Showing : clustering • reset
14
votes
4
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29k
views
heatmap.2() get matrix after hierarchical clustering
Clustering Clustering
updated 12.5 years ago by ★ 1.7k • written 12.5 years ago by ★ 13k
11
votes
8
replies
12k
views
Limma and batch effect
limma differential gene expression clustering removebatcheffect
updated 7.5 years ago by 52k • written 7.5 years ago by ▴ 80
9
votes
10
replies
14k
views
Is the following a correct usage of Limma's removeBatchEffect() for clustered heat map generation?
limma removeBatchEffect heatmap clustering
updated 9.2 years ago by ▴ 610 • written 9.2 years ago by ▴ 80
7
votes
6
replies
6.8k
views
scaling data for clustering heat map
edger heatmap clustering differential gene expression rnaseq
updated 6.8 years ago by 52k • written 6.8 years ago by ▴ 60
6
votes
2
replies
6.2k
views
Cell type specific cell markers for Seurat based analysis.
single cell seurat clustering
updated 7.7 years ago by ▴ 40 • written 7.7 years ago by ▴ 20
6
votes
5
replies
4.8k
views
voom + removeBatchEffect + gene clustering
voom limma clustering removebatcheffect() batch effect
updated 9.7 years ago by 52k • written 9.7 years ago by ▴ 10
6
votes
2
replies
3.9k
views
Is ComBat introducing a signal where there is none?
Microarray Clustering Cancer limma Microarray Clustering Cancer limma
11.3 years ago • updated 9.6 years ago Vegard Nygaard ▴ 120
4
votes
3
replies
2.3k
views
SingleCellExperiment: Edit cluster IDs in colLabels
scran Clustering SingleCellExperiment annotate cluster
updated 2.6 years ago by 68k • written 2.6 years ago by ▴ 10
3
votes
3
replies
1.3k
views
how to plot trends for differentialy expressed genes from normalized count matrix (EdgeR)
edger clustering visualization
updated 6.5 years ago by 68k • written 6.5 years ago by ▴ 10
3
votes
4
replies
2.3k
views
Large differences in sample clustering using cummeRbund (csDendro) and rlog-distance (DESeq2)
deseq2 cummerbund rlog fpkm clustering
9.2 years ago Jon Bråte ▴ 260
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 8.0 years ago by ▴ 20 • written 9.5 years ago by ▴ 840
3
votes
2
replies
3.0k
views
Clustering differentially expressed genes in response to multiple treatments (using edgeR)
edger complexheatmap R clustering
updated 4.9 years ago by 52k • written 4.9 years ago by • 0
2
votes
3
replies
833
views
"could not find function "readTSGE" in package ctsGE" Error occurs when trying to follow ctsGE package instructions.
GeneExpression Clustering ctsGE
13 months ago jbgnielson • 0
2
votes
2
replies
1.7k
views
How to judge DEG analysis of these samples could be done by using limma::voom
limma Clustering voom RNA-Seq
2.7 years ago Yang Shi ▴ 10
2
votes
4
replies
3.0k
views
Silhouette Plots for Clustering Quality (Multiple Algorithm)
scRNA-Seq RNA-Seq Clustering Silhouette Plot
updated 6.1 years ago by ★ 28k • written 6.1 years ago by ▴ 60
2
votes
6
replies
2.1k
views
Change the number of clusters with scater
scater scran scrnaseq clustering
updated 6.4 years ago by ★ 28k • written 6.4 years ago by ▴ 20
2
votes
6
replies
3.5k
views
Clustering and bootstrapping of RNASeq samples
clustering pvclust vsd edgeR rnaseq
written 8.8 years ago by ▴ 90
2
votes
1
reply
2.2k
views
DESeq Variance Stabilizing Transformation (now with non-embedded images)
Normalization Clustering DESeq DESeq2 Normalization Clustering DESeq DESeq2
updated 11.8 years ago by 43k • written 11.8 years ago by ▴ 50
2
votes
5
replies
5.8k
views
Can I use the WGCNA dendrogram to display a heatmap of gene expression?
wgcna heatmap desq2 clustering
updated 9.9 years ago by ★ 1.6k • written 9.9 years ago by ▴ 260
2
votes
3
replies
4.7k
views
Deseq2. Cluster of an specific list
deseq2 heatmap clustering file list
updated 9.5 years ago by 43k • written 9.5 years ago by • 0
2
votes
8
replies
2.7k
views
Clustering RNASeq samples from different libraries using DESeq2
clustering DESeq2
9.0 years ago Jane Merlevede ▴ 90
2
votes
16
replies
4.2k
views
Approaches to group the RNA-Seq samples with large heterogeneity
clustering pca deseq2 edger logfoldchange
updated 9.0 years ago by 43k • written 9.0 years ago by ▴ 10
2
votes
1
reply
3.1k
views
voom transformed data
Clustering limma Clustering limma
updated 11.0 years ago by 52k • written 11.0 years ago by ★ 13k
2
votes
4
replies
3.4k
views
Your thoughts on Limma Array Weights?
Clustering limma Clustering limma
updated 16.8 years ago by 52k • written 16.8 years ago by ▴ 970
2
votes
3
replies
3.6k
views
scran: question on minimum cluster size for computeSumFactors()
scran single cell normalization clustering
8.9 years ago aatsmith • 0
1
vote
1
reply
2.8k
views
ConsensusClusterPlus matrix error
bioconductor clustering consensusclusterplus
8.1 years ago kyn ▴ 10
1
vote
1
reply
1.3k
views
Expected memory usage for analyzing large single-cell seq datasets (> 450,000 cells)?
BigData Clustering memory SingleCellExperiment edgeR
updated 7 months ago by ★ 28k • written 7 months ago by • 0
1
vote
2
replies
1.8k
views
Dunn Index for Clusters from scRNA-Seq
scRNA-Seq clustering scater scran dunn index
updated 6.0 years ago by ★ 28k • written 6.0 years ago by ▴ 60
1
vote
6
replies
2.1k
views
edgeR removing batch effect before using expression data for clustering
edger r batcheffect clustering removeBatchEffect
updated 5.9 years ago by 68k • written 5.9 years ago by ▴ 120
1
vote
4
replies
1.8k
views
OrgDb for Tetrahymena thermophila
annotation clustering
updated 7.8 years ago by ★ 4.1k • written 7.8 years ago by • 0
1
vote
1
reply
7.4k
views
WGCNA: Different Detect Cut Heights Across Multiple Blocks
wgcna clustering gene expression
updated 8.0 years ago by ★ 3.0k • written 8.0 years ago by ▴ 10
1
vote
3
replies
1.9k
views
Selecting genes that best separate between two groups
limma genefilter ttest clustering TPM
7.5 years ago lirongrossmann ▴ 80
1
vote
1
reply
1.0k
views
Clustering like samples with a lot of data
clustering
9.0 years ago gaiusjaugustus • 0
1
vote
2
replies
5.1k
views
WGCNA distance measures, clustering with TOM based on adjacency matrix type = "distance" versus correlation
wgcna microarray clustering
updated 9.1 years ago by ★ 3.0k • written 9.1 years ago by • 0
1
vote
3
replies
2.3k
views
WGCNA clustering configuration
clustering wgcna microarray
updated 8.9 years ago by ★ 3.0k • written 8.9 years ago by ▴ 760
1
vote
0
replies
1.7k
views
Job: UK/EU funded PhD Studentship: Detecting novel subtypes of cancer using data science and machine learning
PhD clustering cancer Job
7.3 years ago • updated 7.0 years ago Daniel Brewer ▴ 100
1
vote
4
replies
1.5k
views
Specifically expressed genes
DESeq2 specific expression rnaseq clustering differential expression
updated 9.9 years ago by 43k • written 9.9 years ago by • 0
1
vote
2
replies
1.8k
views
Binning expression data along with capturing gene identifiers
rnaseqdata clustering
updated 10.2 years ago by ★ 2.1k • written 10.2 years ago by ▴ 150
1
vote
3
replies
2.4k
views
microarray analysis in R without replicates
Microarray Clustering Microarray Clustering
updated 15.5 years ago by ▴ 630 • written 15.5 years ago by ▴ 60
1
vote
1
reply
5.8k
views
Mfuzz: fill.NA - Warning messages: argument is not numeric or logical: returning NA
mfuzz clustering bioinformatics proteomics timecourse
updated 9.1 years ago by 1.6k • written 9.1 years ago by • 0
1
vote
3
replies
2.2k
views
DESeq2 Regularised Log for Clustering of Genes
Clustering DESeq2 Clustering DESeq2
updated 10.9 years ago by ★ 3.8k • written 10.9 years ago by 43k
1
vote
3
replies
1.5k
views
Clustering of samples based on specific gene sets
microarray differential gene expression gene set analysis clustering
7.1 years ago cherlyn.t • 0
0
votes
0
replies
977
views
Fwd: Re: Fwd: Re: Heatmap function
Clustering Clustering
21.4 years ago Marcus ▴ 150
0
votes
0
replies
1.1k
views
Position in Biostatistics and Bioinformatics
Microarray Genetics Normalization Clustering Microarray Genetics Normalization Clustering
21.5 years ago Sophie Gallina ▴ 10
0
votes
3
replies
2.3k
views
Diffbind: Binding Affinity Heatmap
Sequencing GO Clustering GLAD edgeR DESeq DiffBind Sequencing GO Clustering GLAD edgeR
11.6 years ago Rory Stark ★ 5.2k
0
votes
0
replies
875
views
Clustering method
Clustering Clustering
21.5 years ago s0uchi02 ▴ 30
0
votes
0
replies
1.2k
views
Conference announcement: Compstat 2004
Visualization Bayesian Classification Clustering Regression Visualization Bayesian
21.5 years ago Wolfgang Huber ★ 13k
0
votes
0
replies
2.4k
views
Bioconductor Digest, Vol 121, Issue 13
RNASeq Microarray Normalization GO Classification Clustering Cancer Mus musculus probe GO
12.0 years ago Matthew Thornton ▴ 380
0
votes
0
replies
1.4k
views
qPCR Event Calendar - winter 2010
SNP qPCR Genetics Normalization Clustering Regression Cancer Breast Xenopus laevis probe
14.4 years ago qPCR Platform - the reference in real-t… ▴ 170
0
votes
0
replies
993
views
RE: time-course experiments (edoardo missiaglia)
Microarray Clustering Microarray Clustering
21.5 years ago Baker, Stephen ▴ 160
50 results • Page 1 of 1
Recent ...
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Comment: Annotation package for Manduca sexta by GA ▴ 10
Thank you!
Comment: Improving performance of edgeR and limma while adjusting for multiple confounder by ATpoint ★ 4.8k
If 2 minutes is inacceptable to you then you can still fall back to limma-trend which should give a dramatic speedup and finish in seconds.…
Comment: getBM from biomaRt inconsistencies found with .gtf files across multiple species by Mike Smith ★ 6.6k
Great, thanks for the update from Ensembl. So the most relevant part of 'Location: Scaffold HG1277_PATCH: 137,021-141,806 forward strand' …
Answer: Improving performance of edgeR and limma while adjusting for multiple confounder by Gordon Smyth 52k
We recommend that you use voomLmFit() instead of voom+lmFit. We are pretty proud of the speed of glmQLFit and voom, and we hadn't expected…
Answer: Merging EPICV1 and V2 betas by James W. MacDonald 68k
It appears that [SeSAMe][1] has functions meant to do that sort of thing. [1]: https://bioconductor.org/packages/release/bioc/vignet…
Votes
Looking for equivalent EPIC chip v1 vs. v2 annotation variables
Properly constructing a hypergeometric test
A: Is logFC a log2 fold change or some other base in scran::findMarkers
Comment: Error in retrieving clinical data
What is the cheapest day to fly on American Airlines? {Ask_Expert}
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