Showing : Clustering • reset
1
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878
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Expected memory usage for analyzing large single-cell seq datasets (> 450,000 cells)?
BigData Clustering memory SingleCellExperiment edgeR
updated 5 months ago by ★ 28k • written 5 months ago by • 0
2
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3
replies
771
views
"could not find function "readTSGE" in package ctsGE" Error occurs when trying to follow ctsGE package instructions.
GeneExpression Clustering ctsGE
11 months ago jbgnielson • 0
0
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3
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897
views
Clustering coefficient of synteny network
Network syntenet Clustering coefficient
19 months ago Alexandros • 0
0
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2
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1.2k
views
Scaling and normalization by deconvolution of SMART-Seq 2 data
scran Clustering SingleCell Normalization
22 months ago Assa Yeroslaviz ★ 1.5k
0
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0
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645
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maSigPro visualizing individually each plot from each cluster
plot maSigPro Clustering
2.4 years ago oseias.rf.junior • 0
0
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1
reply
1.1k
views
WGCNA - Network construction and module detection
gene Clustering wgcna flashclust
updated 2.4 years ago by ▴ 50 • written 2.4 years ago by ▴ 20
0
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1
reply
821
views
DeSeq Strategies for run to run Replication
DESeq2 Normalization Clustering replicate
updated 2.4 years ago by 43k • written 2.4 years ago by • 0
4
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3
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2.2k
views
SingleCellExperiment: Edit cluster IDs in colLabels
scran Clustering SingleCellExperiment annotate cluster
updated 2.5 years ago by 67k • written 2.5 years ago by ▴ 10
2
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2
replies
1.6k
views
How to judge DEG analysis of these samples could be done by using limma::voom
limma Clustering voom RNA-Seq
2.5 years ago Yang Shi ▴ 10
0
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0
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1.0k
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The gene clusters from the WGCNA dendrogram output are not in order
Clustering WGCNA
2.8 years ago chiwut.wong • 0
0
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0
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979
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Only 1 gene/ feature is present in module after WGCNA analysis
RNASeq Clustering cluster WGCNA
2.8 years ago chiwut.wong • 0
0
votes
1
reply
766
views
Error running hierClust
hierClust R SNPs clustering
updated 2.8 years ago by 67k • written 2.8 years ago by • 0
0
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0
replies
1.1k
views
ConsensusClusterPlus: annotate a class to the heatmap
Clustering ConsensusClusterPlus
3.4 years ago Gian ▴ 30
3
votes
2
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2.8k
views
Clustering differentially expressed genes in response to multiple treatments (using edgeR)
edger complexheatmap R clustering
updated 4.8 years ago by 52k • written 4.8 years ago by • 0
0
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4
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1.8k
views
coseq plotting error: no method for coercing this S4 class to a vector
coseq RNAseq clustering
updated 5.0 years ago by ▴ 80 • written 5.0 years ago by ▴ 40
0
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1
reply
2.2k
views
Evaluating HCPC clusters from FactoMineR using cluster.stats from fpc library
clustering r fpc FactoMineR
5.5 years ago anahochmanova • 0
0
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3
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1.1k
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 5.7 years ago by 67k • written 5.7 years ago by • 0
1
vote
6
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2.0k
views
edgeR removing batch effect before using expression data for clustering
edger r batcheffect clustering removeBatchEffect
updated 5.7 years ago by 67k • written 5.7 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 5.8 years ago by ▴ 420 • written 5.8 years ago by • 0
1
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2
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1.7k
views
Dunn Index for Clusters from scRNA-Seq
scRNA-Seq clustering scater scran dunn index
updated 5.9 years ago by ★ 28k • written 5.9 years ago by ▴ 60
2
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4
replies
2.9k
views
Silhouette Plots for Clustering Quality (Multiple Algorithm)
scRNA-Seq RNA-Seq Clustering Silhouette Plot
updated 6.0 years ago by ★ 28k • written 6.0 years ago by ▴ 60
2
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6
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2.0k
views
Change the number of clusters with scater
scater scran scrnaseq clustering
updated 6.2 years ago by ★ 28k • written 6.2 years ago by ▴ 20
0
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3
replies
1.4k
views
Coverage profile comparison
Targeted sequencing correlation coverage euclid clustering
6.3 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 6.3 years ago by 67k • written 6.3 years ago by ▴ 10
0
votes
0
replies
781
views
DESeq aligned with HOPACH for clustering
clustering
6.5 years ago ss • 0
7
votes
6
replies
6.6k
views
scaling data for clustering heat map
edger heatmap clustering differential gene expression rnaseq
updated 6.7 years ago by 52k • written 6.7 years ago by ▴ 60
0
votes
4
replies
1.8k
views
Why SPADE package has been removed from bioconductor?
spade release remove clustering
updated 6.7 years ago by 67k • written 6.7 years ago by • 0
0
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1
reply
1.2k
views
Global Trend Analysis using results from EdgeR
EdgeR clustering differential gene expression consensusclusterplus kmeans
updated 6.8 years ago by ★ 28k • written 6.8 years ago by • 0
0
votes
0
replies
1.3k
views
Add samples labels with ConsensusClusterPlus
consensusclusterplus microarray clustering
6.8 years ago aagata.szymanek • 0
1
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0
replies
1.6k
views
Job: UK/EU funded PhD Studentship: Detecting novel subtypes of cancer using data science and machine learning
PhD clustering cancer Job
7.1 years ago • updated 6.9 years ago Daniel Brewer ▴ 100
1
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3
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1.5k
views
Clustering of samples based on specific gene sets
microarray differential gene expression gene set analysis clustering
6.9 years ago cherlyn.t • 0
0
votes
1
reply
1.2k
views
ConsensusClusterPlus without figures
clustering
updated 11 months ago by • 0 • written 7.2 years ago by • 0
0
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4
replies
1.6k
views
Gene clusters based on gene expression across samples
kmeans gene expression clustering
7.3 years ago • updated 7.2 years ago Jane Merlevede ▴ 90
0
votes
2
replies
2.3k
views
How to use RUVSeq in clustering problems?
ruvseq rna-seq clustering
updated 7.3 years ago by ▴ 980 • written 7.3 years ago by ▴ 50
0
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5
replies
3.1k
views
Choosing genes for clustering
limma clustering differential gene expression hierarchical clustering feature selection
7.4 years ago • updated 7.3 years ago lirongrossmann ▴ 80
1
vote
3
replies
1.8k
views
Selecting genes that best separate between two groups
limma genefilter ttest clustering TPM
7.4 years ago lirongrossmann ▴ 80
11
votes
8
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12k
views
Limma and batch effect
limma differential gene expression clustering removebatcheffect
updated 7.4 years ago by 52k • written 7.4 years ago by ▴ 80
0
votes
2
replies
5.0k
views
When is centering and scaling needed before doing hierarchical clustering?
clustering hierarchical clustering
written 7.5 years ago by ▴ 20
0
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1
reply
2.3k
views
Observation/case weighting in cluster analysis in R
hclust hierarchical clustering clustering weight
updated 7.5 years ago by ★ 28k • written 7.5 years ago by • 0
6
votes
2
replies
5.9k
views
Cell type specific cell markers for Seurat based analysis.
single cell seurat clustering
updated 7.6 years ago by ▴ 40 • written 7.6 years ago by ▴ 20
1
vote
4
replies
1.7k
views
OrgDb for Tetrahymena thermophila
annotation clustering
updated 7.7 years ago by ★ 4.1k • written 7.7 years ago by • 0
1
vote
1
reply
7.1k
views
WGCNA: Different Detect Cut Heights Across Multiple Blocks
wgcna clustering gene expression
updated 7.8 years ago by ★ 3.0k • written 7.8 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 7.8 years ago by ▴ 20 • written 9.4 years ago by ▴ 840
1
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1
reply
2.7k
views
ConsensusClusterPlus matrix error
bioconductor clustering consensusclusterplus
8.0 years ago kyn ▴ 10
0
votes
5
replies
3.0k
views
Questions on using clusterProfiler
clustering clusterprofiler
8.3 years ago zhangducsu • 0
0
votes
1
reply
1.9k
views
Question about seed in ConsensusClusterPlus, can't repeat the result
bioconductor consensusclusterplus clustering
8.3 years ago afraTW • 0
0
votes
3
replies
2.4k
views
maSigPro genes from clusters
masigpro clustering
updated 8 months ago by • 0 • written 8.6 years ago by • 0
0
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0
replies
1.4k
views
Running Mclust package in R, using maximum a posteriori (MAP)
r mclust clustering
8.6 years ago mabdulsa • 0
0
votes
3
replies
2.7k
views
Prior Control with Mclust package
R mclust clustering
updated 8.7 years ago by ▴ 510 • written 8.7 years ago by • 0
2
votes
6
replies
3.4k
views
Clustering and bootstrapping of RNASeq samples
clustering pvclust vsd edgeR rnaseq
written 8.7 years ago by ▴ 90
50 results • Page 1 of 1
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Comment: build samplesheet and plot profile by yf • 0
![enter image description here][1] [1]: /media/images/8ea93bd0-bc90-443d-a332-4701f54a
Answer: I am having issues with bowtie2_build by James W. MacDonald 67k
Is proof.fa an actual FASTA file? Have you tried using the demo data that comes with the package? See the [vignette under Build Bowtie Inde…
Answer: DEG analysis across multiple timepoints, treatments and tissues by Michael Love 43k
Yes, if you think the entire time course can be modified by tissue effects then you would include another set of interaction terms. I re…
Comment: How to visualize these pathways using pathview by Guido Hooiveld ★ 4.1k
FYI: a similar, if not identical issue has been reported before (`pathview` has problems visualizing some pathways, but not all). You likel…
Comment: Why select top highly expressed genes based on normalized counts, but then plot by Quang NN ▴ 10
I see. Thank you ATpoint!
Votes
A: Doubt about the "zero expression" genes or genes with no reads at all in the co
Answer: Unable to install nloptr
Answer: ensembldb for Homo Sapiens organism containing superfluous SYMBOL genes?
C: How does edgeR cpm function calculate log(CPM) values?
Answer: Selection of correct coefficients or contrasts in DESeq2
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