Showing : clustering • reset
2
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3
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440
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"could not find function "readTSGE" in package ctsGE" Error occurs when trying to follow ctsGE package instructions.
GeneExpression Clustering ctsGE
8 weeks ago jbgnielson • 0
0
votes
3
replies
554
views
Clustering coefficient of synteny network
Network syntenet Clustering coefficient
9 months ago Alexandros • 0
0
votes
2
replies
697
views
Scaling and normalization by deconvolution of SMART-Seq 2 data
scran Clustering SingleCell Normalization
13 months ago Assa Yeroslaviz ★ 1.5k
0
votes
0
replies
421
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maSigPro visualizing individually each plot from each cluster
plot maSigPro Clustering
20 months ago oseias.rf.junior • 0
0
votes
1
reply
805
views
WGCNA - Network construction and module detection
gene Clustering wgcna flashclust
updated 20 months ago by ▴ 50 • written 20 months ago by ▴ 20
0
votes
1
reply
631
views
DeSeq Strategies for run to run Replication
DESeq2 Normalization Clustering replicate
updated 20 months ago by 41k • written 20 months ago by • 0
4
votes
3
replies
1.5k
views
SingleCellExperiment: Edit cluster IDs in colLabels
scran Clustering SingleCellExperiment annotate cluster
updated 20 months ago by 65k • written 20 months ago by ▴ 10
2
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2
replies
1.2k
views
How to judge DEG analysis of these samples could be done by using limma::voom
limma Clustering voom RNA-Seq
21 months ago Yang Shi ▴ 10
0
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0
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746
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The gene clusters from the WGCNA dendrogram output are not in order
Clustering WGCNA
24 months ago chiwut.wong • 0
0
votes
0
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754
views
Only 1 gene/ feature is present in module after WGCNA analysis
RNASeq Clustering cluster WGCNA
2.0 years ago chiwut.wong • 0
0
votes
1
reply
596
views
Error running hierClust
hierClust R SNPs clustering
updated 2.1 years ago by 65k • written 2.1 years ago by • 0
0
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0
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822
views
ConsensusClusterPlus: annotate a class to the heatmap
Clustering ConsensusClusterPlus
2.6 years ago Gian ▴ 30
3
votes
2
replies
2.1k
views
Clustering differentially expressed genes in response to multiple treatments (using edgeR)
edger complexheatmap R clustering
updated 4.0 years ago by 50k • written 4.0 years ago by • 0
0
votes
4
replies
1.3k
views
coseq plotting error: no method for coercing this S4 class to a vector
coseq RNAseq clustering
updated 4.2 years ago by ▴ 80 • written 4.3 years ago by ▴ 30
0
votes
1
reply
1.9k
views
Evaluating HCPC clusters from FactoMineR using cluster.stats from fpc library
clustering r fpc FactoMineR
4.7 years ago anahochmanova • 0
0
votes
3
replies
928
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 4.9 years ago by 65k • written 4.9 years ago by • 0
1
vote
6
replies
1.6k
views
edgeR removing batch effect before using expression data for clustering
edger r batcheffect clustering removeBatchEffect
updated 5.0 years ago by 65k • written 5.0 years ago by ▴ 110
0
votes
1
reply
1.2k
views
Consensus Cluster Plus pre-computed distance matrix
consensusclusterplus distance clustering
updated 5.1 years ago by ▴ 420 • written 5.1 years ago by • 0
1
vote
2
replies
1.4k
views
Dunn Index for Clusters from scRNA-Seq
scRNA-Seq clustering scater scran dunn index
updated 5.1 years ago by ★ 28k • written 5.1 years ago by ▴ 50
2
votes
4
replies
2.3k
views
Silhouette Plots for Clustering Quality (Multiple Algorithm)
scRNA-Seq RNA-Seq Clustering Silhouette Plot
updated 5.2 years ago by ★ 28k • written 5.2 years ago by ▴ 50
2
votes
6
replies
1.7k
views
Change the number of clusters with scater
scater scran scrnaseq clustering
updated 5.4 years ago by ★ 28k • written 5.4 years ago by ▴ 20
0
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3
replies
1.2k
views
Coverage profile comparison
Targeted sequencing correlation coverage euclid clustering
5.5 years ago faramer86 • 0
3
votes
3
replies
1.1k
views
how to plot trends for differentialy expressed genes from normalized count matrix (EdgeR)
edger clustering visualization
updated 5.6 years ago by 65k • written 5.6 years ago by ▴ 10
0
votes
0
replies
662
views
DESeq aligned with HOPACH for clustering
clustering
5.7 years ago ss • 0
7
votes
6
replies
5.7k
views
scaling data for clustering heat map
edger heatmap clustering differential gene expression rnaseq
updated 5.9 years ago by 50k • written 5.9 years ago by ▴ 60
0
votes
4
replies
1.5k
views
Why SPADE package has been removed from bioconductor?
spade release remove clustering
updated 5.9 years ago by 65k • written 5.9 years ago by • 0
0
votes
1
reply
979
views
Global Trend Analysis using results from EdgeR
EdgeR clustering differential gene expression consensusclusterplus kmeans
updated 6.0 years ago by ★ 28k • written 6.0 years ago by • 0
0
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0
replies
1.0k
views
Add samples labels with ConsensusClusterPlus
consensusclusterplus microarray clustering
6.1 years ago aagata.szymanek • 0
1
vote
0
replies
1.4k
views
Job: UK/EU funded PhD Studentship: Detecting novel subtypes of cancer using data science and machine learning
PhD clustering cancer Job
6.3 years ago • updated 6.1 years ago Daniel Brewer ▴ 100
1
vote
3
replies
1.2k
views
Clustering of samples based on specific gene sets
microarray differential gene expression gene set analysis clustering
6.1 years ago cherlyn.t • 0
0
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1
reply
969
views
ConsensusClusterPlus without figures
clustering
updated 7 weeks ago by • 0 • written 6.5 years ago by • 0
0
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4
replies
1.3k
views
Gene clusters based on gene expression across samples
kmeans gene expression clustering
6.5 years ago Jane Merlevede ▴ 90
0
votes
2
replies
1.9k
views
How to use RUVSeq in clustering problems?
ruvseq rna-seq clustering
updated 6.6 years ago by ▴ 950 • written 6.6 years ago by ▴ 50
0
votes
5
replies
2.4k
views
Choosing genes for clustering
limma clustering differential gene expression hierarchical clustering feature selection
6.6 years ago lirongrossmann ▴ 80
1
vote
3
replies
1.5k
views
Selecting genes that best separate between two groups
limma genefilter ttest clustering TPM
6.6 years ago lirongrossmann ▴ 80
11
votes
8
replies
10k
views
Limma and batch effect
limma differential gene expression clustering removebatcheffect
updated 6.6 years ago by 50k • written 6.6 years ago by ▴ 80
0
votes
2
replies
4.5k
views
When is centering and scaling needed before doing hierarchical clustering?
clustering hierarchical clustering
written 6.7 years ago by ▴ 20
0
votes
1
reply
1.9k
views
Observation/case weighting in cluster analysis in R
hclust hierarchical clustering clustering weight
updated 6.8 years ago by ★ 28k • written 6.8 years ago by • 0
6
votes
2
replies
5.3k
views
Cell type specific cell markers for Seurat based analysis.
single cell seurat clustering
updated 6.8 years ago by ▴ 40 • written 6.8 years ago by ▴ 20
1
vote
4
replies
1.4k
views
OrgDb for Tetrahymena thermophila
annotation clustering
updated 6.9 years ago by ★ 3.9k • written 6.9 years ago by • 0
1
vote
1
reply
6.2k
views
WGCNA: Different Detect Cut Heights Across Multiple Blocks
wgcna clustering gene expression
updated 7.1 years ago by ★ 3.0k • written 7.1 years ago by ▴ 10
3
votes
1
reply
9.7k
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 7.1 years ago by ▴ 20 • written 8.6 years ago by ▴ 830
1
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2
replies
2.2k
views
How to adjust the parameters of WGCNA
WGCNA RNA-seq co-expression network module clustering
updated 7.2 years ago by ★ 3.0k • written 7.2 years ago by • 0
1
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1
reply
2.3k
views
ConsensusClusterPlus matrix error
bioconductor clustering consensusclusterplus
7.2 years ago kyn ▴ 10
0
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5
replies
2.6k
views
Questions on using clusterProfiler
clustering clusterprofiler
7.5 years ago zhangducsu • 0
0
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1
reply
1.6k
views
Question about seed in ConsensusClusterPlus, can't repeat the result
bioconductor consensusclusterplus clustering
7.5 years ago afraTW • 0
0
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2
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2.0k
views
maSigPro genes from clusters
masigpro clustering
updated 7.8 years ago by ▴ 90 • written 7.9 years ago by • 0
0
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0
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1.2k
views
Running Mclust package in R, using maximum a posteriori (MAP)
r mclust clustering
7.9 years ago mabdulsa • 0
0
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3
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2.3k
views
Prior Control with Mclust package
R mclust clustering
updated 7.9 years ago by ▴ 510 • written 7.9 years ago by • 0
2
votes
6
replies
2.9k
views
Clustering and bootstrapping of RNASeq samples
clustering pvclust vsd edgeR rnaseq
written 7.9 years ago by ▴ 90
50 results • Page 1 of 1
Recent ...
Replies
Answer: DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR) by Michael Love 41k
> I got many p values that had "1.000000e+00" and padj "1" and stat of "0" when I added the Log threshold of LFC >1 and LFC < -1...is this …
Comment: Trying to use enrichGO by fernanda.backsouza ▴ 10
With all my love, thank you Guido, GOxploreR beeing a big ally for me. I don't know how to be grateful right now.
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
You didn't generate it with an experiment, you made it up: Your PCA doesn't look like a good RNASeq experiment, because it's not.
Answer: Opposite sign of LFC in count plots of DEGs (DESeq2) by swbarnes2 ★ 1.3k
Your contrast is comparing LGR5 to Homeostasis. The bottom 2 are fine, it's the top one that is wrong. Are you sure this step isn't misla…
Comment: get BM error by James W. MacDonald 65k
I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…
Votes
C: when to apply quantile normalization with voom in limma/voom framework with RNA-
A: How to know if I should use voomWithQualityWeights() or not?
A: Weird results (ribosomal proteins / Y-linked genes) in limma/voom
Answer: Log-cpm values from limma
Answer: Log-cpm values from limma
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