Showing : clustering • reset
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47
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The gene clusters from the WGCNA dendrogram output are not in order
Clustering WGCNA
23 days ago chiwut.wong • 0
0
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0
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73
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Only 1 gene/ feature is present in module after WGCNA analysis
RNASeq Clustering cluster WGCNA
5 weeks ago chiwut.wong • 0
0
votes
1
reply
100
views
Error running hierClust
hierClust R SNPs clustering
updated 7 weeks ago by 59k • written 7 weeks ago by • 0
0
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0
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198
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ConsensusClusterPlus: annotate a class to the heatmap
Clustering ConsensusClusterPlus
8 months ago Gian ▴ 30
3
votes
2
replies
642
views
Clustering differentially expressed genes in response to multiple treatments (using edgeR)
edger complexheatmap R clustering
updated 2.1 years ago by 45k • written 2.1 years ago by • 0
0
votes
4
replies
394
views
coseq plotting error: no method for coercing this S4 class to a vector
coseq RNAseq clustering
updated 2.3 years ago by ▴ 80 • written 2.3 years ago by ▴ 20
0
votes
1
reply
1.1k
views
Evaluating HCPC clusters from FactoMineR using cluster.stats from fpc library
clustering r fpc FactoMineR
2.8 years ago anahochmanova • 0
0
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3
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412
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 3.0 years ago by 59k • written 3.0 years ago by • 0
0
votes
6
replies
726
views
edgeR removing batch effect before using expression data for clustering
edger r batcheffect clustering removeBatchEffect
updated 3.0 years ago by 59k • written 3.0 years ago by ▴ 90
0
votes
1
reply
520
views
Consensus Cluster Plus pre-computed distance matrix
consensusclusterplus distance clustering
updated 3.2 years ago by ▴ 400 • written 3.2 years ago by • 0
1
vote
2
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707
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Dunn Index for Clusters from scRNA-Seq
scRNA-Seq clustering scater scran dunn index
updated 3.2 years ago by ★ 27k • written 3.2 years ago by ▴ 50
2
votes
4
replies
1.2k
views
Silhouette Plots for Clustering Quality (Multiple Algorithm)
scRNA-Seq RNA-Seq Clustering Silhouette Plot
updated 3.3 years ago by ★ 27k • written 3.3 years ago by ▴ 50
2
votes
6
replies
787
views
Change the number of clusters with scater
scater scran scrnaseq clustering
updated 3.5 years ago by ★ 27k • written 3.5 years ago by ▴ 20
0
votes
3
replies
580
views
Coverage profile comparison
Targeted sequencing correlation coverage euclid clustering
3.6 years ago faramer86 • 0
3
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3
replies
561
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how to plot trends for differentialy expressed genes from normalized count matrix (EdgeR)
edger clustering visualization
updated 3.6 years ago by 59k • written 3.6 years ago by • 0
0
votes
0
replies
368
views
DESeq aligned with HOPACH for clustering
clustering
3.8 years ago ss • 0
6
votes
6
replies
3.6k
views
scaling data for clustering heat map
edger heatmap clustering differential gene expression rnaseq
updated 4.0 years ago by 45k • written 4.0 years ago by ▴ 50
0
votes
4
replies
814
views
Why SPADE package has been removed from bioconductor?
spade release remove clustering
updated 4.0 years ago by 59k • written 4.0 years ago by • 0
0
votes
1
reply
497
views
Global Trend Analysis using results from EdgeR
EdgeR clustering differential gene expression consensusclusterplus kmeans
updated 4.1 years ago by ★ 27k • written 4.1 years ago by • 0
0
votes
0
replies
505
views
Add samples labels with ConsensusClusterPlus
consensusclusterplus microarray clustering
4.1 years ago aagata.szymanek • 0
1
vote
3
replies
600
views
Clustering of samples based on specific gene sets
microarray differential gene expression gene set analysis clustering
4.2 years ago cherlyn.t • 0
1
vote
0
replies
821
views
Job: UK/EU funded PhD Studentship: Detecting novel subtypes of cancer using data science and machine learning
PhD clustering cancer Job
4.4 years ago • updated 4.2 years ago Daniel Brewer ▴ 90
0
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0
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510
views
ConsensusClusterPlus without figures
clustering
4.5 years ago jasonji_19950808 • 0
0
votes
4
replies
708
views
Gene clusters based on gene expression across samples
kmeans gene expression clustering
4.6 years ago • updated 4.5 years ago Jane Merlevede ▴ 90
0
votes
2
replies
1.1k
views
How to use RUVSeq in clustering problems?
ruvseq rna-seq clustering
updated 4.6 years ago by ▴ 890 • written 4.6 years ago by ▴ 50
1
vote
3
replies
763
views
Selecting genes that best separate between two groups
limma genefilter ttest clustering TPM
4.7 years ago lirongrossmann ▴ 60
0
votes
5
replies
1.2k
views
Choosing genes for clustering
limma clustering differential gene expression hierarchical clustering feature selection
4.7 years ago lirongrossmann ▴ 60
10
votes
8
replies
5.7k
views
Limma and batch effect
limma differential gene expression clustering removebatcheffect
updated 4.7 years ago by 45k • written 4.7 years ago by ▴ 60
0
votes
1
reply
2.9k
views
When is centering and scaling needed before doing hierarchical clustering?
clustering hierarchical clustering
updated 4.8 years ago by ▴ 400 • written 4.8 years ago by ▴ 20
0
votes
1
reply
1.3k
views
Observation/case weighting in cluster analysis in R
hclust hierarchical clustering clustering weight
updated 4.8 years ago by ★ 27k • written 4.8 years ago by • 0
6
votes
2
replies
3.7k
views
Cell type specific cell markers for Seurat based analysis.
single cell seurat clustering
updated 4.9 years ago by ▴ 40 • written 4.9 years ago by ▴ 20
1
vote
4
replies
844
views
OrgDb for Tetrahymena thermophila
annotation clustering
updated 5.0 years ago by ★ 3.2k • written 5.0 years ago by • 0
1
vote
1
reply
4.2k
views
WGCNA: Different Detect Cut Heights Across Multiple Blocks
wgcna clustering gene expression
updated 5.1 years ago by ★ 2.6k • written 5.1 years ago by ▴ 10
1
vote
2
replies
1.5k
views
How to adjust the parameters of WGCNA
WGCNA RNA-seq co-expression network module clustering
updated 5.3 years ago by ★ 2.6k • written 5.3 years ago by • 0
1
vote
1
reply
1.1k
views
ConsensusClusterPlus matrix error
bioconductor clustering consensusclusterplus
5.3 years ago kyn ▴ 10
0
votes
5
replies
1.5k
views
Questions on using clusterProfiler
clustering clusterprofiler
5.6 years ago zhangducsu • 0
0
votes
1
reply
989
views
Question about seed in ConsensusClusterPlus, can't repeat the result
bioconductor consensusclusterplus clustering
5.6 years ago afraTW • 0
0
votes
2
replies
1.3k
views
maSigPro genes from clusters
masigpro clustering
updated 5.9 years ago by ▴ 90 • written 5.9 years ago by • 0
0
votes
0
replies
764
views
Running Mclust package in R, using maximum a posteriori (MAP)
r mclust clustering
6.0 years ago mabdulsa • 0
0
votes
3
replies
1.5k
views
Prior Control with Mclust package
R mclust clustering
updated 6.0 years ago by ▴ 510 • written 6.0 years ago by • 0
2
votes
6
replies
2.1k
views
Clustering and bootstrapping of RNASeq samples
clustering pvclust vsd edgeR rnaseq
written 6.0 years ago by ▴ 90
1
vote
3
replies
1.2k
views
WGCNA clustering configuration
clustering wgcna microarray
updated 6.0 years ago by ★ 2.6k • written 6.0 years ago by ▴ 660
0
votes
0
replies
576
views
Analysis of Various chemical compounds on Cytotoxity Cell lines
clustering normalization
6.0 years ago ramars • 0
2
votes
3
replies
2.3k
views
scran: question on minimum cluster size for computeSumFactors()
scran single cell normalization clustering
6.1 years ago aatsmith • 0
0
votes
1
reply
624
views
Plot with two separated groups of genes.
scatter-plot clustering
updated 6.1 years ago by ▴ 10 • written 6.1 years ago by • 0
1
vote
1
reply
569
views
Clustering like samples with a lot of data
clustering
6.1 years ago gaiusjaugustus • 0
2
votes
8
replies
1.7k
views
Clustering RNASeq samples from different libraries using DESeq2
clustering DESeq2
6.2 years ago Jane Merlevede ▴ 90
2
votes
16
replies
2.6k
views
Approaches to group the RNA-Seq samples with large heterogeneity
clustering pca deseq2 edger logfoldchange
updated 6.2 years ago by 37k • written 6.2 years ago by ▴ 10
1
vote
1
reply
4.8k
views
Mfuzz: fill.NA - Warning messages: argument is not numeric or logical: returning NA
mfuzz clustering bioinformatics proteomics timecourse
updated 6.2 years ago by 1.5k • written 6.2 years ago by • 0
0
votes
2
replies
917
views
clustering analysis of illumina microarray gene expression data
clustering illumina microarray
6.3 years ago kritikamish99 ▴ 10
50 results • Page 1 of 1
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Comment: CPM after RUVseq by James W. MacDonald 59k
Also, you might be confused about something. CPM is counts/million counts, which *uses library size to scale normalize* and logCPM is just…
Comment: CPM after RUVseq by James W. MacDonald 59k
You shouldn't use CPM or logCPM for any of the steps! To use `RUVr` you need to fit a preliminary model using `edgeR`, which takes counts a…
Comment: CPM after RUVseq by Jess • 0
Thank you James! It hadn't occurred to me to input CPM rather than logCPM which is why my df$NormalizedCounts didn't exceed 17ish in valu…
Answer: RPX PXDataset error by Laurent Gatto 1.5k
- From the URL in the error, it looks like you have the latest (or a recent) `rpx` version. It is generally recommended to add the output o…
Answer: Package name already exists due to previous issue by shepherl 3.1k
This has been resolved. There needed to be a manual intervention by the core team to remove the old issue from the issue tracker database.…
Votes
Answer: CPM after RUVseq
Comment: Merging two plated in R
Answer: Merging two plated in R
Answer: Merging two plated in R
A: Can we use glmQLFit instead of glmFit and then glmLRT in edgeR
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