Showing : clustering • reset
1
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723
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Expected memory usage for analyzing large single-cell seq datasets (> 450,000 cells)?
BigData Clustering memory SingleCellExperiment edgeR
updated 4 months ago by ★ 28k • written 4 months ago by • 0
2
votes
3
replies
740
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"could not find function "readTSGE" in package ctsGE" Error occurs when trying to follow ctsGE package instructions.
GeneExpression Clustering ctsGE
9 months ago jbgnielson • 0
0
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3
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785
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Clustering coefficient of synteny network
Network syntenet Clustering coefficient
17 months ago Alexandros • 0
0
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2
replies
1.1k
views
Scaling and normalization by deconvolution of SMART-Seq 2 data
scran Clustering SingleCell Normalization
21 months ago Assa Yeroslaviz ★ 1.5k
0
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0
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624
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maSigPro visualizing individually each plot from each cluster
plot maSigPro Clustering
2.3 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 2.3 years ago by ▴ 50 • written 2.3 years ago by ▴ 20
0
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1
reply
802
views
DeSeq Strategies for run to run Replication
DESeq2 Normalization Clustering replicate
updated 2.3 years ago by 43k • written 2.3 years ago by • 0
4
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3
replies
2.1k
views
SingleCellExperiment: Edit cluster IDs in colLabels
scran Clustering SingleCellExperiment annotate cluster
updated 2.4 years ago by 67k • written 2.4 years ago by ▴ 10
2
votes
2
replies
1.5k
views
How to judge DEG analysis of these samples could be done by using limma::voom
limma Clustering voom RNA-Seq
2.4 years ago Yang Shi ▴ 10
0
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0
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967
views
The gene clusters from the WGCNA dendrogram output are not in order
Clustering WGCNA
2.6 years ago chiwut.wong • 0
0
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0
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955
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Only 1 gene/ feature is present in module after WGCNA analysis
RNASeq Clustering cluster WGCNA
2.7 years ago chiwut.wong • 0
0
votes
1
reply
748
views
Error running hierClust
hierClust R SNPs clustering
updated 2.7 years ago by 67k • written 2.7 years ago by • 0
0
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0
replies
1.1k
views
ConsensusClusterPlus: annotate a class to the heatmap
Clustering ConsensusClusterPlus
3.3 years ago Gian ▴ 30
3
votes
2
replies
2.7k
views
Clustering differentially expressed genes in response to multiple treatments (using edgeR)
edger complexheatmap R clustering
updated 4.6 years ago by 52k • written 4.6 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 4.9 years ago by ▴ 80 • written 4.9 years ago by ▴ 40
0
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1
reply
2.1k
views
Evaluating HCPC clusters from FactoMineR using cluster.stats from fpc library
clustering r fpc FactoMineR
5.4 years ago anahochmanova • 0
0
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3
replies
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 5.6 years ago by 67k • written 5.6 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 5.6 years ago by 67k • written 5.6 years ago by ▴ 120
0
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1
reply
1.4k
views
Consensus Cluster Plus pre-computed distance matrix
consensusclusterplus distance clustering
updated 5.7 years ago by ▴ 420 • written 5.7 years ago by • 0
1
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2
replies
1.7k
views
Dunn Index for Clusters from scRNA-Seq
scRNA-Seq clustering scater scran dunn index
updated 5.8 years ago by ★ 28k • written 5.8 years ago by ▴ 60
2
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4
replies
2.8k
views
Silhouette Plots for Clustering Quality (Multiple Algorithm)
scRNA-Seq RNA-Seq Clustering Silhouette Plot
updated 5.9 years ago by ★ 28k • written 5.9 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 6.1 years ago by ★ 28k • written 6.1 years ago by ▴ 20
0
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3
replies
1.4k
views
Coverage profile comparison
Targeted sequencing correlation coverage euclid clustering
6.2 years ago faramer86 • 0
3
votes
3
replies
1.2k
views
how to plot trends for differentialy expressed genes from normalized count matrix (EdgeR)
edger clustering visualization
updated 6.2 years ago by 67k • written 6.2 years ago by ▴ 10
0
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0
replies
766
views
DESeq aligned with HOPACH for clustering
clustering
6.4 years ago ss • 0
7
votes
6
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6.5k
views
scaling data for clustering heat map
edger heatmap clustering differential gene expression rnaseq
updated 6.6 years ago by 52k • written 6.6 years ago by ▴ 60
0
votes
4
replies
1.8k
views
Why SPADE package has been removed from bioconductor?
spade release remove clustering
updated 6.6 years ago by 67k • written 6.6 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 6.7 years ago by ★ 28k • written 6.7 years ago by • 0
0
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0
replies
1.2k
views
Add samples labels with ConsensusClusterPlus
consensusclusterplus microarray clustering
6.7 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
7.0 years ago • updated 6.8 years ago Daniel Brewer ▴ 100
1
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3
replies
1.4k
views
Clustering of samples based on specific gene sets
microarray differential gene expression gene set analysis clustering
6.8 years ago cherlyn.t • 0
0
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1
reply
1.2k
views
ConsensusClusterPlus without figures
clustering
updated 9 months ago by • 0 • written 7.1 years ago by • 0
0
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4
replies
1.5k
views
Gene clusters based on gene expression across samples
kmeans gene expression clustering
7.2 years ago • updated 7.1 years ago Jane Merlevede ▴ 90
0
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2
replies
2.3k
views
How to use RUVSeq in clustering problems?
ruvseq rna-seq clustering
updated 7.2 years ago by ▴ 980 • written 7.2 years ago by ▴ 50
0
votes
5
replies
3.0k
views
Choosing genes for clustering
limma clustering differential gene expression hierarchical clustering feature selection
7.3 years ago • updated 7.2 years ago lirongrossmann ▴ 80
1
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3
replies
1.8k
views
Selecting genes that best separate between two groups
limma genefilter ttest clustering TPM
7.3 years ago lirongrossmann ▴ 80
11
votes
8
replies
12k
views
Limma and batch effect
limma differential gene expression clustering removebatcheffect
updated 7.3 years ago by 52k • written 7.3 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 7.4 years ago by ▴ 20
0
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1
reply
2.2k
views
Observation/case weighting in cluster analysis in R
hclust hierarchical clustering clustering weight
updated 7.4 years ago by ★ 28k • written 7.4 years ago by • 0
6
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2
replies
5.8k
views
Cell type specific cell markers for Seurat based analysis.
single cell seurat clustering
updated 7.4 years ago by ▴ 40 • written 7.4 years ago by ▴ 20
1
vote
4
replies
1.7k
views
OrgDb for Tetrahymena thermophila
annotation clustering
updated 7.6 years ago by ★ 4.1k • written 7.6 years ago by • 0
1
vote
1
reply
7.0k
views
WGCNA: Different Detect Cut Heights Across Multiple Blocks
wgcna clustering gene expression
updated 7.7 years ago by ★ 3.0k • written 7.7 years ago by ▴ 10
3
votes
1
reply
10k
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 7.7 years ago by ▴ 20 • written 9.3 years ago by ▴ 840
1
vote
2
replies
2.6k
views
How to adjust the parameters of WGCNA
WGCNA RNA-seq co-expression network module clustering
updated 7.9 years ago by ★ 3.0k • written 7.9 years ago by • 0
1
vote
1
reply
2.7k
views
ConsensusClusterPlus matrix error
bioconductor clustering consensusclusterplus
7.9 years ago kyn ▴ 10
0
votes
5
replies
2.9k
views
Questions on using clusterProfiler
clustering clusterprofiler
8.2 years ago zhangducsu • 0
0
votes
1
reply
1.8k
views
Question about seed in ConsensusClusterPlus, can't repeat the result
bioconductor consensusclusterplus clustering
8.2 years ago afraTW • 0
0
votes
3
replies
2.4k
views
maSigPro genes from clusters
masigpro clustering
updated 7 months ago by • 0 • written 8.5 years ago by • 0
0
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0
replies
1.3k
views
Running Mclust package in R, using maximum a posteriori (MAP)
r mclust clustering
8.5 years ago mabdulsa • 0
0
votes
3
replies
2.7k
views
Prior Control with Mclust package
R mclust clustering
updated 8.5 years ago by ▴ 510 • written 8.6 years ago by • 0
50 results • Page 1 of 1
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Answer: Cross-validation with multiple control subgroups in limma by Gordon Smyth 52k
limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Robert Castelo ★ 3.4k
Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS by Aidan ▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings? by Michael Love 43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by xiaofeiwang198266 • 0
Thanks for your reply!
Votes
C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
A: Expected counts from RSEM in DESeq2
A: Using RSEM reads for DESeq2
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