization
2.0 years ago Assa Yeroslaviz ★ 1.5k
0
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0
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688
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maSigPro visualizing individually each plot from each cluster
plot maSigPro Clustering
2.6 years ago oseias.rf.junior • 0
0
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1
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1.2k
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WGCNA - Network construction and module detection
gene Clustering wgcna flashclust
updated 2.6 years ago by ▴ 50 • written 2.6 years ago by ▴ 20
0
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1
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864
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DeSeq Strategies for run to run Replication
DESeq2 Normalization Clustering replicate
updated 2.6 years ago by 43k • written 2.6 years ago by • 0
4
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3
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2.3k
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SingleCellExperiment: Edit cluster IDs in colLabels
scran Clustering SingleCellExperiment annotate cluster
updated 2.7 years ago by 68k • written 2.7 years ago by ▴ 10
2
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2
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1.7k
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How to judge DEG analysis of these samples could be done by using limma::voom
limma Clustering voom RNA-Seq
2.7 years ago Yang Shi ▴ 10
0
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0
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1.1k
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The gene clusters from the WGCNA dendrogram output are not in order
Clustering WGCNA
2.9 years ago chiwut.wong • 0
0
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0
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1.0k
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Only 1 gene/ feature is present in module after WGCNA analysis
RNASeq Clustering cluster WGCNA
3.0 years ago chiwut.wong • 0
0
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1
reply
805
views
Error running hierClust
hierClust R SNPs clustering
updated 3.0 years ago by 68k • written 3.0 years ago by • 0
0
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0
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1.2k
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ConsensusClusterPlus: annotate a class to the heatmap
Clustering ConsensusClusterPlus
3.6 years ago Gian ▴ 30
3
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2
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3.1k
views
Clustering differentially expressed genes in response to multiple treatments (using edgeR)
edger complexheatmap R clustering
updated 4.9 years ago by 52k • written 4.9 years ago by • 0
0
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4
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1.9k
views
coseq plotting error: no method for coercing this S4 class to a vector
coseq RNAseq clustering
updated 5.2 years ago by ▴ 80 • written 5.2 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
5.7 years ago anahochmanova • 0
0
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3
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1.2k
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 5.9 years ago by 68k • written 5.9 years ago by • 0
1
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6
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2.1k
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edgeR removing batch effect before using expression data for clustering
edger r batcheffect clustering removeBatchEffect
updated 5.9 years ago by 68k • written 5.9 years ago by ▴ 120
0
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1
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1.6k
views
Consensus Cluster Plus pre-computed distance matrix
consensusclusterplus distance clustering
updated 6.0 years ago by ▴ 420 • written 6.0 years ago by • 0
1
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2
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1.8k
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Dunn Index for Clusters from scRNA-Seq
scRNA-Seq clustering scater scran dunn index
updated 6.1 years ago by ★ 28k • written 6.1 years ago by ▴ 60
2
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4
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3.1k
views
Silhouette Plots for Clustering Quality (Multiple Algorithm)
scRNA-Seq RNA-Seq Clustering Silhouette Plot
updated 6.2 years ago by ★ 28k • written 6.2 years ago by ▴ 60
2
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6
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2.2k
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Change the number of clusters with scater
scater scran scrnaseq clustering
updated 6.4 years ago by ★ 28k • written 6.4 years ago by ▴ 20
0
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3
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1.5k
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Coverage profile comparison
Targeted sequencing correlation coverage euclid clustering
6.5 years ago faramer86 • 0
3
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3
replies
1.3k
views
how to plot trends for differentialy expressed genes from normalized count matrix (EdgeR)
edger clustering visualization
updated 6.5 years ago by 68k • written 6.5 years ago by ▴ 10
0
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0
replies
816
views
DESeq aligned with HOPACH for clustering
clustering
6.7 years ago ss • 0
7
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6
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6.9k
views
scaling data for clustering heat map
edger heatmap clustering differential gene expression rnaseq
updated 6.9 years ago by 52k • written 6.9 years ago by ▴ 60
0
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4
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1.9k
views
Why SPADE package has been removed from bioconductor?
spade release remove clustering
updated 6.9 years ago by 68k • written 6.9 years ago by • 0
0
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1
reply
1.3k
views
Global Trend Analysis using results from EdgeR
EdgeR clustering differential gene expression consensusclusterplus kmeans
updated 7.0 years ago by ★ 28k • written 7.0 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
7.0 years ago aagata.szymanek • 0
1
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0
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1.7k
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Job: UK/EU funded PhD Studentship: Detecting novel subtypes of cancer using data science and machine learning
PhD clustering cancer Job
7.3 years ago • updated 7.1 years ago Daniel Brewer ▴ 100
1
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3
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1.6k
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Clustering of samples based on specific gene sets
microarray differential gene expression gene set analysis clustering
7.1 years ago cherlyn.t • 0
0
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1
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1.2k
views
ConsensusClusterPlus without figures
clustering
updated 13 months ago by • 0 • written 7.4 years ago by • 0
0
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4
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1.7k
views
Gene clusters based on gene expression across samples
kmeans gene expression clustering
7.5 years ago • updated 7.4 years ago Jane Merlevede ▴ 90
0
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2
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2.4k
views
How to use RUVSeq in clustering problems?
ruvseq rna-seq clustering
updated 7.5 years ago by ▴ 980 • written 7.5 years ago by ▴ 50
0
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5
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3.4k
views
Choosing genes for clustering
limma clustering differential gene expression hierarchical clustering feature selection
7.6 years ago • updated 7.5 years ago lirongrossmann ▴ 80
1
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3
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2.0k
views
Selecting genes that best separate between two groups
limma genefilter ttest clustering TPM
7.6 years ago lirongrossmann ▴ 80
11
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8
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12k
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Limma and batch effect
limma differential gene expression clustering removebatcheffect
updated 7.6 years ago by 52k • written 7.6 years ago by ▴ 80
0
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2
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5.2k
views
When is centering and scaling needed before doing hierarchical clustering?
clustering hierarchical clustering
written 7.6 years ago by ▴ 20
0
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1
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2.3k
views
Observation/case weighting in cluster analysis in R
hclust hierarchical clustering clustering weight
updated 7.7 years ago by ★ 28k • written 7.7 years ago by • 0
6
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2
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6.3k
views
Cell type specific cell markers for Seurat based analysis.
single cell seurat clustering
updated 7.7 years ago by ▴ 40 • written 7.7 years ago by ▴ 20
1
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4
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1.8k
views
OrgDb for Tetrahymena thermophila
annotation clustering
updated 7.9 years ago by ★ 4.1k • written 7.9 years ago by • 0
1
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1
reply
7.4k
views
WGCNA: Different Detect Cut Heights Across Multiple Blocks
wgcna clustering gene expression
updated 8.0 years ago by ★ 3.0k • written 8.0 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 8.0 years ago by ▴ 20 • written 9.6 years ago by ▴ 840
1
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1
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2.8k
views
ConsensusClusterPlus matrix error
bioconductor clustering consensusclusterplus
8.2 years ago kyn ▴ 10
0
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5
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3.1k
views
Questions on using clusterProfiler
clustering clusterprofiler
8.5 years ago zhangducsu • 0
0
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1
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1.9k
views
Question about seed in ConsensusClusterPlus, can't repeat the result
bioconductor consensusclusterplus clustering
8.5 years ago afraTW • 0
0
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3
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2.5k
views
maSigPro genes from clusters
masigpro clustering
updated 10 months ago by • 0 • written 8.8 years ago by • 0
0
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0
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1.4k
views
Running Mclust package in R, using maximum a posteriori (MAP)
r mclust clustering
8.8 years ago mabdulsa • 0
0
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3
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2.8k
views
Prior Control with Mclust package
R mclust clustering
updated 8.8 years ago by ▴ 510 • written 8.8 years ago by • 0
2
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6
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3.5k
views
Clustering and bootstrapping of RNASeq samples
clustering pvclust vsd edgeR rnaseq
written 8.9 years ago by ▴ 90
50 results • Page 1 of 1
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Comment: DiffBind can't find a DAR by ATpoint ★ 4.8k
"My cake does not look as advertised in the recipe", with this sloppy sentence I hope you understand that you need to give people details, …
Comment: DESeq - help with pair wise comparisons by bd2000 ▴ 30
Follow up question, is this the correct way to extract results? ```r results <- results(ddsObj, list(c("GroupControl.Followup", "GroupTrea…
Comment: DESeq: Gene is not flagged as differentially expressed despite count data showin by ktz • 0
Thank you for your reply! I would love to know your thoughts on the plots I've included above. > 'Are the differences between groups lar…
Comment: DESeq: Gene is not flagged as differentially expressed despite count data showin by ktz • 0
I also realised that the other gene I pointed out that was flagged as DE but had similar count differences also shows that rep1 is lower th…
Comment: DESeq - help with pair wise comparisons by bd2000 ▴ 30
Thanks that's great!! I've followed the instructions from the link you sent, is my code correct? By correct I mean, is my code comparing fo…
Votes
Comment: DESeq - help with pair wise comparisons
Answer: Is random access by row index possible for an indexed VCF file?
Answer: Is random access by row index possible for an indexed VCF file?
Answer: SingleR with multiple single cell references
Answer: SingleR with multiple single cell references
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