Showing : Clustering • reset
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130
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Scaling and normalization by deconvolution of SMART-Seq 2 data
scran Clustering SingleCell Normalization
8 weeks ago Assa Yeroslaviz ★ 1.5k
0
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0
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172
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maSigPro visualizing individually each plot from each cluster
plot maSigPro Clustering
9 months ago oseias.rf.junior • 0
0
votes
1
reply
345
views
WGCNA - Network construction and module detection
gene Clustering wgcna flashclust
updated 9 months ago by ▴ 50 • written 9 months ago by ▴ 20
0
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1
reply
301
views
DeSeq Strategies for run to run Replication
DESeq2 Normalization Clustering replicate
updated 9 months ago by 40k • written 9 months ago by • 0
4
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3
replies
585
views
SingleCellExperiment: Edit cluster IDs in colLabels
scran Clustering SingleCellExperiment annotate cluster
updated 9 months ago by 63k • written 9 months ago by ▴ 10
2
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2
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495
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How to judge DEG analysis of these samples could be done by using limma::voom
limma Clustering voom RNA-Seq
10 months ago Yang Shi ▴ 10
0
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0
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360
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The gene clusters from the WGCNA dendrogram output are not in order
Clustering WGCNA
13 months ago chiwut.wong • 0
0
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0
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404
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Only 1 gene/ feature is present in module after WGCNA analysis
RNASeq Clustering cluster WGCNA
13 months ago chiwut.wong • 0
0
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1
reply
328
views
Error running hierClust
hierClust R SNPs clustering
updated 14 months ago by 63k • written 14 months ago by • 0
0
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0
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479
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ConsensusClusterPlus: annotate a class to the heatmap
Clustering ConsensusClusterPlus
21 months ago Gian ▴ 30
3
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2
replies
1.3k
views
Clustering differentially expressed genes in response to multiple treatments (using edgeR)
edger complexheatmap R clustering
updated 3.1 years ago by 47k • written 3.1 years ago by • 0
0
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4
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786
views
coseq plotting error: no method for coercing this S4 class to a vector
coseq RNAseq clustering
updated 3.3 years ago by ▴ 80 • written 3.4 years ago by ▴ 30
0
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1
reply
1.5k
views
Evaluating HCPC clusters from FactoMineR using cluster.stats from fpc library
clustering r fpc FactoMineR
3.8 years ago anahochmanova • 0
0
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3
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614
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 4.0 years ago by 63k • written 4.0 years ago by • 0
1
vote
6
replies
1.1k
views
edgeR removing batch effect before using expression data for clustering
edger r batcheffect clustering removeBatchEffect
updated 4.0 years ago by 63k • written 4.0 years ago by ▴ 110
0
votes
1
reply
787
views
Consensus Cluster Plus pre-computed distance matrix
consensusclusterplus distance clustering
updated 4.2 years ago by ▴ 400 • written 4.2 years ago by • 0
1
vote
2
replies
986
views
Dunn Index for Clusters from scRNA-Seq
scRNA-Seq clustering scater scran dunn index
updated 4.2 years ago by ★ 28k • written 4.2 years ago by ▴ 50
2
votes
4
replies
1.7k
views
Silhouette Plots for Clustering Quality (Multiple Algorithm)
scRNA-Seq RNA-Seq Clustering Silhouette Plot
updated 4.3 years ago by ★ 28k • written 4.3 years ago by ▴ 50
2
votes
6
replies
1.2k
views
Change the number of clusters with scater
scater scran scrnaseq clustering
updated 4.5 years ago by ★ 28k • written 4.5 years ago by ▴ 20
0
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3
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839
views
Coverage profile comparison
Targeted sequencing correlation coverage euclid clustering
4.6 years ago faramer86 • 0
3
votes
3
replies
768
views
how to plot trends for differentialy expressed genes from normalized count matrix (EdgeR)
edger clustering visualization
updated 4.7 years ago by 63k • written 4.7 years ago by • 0
0
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0
replies
497
views
DESeq aligned with HOPACH for clustering
clustering
4.8 years ago ss • 0
7
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6
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4.7k
views
scaling data for clustering heat map
edger heatmap clustering differential gene expression rnaseq
updated 5.0 years ago by 47k • written 5.0 years ago by ▴ 50
0
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4
replies
1.2k
views
Why SPADE package has been removed from bioconductor?
spade release remove clustering
updated 5.0 years ago by 63k • written 5.0 years ago by • 0
0
votes
1
reply
698
views
Global Trend Analysis using results from EdgeR
EdgeR clustering differential gene expression consensusclusterplus kmeans
updated 5.1 years ago by ★ 28k • written 5.1 years ago by • 0
0
votes
0
replies
752
views
Add samples labels with ConsensusClusterPlus
consensusclusterplus microarray clustering
5.2 years ago aagata.szymanek • 0
1
vote
0
replies
1.1k
views
Job: UK/EU funded PhD Studentship: Detecting novel subtypes of cancer using data science and machine learning
PhD clustering cancer Job
5.4 years ago • updated 5.2 years ago Daniel Brewer ▴ 90
1
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3
replies
838
views
Clustering of samples based on specific gene sets
microarray differential gene expression gene set analysis clustering
5.2 years ago cherlyn.t • 0
0
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0
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692
views
ConsensusClusterPlus without figures
clustering
5.6 years ago jasonji_19950808 • 0
0
votes
4
replies
899
views
Gene clusters based on gene expression across samples
kmeans gene expression clustering
5.6 years ago Jane Merlevede ▴ 90
0
votes
2
replies
1.5k
views
How to use RUVSeq in clustering problems?
ruvseq rna-seq clustering
updated 5.7 years ago by ▴ 920 • written 5.7 years ago by ▴ 50
0
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5
replies
1.7k
views
Choosing genes for clustering
limma clustering differential gene expression hierarchical clustering feature selection
5.7 years ago lirongrossmann ▴ 80
1
vote
3
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1.1k
views
Selecting genes that best separate between two groups
limma genefilter ttest clustering TPM
5.7 years ago lirongrossmann ▴ 80
11
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8
replies
8.2k
views
Limma and batch effect
limma differential gene expression clustering removebatcheffect
updated 5.7 years ago by 47k • written 5.7 years ago by ▴ 80
0
votes
2
replies
3.9k
views
When is centering and scaling needed before doing hierarchical clustering?
clustering hierarchical clustering
written 5.8 years ago by ▴ 20
0
votes
1
reply
1.6k
views
Observation/case weighting in cluster analysis in R
hclust hierarchical clustering clustering weight
updated 5.9 years ago by ★ 28k • written 5.9 years ago by • 0
6
votes
2
replies
4.6k
views
Cell type specific cell markers for Seurat based analysis.
single cell seurat clustering
updated 5.9 years ago by ▴ 40 • written 5.9 years ago by ▴ 20
1
vote
4
replies
1.1k
views
OrgDb for Tetrahymena thermophila
annotation clustering
updated 6.0 years ago by ★ 3.6k • written 6.0 years ago by • 0
1
vote
1
reply
5.1k
views
WGCNA: Different Detect Cut Heights Across Multiple Blocks
wgcna clustering gene expression
updated 6.1 years ago by ★ 2.8k • written 6.2 years ago by ▴ 10
3
votes
1
reply
8.6k
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 6.2 years ago by ▴ 20 • written 7.7 years ago by ▴ 810
1
vote
2
replies
1.8k
views
How to adjust the parameters of WGCNA
WGCNA RNA-seq co-expression network module clustering
updated 6.3 years ago by ★ 2.8k • written 6.3 years ago by • 0
1
vote
1
reply
1.8k
views
ConsensusClusterPlus matrix error
bioconductor clustering consensusclusterplus
6.3 years ago kyn ▴ 10
0
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5
replies
2.1k
views
Questions on using clusterProfiler
clustering clusterprofiler
6.6 years ago zhangducsu • 0
0
votes
1
reply
1.2k
views
Question about seed in ConsensusClusterPlus, can't repeat the result
bioconductor consensusclusterplus clustering
6.6 years ago afraTW • 0
0
votes
2
replies
1.6k
views
maSigPro genes from clusters
masigpro clustering
updated 6.9 years ago by ▴ 90 • written 7.0 years ago by • 0
0
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0
replies
966
views
Running Mclust package in R, using maximum a posteriori (MAP)
r mclust clustering
7.0 years ago mabdulsa • 0
0
votes
3
replies
1.9k
views
Prior Control with Mclust package
R mclust clustering
updated 7.0 years ago by ▴ 510 • written 7.0 years ago by • 0
2
votes
6
replies
2.5k
views
Clustering and bootstrapping of RNASeq samples
clustering pvclust vsd edgeR rnaseq
written 7.0 years ago by ▴ 90
1
vote
3
replies
1.4k
views
WGCNA clustering configuration
clustering wgcna microarray
updated 7.0 years ago by ★ 2.8k • written 7.1 years ago by ▴ 710
0
votes
0
replies
709
views
Analysis of Various chemical compounds on Cytotoxity Cell lines
clustering normalization
7.1 years ago ramars • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Question on constructing design matrix and defining contrasts for analysis by mohammedtoufiq91 ▴ 10
@gordonsmyth thank you, yes, please find the targets frame below. Basically, I want to create a design matrix and binarize by 0 and 1 to be…
Comment: WGCNA: many over and under-expressed features in modules of a signed network by andres.firrincieli ▴ 50
answered in Biostars: https://www.biostars.org/p/9564943/
Comment: Multitasking and Rbwa by Jean-Philippe Fortin • 0
Indeed, one can pass additional arguments to the `bwa_aln` function in `Rbwa`: bwa_aln(type="single", index_prefix=index_pr…
Comment: biomaRt error: database disk image is malformed by Emile • 0
UNBORKING the bioMaRt cache `biomaRt::biomartCacheClear()` also fixes the troubles with PANTHER.db installation which have also something t…
Answer: Proteomics data with NA values by Laurent Gatto 1.6k
- First, you need to assess how many missing values you have. - I would recommend not to impute your data by 0 (or any arbitrary small …
Votes
Answer: Question on constructing design matrix and defining contrasts for analysis
WGCNA: many over and under-expressed features in modules of a signed network
Comment: WGCNA: many over and under-expressed features in modules of a signed network
Answer: DESeq2 or edgeR for Presence and Absence of Proteins
Answer: Normalized counts from LRT or Wald test?
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