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Showing :
clustering
•
reset
2
votes
3
replies
487
views
"could not find function "readTSGE" in package ctsGE" Error occurs when trying to follow ctsGE package instructions.
GeneExpression
Clustering
ctsGE
3 months ago
jbgnielson
• 0
0
votes
3
replies
602
views
Clustering coefficient of synteny network
Network
syntenet
Clustering
coefficient
11 months ago • updated 10 months ago
Alexandros
• 0
0
votes
2
replies
777
views
Scaling and normalization by deconvolution of SMART-Seq 2 data
scran
Clustering
SingleCell
Normalization
14 months ago
Assa Yeroslaviz
★ 1.5k
0
votes
0
replies
452
views
maSigPro visualizing individually each plot from each cluster
plot
maSigPro
Clustering
21 months ago
oseias.rf.junior
• 0
0
votes
1
reply
850
views
WGCNA - Network construction and module detection
gene
Clustering
wgcna
flashclust
updated 21 months ago by
andres.firrincieli
▴ 50 • written 21 months ago by
Recep
▴ 20
0
votes
1
reply
655
views
DeSeq Strategies for run to run Replication
DESeq2
Normalization
Clustering
replicate
updated 21 months ago by
Michael Love
42k • written 21 months ago by
Giorgio
• 0
4
votes
3
replies
1.6k
views
SingleCellExperiment: Edit cluster IDs in colLabels
scran
Clustering
SingleCellExperiment
annotate
cluster
updated 22 months ago by
James W. MacDonald
66k • written 22 months ago by
achoppe
▴ 10
2
votes
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
22 months ago
Yang Shi
▴ 10
0
votes
0
replies
782
views
The gene clusters from the WGCNA dendrogram output are not in order
Clustering
WGCNA
2.1 years ago
chiwut.wong
• 0
0
votes
0
replies
789
views
Only 1 gene/ feature is present in module after WGCNA analysis
RNASeq
Clustering
cluster
WGCNA
2.1 years ago
chiwut.wong
• 0
0
votes
1
reply
616
views
Error running hierClust
hierClust
R
SNPs
clustering
updated 2.2 years ago by
James W. MacDonald
66k • written 2.2 years ago by
sekhwal
• 0
0
votes
0
replies
877
views
ConsensusClusterPlus: annotate a class to the heatmap
Clustering
ConsensusClusterPlus
2.7 years ago
Gian
▴ 30
3
votes
2
replies
2.2k
views
Clustering differentially expressed genes in response to multiple treatments (using edgeR)
edger
complexheatmap
R
clustering
updated 4.1 years ago by
Gordon Smyth
50k • written 4.1 years ago by
eggrandio
• 0
0
votes
4
replies
1.4k
views
coseq plotting error: no method for coercing this S4 class to a vector
coseq
RNAseq
clustering
updated 4.3 years ago by
andrea.rau
▴ 80 • written 4.4 years ago by
minyaaa9058
▴ 30
0
votes
1
reply
1.9k
views
Evaluating HCPC clusters from FactoMineR using cluster.stats from fpc library
clustering
r
fpc
FactoMineR
4.8 years ago
anahochmanova
• 0
0
votes
3
replies
953
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 5.0 years ago by
James W. MacDonald
66k • written 5.0 years ago by
v.yuvanesh
• 0
1
vote
6
replies
1.7k
views
edgeR removing batch effect before using expression data for clustering
edger
r
batcheffect
clustering
removeBatchEffect
updated 5.0 years ago by
James W. MacDonald
66k • written 5.0 years ago by
Biologist
▴ 110
0
votes
1
reply
1.2k
views
Consensus Cluster Plus pre-computed distance matrix
consensusclusterplus
distance
clustering
updated 5.2 years ago by
chris86
▴ 420 • written 5.2 years ago by
neuro3030
• 0
1
vote
2
replies
1.4k
views
Dunn Index for Clusters from scRNA-Seq
scRNA-Seq
clustering
scater
scran
dunn index
updated 5.2 years ago by
Aaron Lun
★ 28k • written 5.2 years ago by
hamza_karakurt
▴ 60
2
votes
4
replies
2.4k
views
Silhouette Plots for Clustering Quality (Multiple Algorithm)
scRNA-Seq
RNA-Seq
Clustering
Silhouette Plot
updated 5.3 years ago by
Aaron Lun
★ 28k • written 5.3 years ago by
hamza_karakurt
▴ 60
2
votes
6
replies
1.7k
views
Change the number of clusters with scater
scater
scran
scrnaseq
clustering
updated 5.5 years ago by
Aaron Lun
★ 28k • written 5.5 years ago by
shbrief
▴ 20
0
votes
3
replies
1.2k
views
Coverage profile comparison
Targeted sequencing
correlation
coverage
euclid
clustering
5.6 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 5.7 years ago by
James W. MacDonald
66k • written 5.7 years ago by
thindmarsmission
▴ 10
0
votes
0
replies
677
views
DESeq aligned with HOPACH for clustering
clustering
5.8 years ago
ss
• 0
7
votes
6
replies
5.8k
views
scaling data for clustering heat map
edger
heatmap
clustering
differential gene expression
rnaseq
updated 6.0 years ago by
Gordon Smyth
50k • written 6.0 years ago by
Beginner
▴ 60
0
votes
4
replies
1.6k
views
Why SPADE package has been removed from bioconductor?
spade
release
remove
clustering
updated 6.0 years ago by
James W. MacDonald
66k • written 6.0 years ago by
a.n.horvath
• 0
0
votes
1
reply
1.0k
views
Global Trend Analysis using results from EdgeR
EdgeR
clustering
differential gene expression
consensusclusterplus
kmeans
updated 6.1 years ago by
Aaron Lun
★ 28k • written 6.1 years ago by
anupriya.dalmia
• 0
0
votes
0
replies
1.1k
views
Add samples labels with ConsensusClusterPlus
consensusclusterplus
microarray
clustering
6.2 years ago
aagata.szymanek
• 0
1
vote
3
replies
1.2k
views
Clustering of samples based on specific gene sets
microarray
differential gene expression
gene set analysis
clustering
6.2 years ago
cherlyn.t
• 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
6.4 years ago • updated 6.2 years ago
Daniel Brewer
▴ 100
0
votes
1
reply
997
views
ConsensusClusterPlus without figures
clustering
updated 12 weeks ago by
fatmaserrt
• 0 • written 6.6 years ago by
jasonji_19950808
• 0
0
votes
4
replies
1.3k
views
Gene clusters based on gene expression across samples
kmeans
gene expression
clustering
6.6 years ago
Jane Merlevede
▴ 90
0
votes
2
replies
2.0k
views
How to use RUVSeq in clustering problems?
ruvseq
rna-seq
clustering
updated 6.6 years ago by
davide risso
▴ 950 • written 6.7 years ago by
paul.alto
▴ 50
1
vote
3
replies
1.5k
views
Selecting genes that best separate between two groups
limma
genefilter
ttest
clustering
TPM
6.7 years ago
lirongrossmann
▴ 80
0
votes
5
replies
2.5k
views
Choosing genes for clustering
limma
clustering
differential gene expression
hierarchical clustering
feature selection
6.7 years ago
lirongrossmann
▴ 80
11
votes
8
replies
10k
views
Limma and batch effect
limma
differential gene expression
clustering
removebatcheffect
updated 6.7 years ago by
Gordon Smyth
50k • written 6.7 years ago by
lirongrossmann
▴ 80
0
votes
2
replies
4.6k
views
When is centering and scaling needed before doing hierarchical clustering?
clustering
hierarchical clustering
written 6.8 years ago by
hrishi27n
▴ 20
0
votes
1
reply
1.9k
views
Observation/case weighting in cluster analysis in R
hclust
hierarchical clustering
clustering
weight
updated 6.9 years ago by
Aaron Lun
★ 28k • written 6.9 years ago by
danielle.newby
• 0
6
votes
2
replies
5.4k
views
Cell type specific cell markers for Seurat based analysis.
single cell
seurat
clustering
updated 6.9 years ago by
ankur.chakravarthy.10
▴ 40 • written 6.9 years ago by
hrishi27n
▴ 20
1
vote
4
replies
1.5k
views
OrgDb for Tetrahymena thermophila
annotation
clustering
updated 7.0 years ago by
Guido Hooiveld
★ 4.0k • written 7.0 years ago by
lin.ying.zhang
• 0
1
vote
1
reply
6.3k
views
WGCNA: Different Detect Cut Heights Across Multiple Blocks
wgcna
clustering
gene expression
updated 7.1 years ago by
Peter Langfelder
★ 3.0k • written 7.1 years ago by
ngeraci
▴ 10
1
vote
2
replies
2.2k
views
How to adjust the parameters of WGCNA
WGCNA
RNA-seq
co-expression network
module
clustering
updated 7.3 years ago by
Peter Langfelder
★ 3.0k • written 7.3 years ago by
xie186
• 0
1
vote
1
reply
2.4k
views
ConsensusClusterPlus matrix error
bioconductor
clustering
consensusclusterplus
7.3 years ago
kyn
▴ 10
0
votes
5
replies
2.6k
views
Questions on using clusterProfiler
clustering
clusterprofiler
7.6 years ago
zhangducsu
• 0
0
votes
1
reply
1.6k
views
Question about seed in ConsensusClusterPlus, can't repeat the result
bioconductor
consensusclusterplus
clustering
7.6 years ago
afraTW
• 0
0
votes
3
replies
2.1k
views
maSigPro genes from clusters
masigpro
clustering
updated 13 days ago by
anne-laure
• 0 • written 8.0 years ago by
ls299
• 0
0
votes
0
replies
1.2k
views
Running Mclust package in R, using maximum a posteriori (MAP)
r
mclust
clustering
8.0 years ago
mabdulsa
• 0
0
votes
3
replies
2.4k
views
Prior Control with Mclust package
R
mclust
clustering
updated 8.0 years ago by
Aedin Culhane
▴ 510 • written 8.0 years ago by
mabdulsa
• 0
2
votes
6
replies
3.0k
views
Clustering and bootstrapping of RNASeq samples
clustering
pvclust
vsd
edgeR
rnaseq
written 8.0 years ago by
Jane Merlevede
▴ 90
1
vote
3
replies
1.9k
views
WGCNA clustering configuration
clustering
wgcna
microarray
updated 8.0 years ago by
Peter Langfelder
★ 3.0k • written 8.1 years ago by
Lluís Revilla Sancho
▴ 730
50 results • Page
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Comment: Deseq2
by
Ram
▴ 210
Cross-posted on biostars: https://www.biostars.org/p/9596031/
Comment: SpliceWiz collateData error
by
giulia.nicoletto.1
• 0
Hi there, I am facing a similar error. When I try the collateData command collateData( Experiment = expr, reference_path = "./Referen…
Answer: Best way to describe DEseq2 design
by
SamGG
▴ 350
Hi, My own opinion. In the design `~ Batch`, ChemicalA_t1 is the intercept. So, all coefficients refer to this level as a reference. …
Answer: Deseq2
by
ATpoint
★ 4.2k
Ser the vignette https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html It covers prefiltering (and everyt…
Comment: Counter-directional LFC shrinkage
by
Michael Love
42k
Gene 1 is hard to predict given the paucity of data for the comparison of interest. What is happening is that the relatively low dispersion…
Votes
Answer: Deseq2
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: When should I correct for batch effects
Answer: When should I correct for batch effects
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