Showing : Clustering • reset
2
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2.1k
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Expected memory usage for analyzing large single-cell seq datasets (> 450,000 cells)?
BigData Clustering memory SingleCellExperiment edgeR
updated 15 months ago by ★ 29k • written 15 months ago by • 0
2
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3
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1.1k
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"could not find function "readTSGE" in package ctsGE" Error occurs when trying to follow ctsGE package instructions.
GeneExpression Clustering ctsGE
21 months ago • updated 20 months ago jbgnielson • 0
0
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3
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1.3k
views
Clustering coefficient of synteny network
Network syntenet Clustering coefficient
2.4 years ago Alexandros • 0
0
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2
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1.6k
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Scaling and normalization by deconvolution of SMART-Seq 2 data
scran Clustering SingleCell Normalization
2.6 years ago Assa Yeroslaviz ★ 1.5k
0
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0
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821
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maSigPro visualizing individually each plot from each cluster
plot maSigPro Clustering
3.2 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 3.2 years ago by ▴ 50 • written 3.2 years ago by ▴ 20
0
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5
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2.4k
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DeSeq Strategies for run to run Replication
DESeq2 Normalization Clustering replicate
updated 5 months ago by 43k • written 3.2 years ago by • 0
4
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3
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2.7k
views
SingleCellExperiment: Edit cluster IDs in colLabels
scran Clustering SingleCellExperiment annotate cluster
updated 3.3 years ago by 68k • written 3.3 years ago by ▴ 10
2
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2
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2.0k
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How to judge DEG analysis of these samples could be done by using limma::voom
limma Clustering voom RNA-Seq
3.3 years ago Yang Shi ▴ 10
0
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0
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1.3k
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The gene clusters from the WGCNA dendrogram output are not in order
Clustering WGCNA
3.6 years ago chiwut.wong • 0
0
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0
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1.2k
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Only 1 gene/ feature is present in module after WGCNA analysis
RNASeq Clustering cluster WGCNA
3.6 years ago chiwut.wong • 0
0
votes
1
reply
929
views
Error running hierClust
hierClust R SNPs clustering
updated 3.6 years ago by 68k • written 3.6 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
4.2 years ago Gian ▴ 30
3
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2
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3.5k
views
Clustering differentially expressed genes in response to multiple treatments (using edgeR)
edger complexheatmap R clustering
updated 5.6 years ago by 53k • written 5.6 years ago by • 0
0
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4
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2.2k
views
coseq plotting error: no method for coercing this S4 class to a vector
coseq RNAseq clustering
updated 5.8 years ago by ▴ 80 • written 5.8 years ago by ▴ 40
0
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1
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2.5k
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Evaluating HCPC clusters from FactoMineR using cluster.stats from fpc library
clustering r fpc FactoMineR
6.3 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 6.5 years ago by 68k • written 6.5 years ago by • 0
1
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6
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2.4k
views
edgeR removing batch effect before using expression data for clustering
edger r batcheffect clustering removeBatchEffect
updated 6.5 years ago by 68k • written 6.5 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 6.7 years ago by ▴ 420 • written 6.7 years ago by • 0
1
vote
2
replies
2.1k
views
Dunn Index for Clusters from scRNA-Seq
scRNA-Seq clustering scater scran dunn index
updated 6.7 years ago by ★ 29k • written 6.7 years ago by ▴ 60
2
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4
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3.4k
views
Silhouette Plots for Clustering Quality (Multiple Algorithm)
scRNA-Seq RNA-Seq Clustering Silhouette Plot
updated 6.8 years ago by ★ 29k • written 6.8 years ago by ▴ 60
2
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6
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2.5k
views
Change the number of clusters with scater
scater scran scrnaseq clustering
updated 7.0 years ago by ★ 29k • written 7.0 years ago by ▴ 20
0
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3
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1.7k
views
Coverage profile comparison
Targeted sequencing correlation coverage euclid clustering
7.1 years ago faramer86 • 0
3
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3
replies
1.5k
views
how to plot trends for differentialy expressed genes from normalized count matrix (EdgeR)
edger clustering visualization
updated 7.1 years ago by 68k • written 7.1 years ago by ▴ 10
0
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0
replies
908
views
DESeq aligned with HOPACH for clustering
clustering
7.3 years ago ss • 0
7
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6
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7.3k
views
scaling data for clustering heat map
edger heatmap clustering differential gene expression rnaseq
updated 7.5 years ago by 53k • written 7.5 years ago by ▴ 60
0
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4
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2.1k
views
Why SPADE package has been removed from bioconductor?
spade release remove clustering
updated 7.5 years ago by 68k • written 7.5 years ago by • 0
0
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1
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1.5k
views
Global Trend Analysis using results from EdgeR
EdgeR clustering differential gene expression consensusclusterplus kmeans
updated 7.6 years ago by ★ 29k • written 7.6 years ago by • 0
0
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0
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1.4k
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Add samples labels with ConsensusClusterPlus
consensusclusterplus microarray clustering
7.6 years ago aagata.szymanek • 0
1
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0
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1.8k
views
Job: UK/EU funded PhD Studentship: Detecting novel subtypes of cancer using data science and machine learning
PhD clustering cancer Job
7.9 years ago • updated 7.7 years ago Daniel Brewer ▴ 100
1
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3
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1.7k
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Clustering of samples based on specific gene sets
microarray differential gene expression gene set analysis clustering
7.7 years ago cherlyn.t • 0
0
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1
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1.4k
views
ConsensusClusterPlus without figures
clustering
updated 20 months ago by • 0 • written 8.0 years ago by • 0
0
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4
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1.9k
views
Gene clusters based on gene expression across samples
kmeans gene expression clustering
8.1 years ago • updated 8.0 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 8.1 years ago by ▴ 980 • written 8.1 years ago by ▴ 50
0
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5
replies
3.9k
views
Choosing genes for clustering
limma clustering differential gene expression hierarchical clustering feature selection
8.2 years ago • updated 8.1 years ago lirongrossmann ▴ 80
1
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3
replies
2.2k
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Selecting genes that best separate between two groups
limma genefilter ttest clustering TPM
8.2 years ago lirongrossmann ▴ 80
11
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8
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13k
views
Limma and batch effect
limma differential gene expression clustering removebatcheffect
updated 8.2 years ago by 53k • written 8.2 years ago by ▴ 80
0
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2
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5.5k
views
When is centering and scaling needed before doing hierarchical clustering?
clustering hierarchical clustering
written 8.3 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 8.3 years ago by ★ 29k • written 8.3 years ago by • 0
6
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2
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6.7k
views
Cell type specific cell markers for Seurat based analysis.
single cell seurat clustering
updated 8.4 years ago by ▴ 40 • written 8.4 years ago by ▴ 20
1
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4
replies
2.1k
views
OrgDb for Tetrahymena thermophila
annotation clustering
updated 8.5 years ago by ★ 4.1k • written 8.5 years ago by • 0
1
vote
1
reply
7.9k
views
WGCNA: Different Detect Cut Heights Across Multiple Blocks
wgcna clustering gene expression
updated 8.6 years ago by ★ 3.0k • written 8.6 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 8.6 years ago by ▴ 20 • written 10.2 years ago by ▴ 840
1
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1
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3.1k
views
ConsensusClusterPlus matrix error
bioconductor clustering consensusclusterplus
8.8 years ago kyn ▴ 10
0
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5
replies
3.3k
views
Questions on using clusterProfiler
clustering clusterprofiler
9.1 years ago zhangducsu • 0
0
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1
reply
2.1k
views
Question about seed in ConsensusClusterPlus, can't repeat the result
bioconductor consensusclusterplus clustering
9.1 years ago afraTW • 0
0
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3
replies
2.8k
views
maSigPro genes from clusters
masigpro clustering
updated 18 months ago by • 0 • written 9.4 years ago by • 0
0
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0
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1.5k
views
Running Mclust package in R, using maximum a posteriori (MAP)
r mclust clustering
9.5 years ago mabdulsa • 0
0
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3
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3.1k
views
Prior Control with Mclust package
R mclust clustering
updated 9.5 years ago by ▴ 510 • written 9.5 years ago by • 0
2
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6
replies
3.8k
views
Clustering and bootstrapping of RNASeq samples
clustering pvclust vsd edgeR rnaseq
written 9.5 years ago by ▴ 90
374 results • Page 1 of 8
Recent ...
Replies
Answer: mzR-Rcpp compiler version issue by Laurent Gatto 1.6k
There are two issues here. First, a warning about mzR, that you can safely ignore. It tells you that mzR was compiled using a different …
Comment: Identifying differentially expressed genes in individual samples from a large co by jamie.gearing ▴ 60
Great. Yes, something descriptive is probably good enough, even if the p-values themselves are not so rigorous. Thanks very much Gordon!
Comment: Co-occurrence Network Analysis between Algae and Bacteria by Stefano Mangiola ▴ 40
Just a placeholder, that we are extending `sccomp` to co-occurrence analyses. Yours could be a good use-case to test first. We will be in t…
Answer: DESeq2 design for haplotype MPRA by aimesd808 • 0
I appreciate you telling me about this. Now it's crystal plain to me. Publish this: https://support.bioconductor.org/p/9162649/
Answer: Extract snp information from genomic regions with biomaRt -> "oaries_snp" by Kevin Blighe ★ 4.0k
My sincere apologies that my colleagues had ignored your question. The error occurs because the "chromosomal_region" filter is not valid…
Votes
Answer: Identifying differentially expressed genes in individual samples from a large co
Answer: Identifying differentially expressed genes in individual samples from a large co
Bioconductor Seminar Series - Dec 2: Deep-learning Gene Perturbation Effect Prediction
Comment: What R/Bioconductor tools would you recommend for the analysis of sncRNA, specif
Comment: Error installing Seqinfo
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Popular Question to Gordon Smyth 53k
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