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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852
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"could not find function "readTSGE" in package ctsGE" Error occurs when trying to follow ctsGE package instructions.
GeneExpression Clustering ctsGE
14 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
22 months ago • updated 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
2.1 years ago Assa Yeroslaviz ★ 1.5k
0
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0
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699
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maSigPro visualizing individually each plot from each cluster
plot maSigPro Clustering
2.7 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 2.7 years ago by ▴ 20
0
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3
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1.7k
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DeSeq Strategies for run to run Replication
DESeq2 Normalization Clustering replicate
updated 7 days ago by 43k • written 2.7 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
2.8 years ago Yang Shi ▴ 10
0
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0
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1.2k
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The gene clusters from the WGCNA dendrogram output are not in order
Clustering WGCNA
3.0 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
votes
1
reply
816
views
Error running hierClust
hierClust R SNPs clustering
updated 3.1 years ago by 68k • written 3.1 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
3.7 years ago Gian ▴ 30
3
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2
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3.2k
views
Clustering differentially expressed genes in response to multiple treatments (using edgeR)
edger complexheatmap R clustering
updated 5.0 years ago by 52k • written 5.0 years ago by • 0
0
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4
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2.0k
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 5.3 years ago by ▴ 40
0
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1
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2.3k
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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
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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 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 6.0 years ago by 68k • written 6.0 years ago by ▴ 120
0
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1
reply
1.6k
views
Consensus Cluster Plus pre-computed distance matrix
consensusclusterplus distance clustering
updated 6.1 years ago by ▴ 420 • written 6.1 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
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1.3k
views
how to plot trends for differentialy expressed genes from normalized count matrix (EdgeR)
edger clustering visualization
updated 6.6 years ago by 68k • written 6.6 years ago by ▴ 10
0
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0
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821
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
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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
7.1 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
7.4 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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1.3k
views
ConsensusClusterPlus without figures
clustering
updated 13 months ago by • 0 • written 7.5 years ago by • 0
0
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4
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1.7k
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Gene clusters based on gene expression across samples
kmeans gene expression clustering
7.5 years ago Jane Merlevede ▴ 90
0
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2
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2.5k
views
How to use RUVSeq in clustering problems?
ruvseq rna-seq clustering
updated 7.6 years ago by ▴ 980 • written 7.6 years ago by ▴ 50
0
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5
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3.5k
views
Choosing genes for clustering
limma clustering differential gene expression hierarchical clustering feature selection
7.6 years ago lirongrossmann ▴ 80
1
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3
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2.0k
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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
views
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 7.7 years ago by ▴ 20
0
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1
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2.4k
views
Observation/case weighting in cluster analysis in R
hclust hierarchical clustering clustering weight
updated 7.8 years ago by ★ 28k • written 7.8 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 7.8 years ago by ▴ 40 • written 7.8 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
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7.5k
views
WGCNA: Different Detect Cut Heights Across Multiple Blocks
wgcna clustering gene expression
updated 8.1 years ago by ★ 3.0k • written 8.1 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 8.1 years ago by ▴ 20 • written 9.6 years ago by ▴ 840
1
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1
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2.9k
views
ConsensusClusterPlus matrix error
bioconductor clustering consensusclusterplus
8.2 years ago kyn ▴ 10
0
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5
replies
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
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Question about seed in ConsensusClusterPlus, can't repeat the result
bioconductor consensusclusterplus clustering
8.6 years ago afraTW • 0
0
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3
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2.5k
views
maSigPro genes from clusters
masigpro clustering
updated 11 months ago by • 0 • written 8.9 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
8.9 years ago mabdulsa • 0
0
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3
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2.9k
views
Prior Control with Mclust package
R mclust clustering
updated 8.9 years ago by ▴ 510 • written 8.9 years ago by • 0
2
votes
6
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3.6k
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; Error: No sites have activity greater than filter value by etiennedanis • 0
Same issue here as well. This is very weird because I never had this issue before. I started observing this issue with a new ATAC-seq da…
Comment: GSEA preranked analysis downstream of DEseq2 by Ajay • 0
`logFC * -log10(pval)` seems to be the pi-score proposed in this [paper][1] [1]: https://pmc.ncbi.nlm.nih.gov/articles/PMC3957066/
Comment: error in ChAMP loading file by janwilseo • 0
Any update on this post? I also had an issue with this. [erosion control](https://charlestonhydroseeding.com/)
Answer: CluserProfiler message "No gene can be mapped" by James W. MacDonald 68k
Two things. First, the order of your term2gene is backwards (should be term and then gene, like the name), and by default `enricher` adjust…
Comment: Controlling for batch and estrus cycle using DESeq2 in RNA-seq analysis by donnycrimson • 0
One potential workaround might be to adjust for these factors using a combination of design matrices perhaps including batch as a covariate…
Votes
Answer: DiffBind; Error: No sites have activity greater than filter value
DiffBind; Error: No sites have activity greater than filter value
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
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