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Showing :
clustering
•
reset
2
votes
3
replies
389
views
"could not find function "readTSGE" in package ctsGE" Error occurs when trying to follow ctsGE package instructions.
GeneExpression
Clustering
ctsGE
4 weeks ago • updated 29 days ago
jbgnielson
• 0
0
votes
3
replies
522
views
Clustering coefficient of synteny network
Network
syntenet
Clustering
coefficient
8 months ago
Alexandros
• 0
0
votes
2
replies
637
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
397
views
maSigPro visualizing individually each plot from each cluster
plot
maSigPro
Clustering
19 months ago
oseias.rf.junior
• 0
0
votes
1
reply
774
views
WGCNA - Network construction and module detection
gene
Clustering
wgcna
flashclust
updated 19 months ago by
andres.firrincieli
▴ 50 • written 19 months ago by
Recep
▴ 20
0
votes
1
reply
608
views
DeSeq Strategies for run to run Replication
DESeq2
Normalization
Clustering
replicate
updated 19 months ago by
Michael Love
41k • written 19 months ago by
Giorgio
• 0
4
votes
3
replies
1.4k
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
1.1k
views
How to judge DEG analysis of these samples could be done by using limma::voom
limma
Clustering
voom
RNA-Seq
20 months ago
Yang Shi
▴ 10
0
votes
0
replies
704
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
708
views
Only 1 gene/ feature is present in module after WGCNA analysis
RNASeq
Clustering
cluster
WGCNA
23 months ago
chiwut.wong
• 0
0
votes
1
reply
558
views
Error running hierClust
hierClust
R
SNPs
clustering
updated 24 months ago by
James W. MacDonald
65k • written 24 months ago by
sekhwal
• 0
0
votes
0
replies
775
views
ConsensusClusterPlus: annotate a class to the heatmap
Clustering
ConsensusClusterPlus
2.6 years ago
Gian
▴ 30
3
votes
2
replies
2.0k
views
Clustering differentially expressed genes in response to multiple treatments (using edgeR)
edger
complexheatmap
R
clustering
updated 3.9 years ago by
Gordon Smyth
50k • written 3.9 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
906
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 4.8 years ago by
James W. MacDonald
65k • written 4.8 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
1.1k
views
Consensus Cluster Plus pre-computed distance matrix
consensusclusterplus
distance
clustering
updated 5.0 years ago by
chris86
▴ 420 • written 5.0 years ago by
neuro3030
• 0
1
vote
2
replies
1.3k
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
2.2k
views
Silhouette Plots for Clustering Quality (Multiple Algorithm)
scRNA-Seq
RNA-Seq
Clustering
Silhouette Plot
updated 5.1 years ago by
Aaron Lun
★ 28k • written 5.1 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
5.4 years ago
faramer86
• 0
3
votes
3
replies
1.0k
views
how to plot trends for differentialy expressed genes from normalized count matrix (EdgeR)
edger
clustering
visualization
updated 5.5 years ago by
James W. MacDonald
65k • written 5.5 years ago by
thindmarsmission
▴ 10
0
votes
0
replies
642
views
DESeq aligned with HOPACH for clustering
clustering
5.7 years ago
ss
• 0
7
votes
6
replies
5.6k
views
scaling data for clustering heat map
edger
heatmap
clustering
differential gene expression
rnaseq
updated 5.8 years ago by
Gordon Smyth
50k • written 5.8 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
952
views
Global Trend Analysis using results from EdgeR
EdgeR
clustering
differential gene expression
consensusclusterplus
kmeans
updated 5.9 years ago by
Aaron Lun
★ 28k • written 5.9 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 6.0 years ago
Daniel Brewer
▴ 100
1
vote
3
replies
1.1k
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
945
views
ConsensusClusterPlus without figures
clustering
updated 23 days ago by
fatmaserrt
• 0 • written 6.4 years ago by
jasonji_19950808
• 0
0
votes
4
replies
1.2k
views
Gene clusters based on gene expression across samples
kmeans
gene expression
clustering
6.5 years ago • updated 6.4 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
2.3k
views
Choosing genes for clustering
limma
clustering
differential gene expression
hierarchical clustering
feature selection
6.5 years ago
lirongrossmann
▴ 80
1
vote
3
replies
1.4k
views
Selecting genes that best separate between two groups
limma
genefilter
ttest
clustering
TPM
6.5 years ago
lirongrossmann
▴ 80
11
votes
8
replies
10k
views
Limma and batch effect
limma
differential gene expression
clustering
removebatcheffect
updated 6.5 years ago by
Gordon Smyth
50k • written 6.5 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 6.6 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
5.2k
views
Cell type specific cell markers for Seurat based analysis.
single cell
seurat
clustering
updated 6.7 years ago by
ankur.chakravarthy.10
▴ 40 • written 6.7 years ago by
hrishi27n
▴ 20
1
vote
4
replies
1.4k
views
OrgDb for Tetrahymena thermophila
annotation
clustering
updated 6.8 years ago by
Guido Hooiveld
★ 3.9k • written 6.8 years ago by
lin.ying.zhang
• 0
1
vote
1
reply
6.1k
views
WGCNA: Different Detect Cut Heights Across Multiple Blocks
wgcna
clustering
gene expression
updated 7.0 years ago by
Peter Langfelder
★ 2.9k • written 7.0 years ago by
ngeraci
▴ 10
3
votes
1
reply
9.6k
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 7.0 years ago by
james.tsakalos
▴ 20 • written 8.5 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 7.1 years ago by
Peter Langfelder
★ 2.9k • written 7.1 years ago by
xie186
• 0
1
vote
1
reply
2.3k
views
ConsensusClusterPlus matrix error
bioconductor
clustering
consensusclusterplus
7.1 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 7.7 years ago by
Mª José Nueda
▴ 90 • written 7.8 years ago by
ls299
• 0
0
votes
0
replies
1.1k
views
Running Mclust package in R, using maximum a posteriori (MAP)
r
mclust
clustering
7.8 years ago
mabdulsa
• 0
0
votes
3
replies
2.2k
views
Prior Control with Mclust package
R
mclust
clustering
updated 7.8 years ago by
Aedin Culhane
▴ 510 • written 7.8 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: limma models out of memory issue on Slurm HPC
by
Jitendra
▴ 10
thanks Gordon, but our methylation epic array input file is quite big and we can't read it in R by just using laptop memory so we need to …
Comment: Doing comparison of RNA-seq data using EdgeR
by
Michael Love
41k
Just to clarify, when I originally posted the title and tags had listed "DESeq2" and then the post was changed after my answer was added. …
Comment: fgsea fork
by
shepherl
3.8k
Not quite sure what you mean by clone or fork the package on latest version of R. Bioconductor runs all builds on the latest version of R.…
Answer: Doing comparison of RNA-seq data using EdgeR
by
Gordon Smyth
50k
It's pretty easy to do a two-group comparison using edgeR, but you seem to be stuck at the initial stage of reading data into R. If you exp…
Answer: Differing results from plotMDS and PCAtools
by
Gordon Smyth
50k
The reason why the two plots are different is that the first plot is a PCA plot while the second is a biplot. Quite different plots. The P…
Votes
transcript name mapping between human and mouse
transcript name mapping between human and mouse
A: Error object and replacement value dimnames differ, when changing column names o
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
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