Showing : clustering • reset
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1.3k
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Expected memory usage for analyzing large single-cell seq datasets (> 450,000 cells)?
BigData Clustering memory SingleCellExperiment edgeR
updated 7 months ago by ★ 28k • written 7 months ago by • 0
2
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3
replies
832
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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
20 months ago Alexandros • 0
0
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2
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1.3k
views
Scaling and normalization by deconvolution of SMART-Seq 2 data
scran Clustering SingleCell Normalization
24 months ago Assa Yeroslaviz ★ 1.5k
0
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0
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685
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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
reply
1.2k
views
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
reply
861
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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
views
SingleCellExperiment: Edit cluster IDs in colLabels
scran Clustering SingleCellExperiment annotate cluster
updated 2.6 years ago by 68k • written 2.6 years ago by ▴ 10
2
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2
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1.6k
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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
views
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
2.9 years ago chiwut.wong • 0
0
votes
1
reply
801
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
views
ConsensusClusterPlus: annotate a class to the heatmap
Clustering ConsensusClusterPlus
3.6 years ago Gian ▴ 30
3
votes
2
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3.0k
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 5.8 years ago by 68k • written 5.8 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
reply
1.5k
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
views
Dunn Index for Clusters from scRNA-Seq
scRNA-Seq clustering scater scran dunn index
updated 6.0 years ago by ★ 28k • written 6.0 years ago by ▴ 60
2
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4
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3.0k
views
Silhouette Plots for Clustering Quality (Multiple Algorithm)
scRNA-Seq RNA-Seq Clustering Silhouette Plot
updated 6.1 years ago by ★ 28k • written 6.1 years ago by ▴ 60
2
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6
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2.1k
views
Change the number of clusters with scater
scater scran scrnaseq clustering
updated 6.3 years ago by ★ 28k • written 6.3 years ago by ▴ 20
0
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3
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1.5k
views
Coverage profile comparison
Targeted sequencing correlation coverage euclid clustering
6.4 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 6.5 years ago by 68k • written 6.5 years ago by ▴ 10
0
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0
replies
812
views
DESeq aligned with HOPACH for clustering
clustering
6.7 years ago ss • 0
7
votes
6
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6.8k
views
scaling data for clustering heat map
edger heatmap clustering differential gene expression rnaseq
updated 6.8 years ago by 52k • written 6.8 years ago by ▴ 60
0
votes
4
replies
1.9k
views
Why SPADE package has been removed from bioconductor?
spade release remove clustering
updated 6.8 years ago by 68k • written 6.8 years ago by • 0
0
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1
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1.3k
views
Global Trend Analysis using results from EdgeR
EdgeR clustering differential gene expression consensusclusterplus kmeans
updated 6.9 years ago by ★ 28k • written 6.9 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 7.0 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
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 12 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
7.4 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
replies
3.4k
views
Choosing genes for clustering
limma clustering differential gene expression hierarchical clustering feature selection
7.5 years ago lirongrossmann ▴ 80
1
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3
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1.9k
views
Selecting genes that best separate between two groups
limma genefilter ttest clustering TPM
7.5 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 7.5 years ago by 52k • written 7.5 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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6.2k
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
replies
1.8k
views
OrgDb for Tetrahymena thermophila
annotation clustering
updated 7.8 years ago by ★ 4.1k • written 7.8 years ago by • 0
1
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1
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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 9.5 years ago by ▴ 840
1
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1
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2.8k
views
ConsensusClusterPlus matrix error
bioconductor clustering consensusclusterplus
8.1 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
reply
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 8.8 years ago by ▴ 90
50 results • Page 1 of 1
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Answer: Improving performance of edgeR and limma while adjusting for multiple confounder by Gordon Smyth 52k
We recommend that you use voomLmFit() instead of voom+lmFit. We are pretty proud of the speed of glmQLFit and voom, and we hadn't expected…
Answer: Merging EPICV1 and V2 betas by James W. MacDonald 68k
It appears that [SeSAMe][1] has functions meant to do that sort of thing. [1]: https://bioconductor.org/packages/release/bioc/vignet…
Comment: getBM from biomaRt inconsistencies found with .gtf files across multiple species by Benjamin ▴ 20
I have received a response from Ensembl regarding the items I have listed above. I wanted to post it here and will continue to post update…
Answer: Error in cnetplot by Guido Hooiveld ★ 4.1k
Unfortunately you did not show how you generated your input data (the object `enrichment`), nor did you show the output from `sessionInfo()…
Answer: getBM from biomaRt inconsistencies found with .gtf files across multiple species by Mike Smith ★ 6.6k
I think this is because Ensembl can assign different Gene IDs to "the same gene" if it is found both on a standard chromosome and a scaffol…
Votes
Answer: Merging annotation with differential expression output
Answer: Explannation for ROAST results
Comment: Limma comparing gene expression between base line and one treatment
Answer: Is there any chance to solve "the model matrix is not full rank" in DESeq2?
clusterProfiler-GO enrichment Error
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