Showing : clustering • reset
1
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2.0k
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Expected memory usage for analyzing large single-cell seq datasets (> 450,000 cells)?
BigData Clustering memory SingleCellExperiment edgeR
updated 13 months ago by ★ 29k • written 13 months ago by • 0
2
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3
replies
951
views
"could not find function "readTSGE" in package ctsGE" Error occurs when trying to follow ctsGE package instructions.
GeneExpression Clustering ctsGE
18 months ago jbgnielson • 0
0
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3
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1.2k
views
Clustering coefficient of synteny network
Network syntenet Clustering coefficient
2.2 years ago Alexandros • 0
0
votes
2
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1.5k
views
Scaling and normalization by deconvolution of SMART-Seq 2 data
scran Clustering SingleCell Normalization
2.5 years ago Assa Yeroslaviz ★ 1.5k
0
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0
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776
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maSigPro visualizing individually each plot from each cluster
plot maSigPro Clustering
3.0 years ago oseias.rf.junior • 0
0
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1
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1.6k
views
WGCNA - Network construction and module detection
gene Clustering wgcna flashclust
updated 3.0 years ago by ▴ 50 • written 3.0 years ago by ▴ 20
0
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5
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2.3k
views
DeSeq Strategies for run to run Replication
DESeq2 Normalization Clustering replicate
updated 3 months ago by 43k • written 3.0 years ago by • 0
4
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3
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2.6k
views
SingleCellExperiment: Edit cluster IDs in colLabels
scran Clustering SingleCellExperiment annotate cluster
updated 3.1 years ago by 68k • written 3.1 years ago by ▴ 10
2
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2
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1.9k
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How to judge DEG analysis of these samples could be done by using limma::voom
limma Clustering voom RNA-Seq
3.1 years ago Yang Shi ▴ 10
0
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0
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1.3k
views
The gene clusters from the WGCNA dendrogram output are not in order
Clustering WGCNA
3.4 years ago chiwut.wong • 0
0
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0
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1.1k
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Only 1 gene/ feature is present in module after WGCNA analysis
RNASeq Clustering cluster WGCNA
3.4 years ago chiwut.wong • 0
0
votes
1
reply
889
views
Error running hierClust
hierClust R SNPs clustering
updated 3.4 years ago by 68k • written 3.5 years ago by • 0
0
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0
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1.3k
views
ConsensusClusterPlus: annotate a class to the heatmap
Clustering ConsensusClusterPlus
4.0 years ago Gian ▴ 30
3
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2
replies
3.5k
views
Clustering differentially expressed genes in response to multiple treatments (using edgeR)
edger complexheatmap R clustering
updated 5.4 years ago by 53k • written 5.4 years ago by • 0
0
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4
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2.1k
views
coseq plotting error: no method for coercing this S4 class to a vector
coseq RNAseq clustering
updated 5.6 years ago by ▴ 80 • written 5.6 years ago by ▴ 40
0
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1
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2.4k
views
Evaluating HCPC clusters from FactoMineR using cluster.stats from fpc library
clustering r fpc FactoMineR
6.1 years ago anahochmanova • 0
0
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3
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1.3k
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 6.3 years ago by 68k • written 6.3 years ago by • 0
1
vote
6
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2.3k
views
edgeR removing batch effect before using expression data for clustering
edger r batcheffect clustering removeBatchEffect
updated 6.3 years ago by 68k • written 6.3 years ago by ▴ 120
0
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1
reply
1.8k
views
Consensus Cluster Plus pre-computed distance matrix
consensusclusterplus distance clustering
updated 6.5 years ago by ▴ 420 • written 6.5 years ago by • 0
1
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2
replies
2.0k
views
Dunn Index for Clusters from scRNA-Seq
scRNA-Seq clustering scater scran dunn index
updated 6.5 years ago by ★ 29k • written 6.5 years ago by ▴ 60
2
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4
replies
3.3k
views
Silhouette Plots for Clustering Quality (Multiple Algorithm)
scRNA-Seq RNA-Seq Clustering Silhouette Plot
updated 6.6 years ago by ★ 29k • written 6.6 years ago by ▴ 60
2
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6
replies
2.4k
views
Change the number of clusters with scater
scater scran scrnaseq clustering
updated 6.8 years ago by ★ 29k • written 6.8 years ago by ▴ 20
0
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3
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1.6k
views
Coverage profile comparison
Targeted sequencing correlation coverage euclid clustering
6.9 years ago faramer86 • 0
3
votes
3
replies
1.4k
views
how to plot trends for differentialy expressed genes from normalized count matrix (EdgeR)
edger clustering visualization
updated 7.0 years ago by 68k • written 7.0 years ago by ▴ 10
0
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0
replies
882
views
DESeq aligned with HOPACH for clustering
clustering
7.1 years ago ss • 0
7
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6
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7.2k
views
scaling data for clustering heat map
edger heatmap clustering differential gene expression rnaseq
updated 7.3 years ago by 53k • written 7.3 years ago by ▴ 60
0
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4
replies
2.0k
views
Why SPADE package has been removed from bioconductor?
spade release remove clustering
updated 7.3 years ago by 68k • written 7.3 years ago by • 0
0
votes
1
reply
1.4k
views
Global Trend Analysis using results from EdgeR
EdgeR clustering differential gene expression consensusclusterplus kmeans
updated 7.4 years ago by ★ 29k • written 7.4 years ago by • 0
0
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0
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1.4k
views
Add samples labels with ConsensusClusterPlus
consensusclusterplus microarray clustering
7.4 years ago aagata.szymanek • 0
1
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0
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1.8k
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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
7.7 years ago • updated 7.5 years ago Daniel Brewer ▴ 100
1
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3
replies
1.7k
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Clustering of samples based on specific gene sets
microarray differential gene expression gene set analysis clustering
7.5 years ago cherlyn.t • 0
0
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1
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1.4k
views
ConsensusClusterPlus without figures
clustering
updated 18 months ago by • 0 • written 7.8 years ago by • 0
0
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4
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1.8k
views
Gene clusters based on gene expression across samples
kmeans gene expression clustering
7.9 years ago • updated 7.8 years ago Jane Merlevede ▴ 90
0
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2
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2.6k
views
How to use RUVSeq in clustering problems?
ruvseq rna-seq clustering
updated 7.9 years ago by ▴ 980 • written 7.9 years ago by ▴ 50
0
votes
5
replies
3.8k
views
Choosing genes for clustering
limma clustering differential gene expression hierarchical clustering feature selection
8.0 years ago lirongrossmann ▴ 80
1
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3
replies
2.1k
views
Selecting genes that best separate between two groups
limma genefilter ttest clustering TPM
8.0 years ago lirongrossmann ▴ 80
11
votes
8
replies
13k
views
Limma and batch effect
limma differential gene expression clustering removebatcheffect
updated 8.0 years ago by 53k • written 8.0 years ago by ▴ 80
0
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2
replies
5.4k
views
When is centering and scaling needed before doing hierarchical clustering?
clustering hierarchical clustering
written 8.1 years ago by ▴ 20
0
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1
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2.5k
views
Observation/case weighting in cluster analysis in R
hclust hierarchical clustering clustering weight
updated 8.1 years ago by ★ 29k • written 8.1 years ago by • 0
6
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2
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6.6k
views
Cell type specific cell markers for Seurat based analysis.
single cell seurat clustering
updated 8.2 years ago by ▴ 40 • written 8.2 years ago by ▴ 20
1
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4
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2.0k
views
OrgDb for Tetrahymena thermophila
annotation clustering
updated 8.3 years ago by ★ 4.1k • written 8.3 years ago by • 0
1
vote
1
reply
7.8k
views
WGCNA: Different Detect Cut Heights Across Multiple Blocks
wgcna clustering gene expression
updated 8.4 years ago by ★ 3.0k • written 8.4 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 8.5 years ago by ▴ 20 • written 10.0 years ago by ▴ 840
1
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1
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3.0k
views
ConsensusClusterPlus matrix error
bioconductor clustering consensusclusterplus
8.6 years ago kyn ▴ 10
0
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5
replies
3.3k
views
Questions on using clusterProfiler
clustering clusterprofiler
8.9 years ago zhangducsu • 0
0
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1
reply
2.0k
views
Question about seed in ConsensusClusterPlus, can't repeat the result
bioconductor consensusclusterplus clustering
8.9 years ago afraTW • 0
0
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3
replies
2.7k
views
maSigPro genes from clusters
masigpro clustering
updated 16 months ago by • 0 • written 9.2 years ago by • 0
0
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0
replies
1.5k
views
Running Mclust package in R, using maximum a posteriori (MAP)
r mclust clustering
9.3 years ago mabdulsa • 0
0
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3
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3.0k
views
Prior Control with Mclust package
R mclust clustering
updated 9.3 years ago by ▴ 510 • written 9.3 years ago by • 0
2
votes
6
replies
3.7k
views
Clustering and bootstrapping of RNASeq samples
clustering pvclust vsd edgeR rnaseq
written 9.3 years ago by ▴ 90
374 results • Page 1 of 8
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Comment: Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg? by Michael Love 43k
I moved your post from an "answer" to a "comment". I don't know about `offst()` function, what is the scale or direction, or whether you a…
Comment: Average biological replicates in RNA-seq by boczniak767 ▴ 740
@atpoint Should I first standardise data and then average replicates?
Comment: 3-factor DESeq2 trime-series analysis by gogeni5529 • 0
Thans you @swbarnes2 for the answer. I can see why trying to include all three parameters might be difficult to interpret. But we're inte…
Comment: 3-factor DESeq2 trime-series analysis by swbarnes2 ★ 1.4k
What does your PCA look like? A lot of times, I find that different cell lines are so different from each other, that they should not be d…
Comment: Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg? by yongjie.wang • 0
Thanks for your reply. " normFactors <- exp(-1 * offst(set2)) normFactors <- normFactors / exp(rowMeans(log(normFactors))) normalizat…
Votes
Answer: Limpa Pipeline Order
A: How barcode-plot enrichment is calculated?
A: How barcode-plot enrichment is calculated?
Answer: ROAST compare results with complex design
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
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