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Showing :
clustering
•
reset
2
votes
3
replies
434
views
"could not find function "readTSGE" in package ctsGE" Error occurs when trying to follow ctsGE package instructions.
GeneExpression
Clustering
ctsGE
7 weeks ago
jbgnielson
• 0
0
votes
3
replies
546
views
Clustering coefficient of synteny network
Network
syntenet
Clustering
coefficient
9 months ago
Alexandros
• 0
0
votes
2
replies
687
views
Scaling and normalization by deconvolution of SMART-Seq 2 data
scran
Clustering
SingleCell
Normalization
12 months ago
Assa Yeroslaviz
★ 1.5k
0
votes
0
replies
411
views
maSigPro visualizing individually each plot from each cluster
plot
maSigPro
Clustering
19 months ago
oseias.rf.junior
• 0
0
votes
1
reply
798
views
WGCNA - Network construction and module detection
gene
Clustering
wgcna
flashclust
updated 19 months ago by
andres.firrincieli
▴ 50 • written 20 months ago by
Recep
▴ 20
0
votes
1
reply
627
views
DeSeq Strategies for run to run Replication
DESeq2
Normalization
Clustering
replicate
updated 20 months ago by
Michael Love
41k • written 20 months ago by
Giorgio
• 0
4
votes
3
replies
1.5k
views
SingleCellExperiment: Edit cluster IDs in colLabels
scran
Clustering
SingleCellExperiment
annotate
cluster
updated 20 months ago by
James W. MacDonald
65k • written 20 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
21 months ago
Yang Shi
▴ 10
0
votes
0
replies
735
views
The gene clusters from the WGCNA dendrogram output are not in order
Clustering
WGCNA
23 months ago
chiwut.wong
• 0
0
votes
0
replies
743
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
587
views
Error running hierClust
hierClust
R
SNPs
clustering
updated 2.1 years ago by
James W. MacDonald
65k • written 2.1 years ago by
sekhwal
• 0
0
votes
0
replies
811
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
Gordon Smyth
50k • written 4.0 years ago by
eggrandio
• 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
andrea.rau
▴ 80 • written 4.2 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
4.7 years ago
anahochmanova
• 0
0
votes
3
replies
923
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
James W. MacDonald
65k • written 4.9 years ago by
v.yuvanesh
• 0
1
vote
6
replies
1.6k
views
edgeR removing batch effect before using expression data for clustering
edger
r
batcheffect
clustering
removeBatchEffect
updated 4.9 years ago by
James W. MacDonald
65k • written 4.9 years ago by
Biologist
▴ 110
0
votes
1
reply
1.2k
views
Consensus Cluster Plus pre-computed distance matrix
consensusclusterplus
distance
clustering
updated 5.1 years ago by
chris86
▴ 420 • written 5.1 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 5.1 years ago by
Aaron Lun
★ 28k • written 5.1 years ago by
hamza_karakurt
▴ 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
Aaron Lun
★ 28k • written 5.2 years ago by
hamza_karakurt
▴ 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
Aaron Lun
★ 28k • written 5.4 years ago by
shbrief
▴ 20
0
votes
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
James W. MacDonald
65k • written 5.6 years ago by
thindmarsmission
▴ 10
0
votes
0
replies
657
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
Gordon Smyth
50k • written 5.9 years ago by
Beginner
▴ 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
James W. MacDonald
65k • written 5.9 years ago by
a.n.horvath
• 0
0
votes
1
reply
970
views
Global Trend Analysis using results from EdgeR
EdgeR
clustering
differential gene expression
consensusclusterplus
kmeans
updated 6.0 years ago by
Aaron Lun
★ 28k • written 6.0 years ago by
anupriya.dalmia
• 0
0
votes
0
replies
1.0k
views
Add samples labels with ConsensusClusterPlus
consensusclusterplus
microarray
clustering
6.0 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
votes
1
reply
962
views
ConsensusClusterPlus without figures
clustering
updated 6 weeks ago by
fatmaserrt
• 0 • written 6.4 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
6.5 years ago
Jane Merlevede
▴ 90
0
votes
2
replies
1.9k
views
How to use RUVSeq in clustering problems?
ruvseq
rna-seq
clustering
updated 6.5 years ago by
davide risso
▴ 950 • written 6.5 years ago by
paul.alto
▴ 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
Gordon Smyth
50k • written 6.6 years ago by
lirongrossmann
▴ 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
hrishi27n
▴ 20
0
votes
1
reply
1.9k
views
Observation/case weighting in cluster analysis in R
hclust
hierarchical clustering
clustering
weight
updated 6.7 years ago by
Aaron Lun
★ 28k • written 6.7 years ago by
danielle.newby
• 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
ankur.chakravarthy.10
▴ 40 • written 6.8 years ago by
hrishi27n
▴ 20
1
vote
4
replies
1.4k
views
OrgDb for Tetrahymena thermophila
annotation
clustering
updated 6.9 years ago by
Guido Hooiveld
★ 3.9k • written 6.9 years ago by
lin.ying.zhang
• 0
1
vote
1
reply
6.2k
views
WGCNA: Different Detect Cut Heights Across Multiple Blocks
wgcna
clustering
gene expression
updated 7.0 years ago by
Peter Langfelder
★ 3.0k • written 7.0 years ago by
ngeraci
▴ 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
james.tsakalos
▴ 20 • written 8.6 years ago by
svlachavas
▴ 830
1
vote
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
Peter Langfelder
★ 3.0k • written 7.2 years ago by
xie186
• 0
1
vote
1
reply
2.3k
views
ConsensusClusterPlus matrix error
bioconductor
clustering
consensusclusterplus
7.2 years ago
kyn
▴ 10
0
votes
5
replies
2.6k
views
Questions on using clusterProfiler
clustering
clusterprofiler
7.5 years ago
zhangducsu
• 0
0
votes
1
reply
1.6k
views
Question about seed in ConsensusClusterPlus, can't repeat the result
bioconductor
consensusclusterplus
clustering
7.5 years ago
afraTW
• 0
0
votes
2
replies
2.0k
views
maSigPro genes from clusters
masigpro
clustering
updated 7.8 years ago by
Mª José Nueda
▴ 90 • written 7.8 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
7.9 years ago
mabdulsa
• 0
0
votes
3
replies
2.3k
views
Prior Control with Mclust package
R
mclust
clustering
updated 7.9 years ago by
Aedin Culhane
▴ 510 • written 7.9 years ago by
mabdulsa
• 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
Jane Merlevede
▴ 90
50 results • Page
1 of 1
Recent ...
Replies
Comment: DESeq filtering specific to contrasts
by
Michael Love
41k
It will likely not filter it out, but really the per-dataset details would affect the results.
Comment: DESeq filtering specific to contrasts
by
Carlin95
• 0
Thanks for clarifying. Could I ask maybe one more thing for my sanity? Let's say you had a multi-factor experiment with contrasts including…
Comment: FilterByExpr low counts with small sample size
by
Jonathan
▴ 10
Thank you for your answer; However, I have some follow-up questions. Following up in In your [1-2-3 article][1], you say that > "... the…
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa
by
Seyram M.
• 0
Thank you very much for your reply! I will do so. Kind regards, Seyram
Comment: Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
by
isaac.vock
• 0
Thank you for your response. I can confirm that setting `-t exon` and/or removing `-s 1` and adding `-O` has no impact on the number of suc…
Votes
Install/Switch between multiple versions of R, Rstudio, and Bioconductor
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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