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coexpression
•
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0
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0
replies
1.0k
views
Sample size on Differential Network Analysis
coexpression
WGCNA
3.7 years ago
Hanna
▴ 10
15
votes
17
replies
26k
views
WGCNA: What is `soft thresholding`?
wgcna
network analysis
network
correlation
coexpression
updated 4.0 years ago by
Lluís Revilla Sancho
▴ 760 • written 8.2 years ago by
jol.espinoz
▴ 40
1
vote
1
reply
1.9k
views
WGCNA gene clusters vs eigengenes
wgcna
network
coexpression
eigengenes
updated 5.2 years ago by
Gordon Smyth
52k • written 5.2 years ago by
bioming
▴ 10
5
votes
3
replies
2.6k
views
Adjusting for known covariates before coexpression analysis with WGCNA
wgcna
coexpression
sva
updated 5.5 years ago by
Peter Langfelder
★ 3.0k • written 5.5 years ago by
mikhael.manurung
▴ 280
3
votes
7
replies
2.7k
views
novice: building gene co-expression network using RNA-Seq data
rna-seq
WGCNA
deseq
method
coexpression
updated 6.6 years ago by
Peter Langfelder
★ 3.0k • written 6.6 years ago by
7kemZmani
▴ 10
0
votes
0
replies
984
views
Principle in selecting the "appropriate" merging value for module generation
wgcna
module
mergecutheight
coexpression
6.7 years ago
tarun2
• 0
0
votes
1
reply
1.3k
views
Differential Coexpression Analysis
differential analysis
differential gene expression
coexpression
correlation
updated 6.7 years ago by
Peter Langfelder
★ 3.0k • written 6.7 years ago by
hkarakurt
▴ 20
0
votes
0
replies
2.0k
views
How to interpret WGCNA's modulePreservation output when comparing 2 networks?
wgcna
modules
coexpression
networks
6.7 years ago
jol.espinoz
▴ 40
0
votes
0
replies
832
views
correlation between PCGs and the neighboring lncRNAs using LINC
coexpression
linc
LINC package
6.8 years ago
edoardobertolini
• 0
2
votes
1
reply
1.6k
views
How to know which soft threshold to use for blockwise modules in WGCNA?
wgcna
coexpression
transcriptome
updated 6.8 years ago by
Peter Langfelder
★ 3.0k • written 6.8 years ago by
jol.espinoz
▴ 40
1
vote
1
reply
1.5k
views
Setting soft threshold when comparing 2 networks in WGCNA?
wgcna
coexpression
cooccurrence
coabundance
network
updated 7.1 years ago by
Lluís Revilla Sancho
▴ 760 • written 7.2 years ago by
jol.espinoz
▴ 40
0
votes
2
replies
2.0k
views
Cutoff for coexpressed gene pairs using Pearson/Spearman correlation
microarray
pearsoncorrelation
coexpression
spearman
updated 7.8 years ago by
James W. MacDonald
67k • written 7.8 years ago by
juls
• 0
1
vote
0
replies
1.5k
views
Gene Set Testing or GSEA for functional annotation of co-expressed ncRNA and coding genes
gsea
ncrna
coexpression
gene set analysis
gene set testing
8.6 years ago
m.fletcher
▴ 20
3
votes
2
replies
2.8k
views
Finding nearest neighbors of given hub gene in a co-expression network module
wgcna
rbgl
graph
coexpression
hub genes
updated 8.7 years ago by
Peter Langfelder
★ 3.0k • written 8.7 years ago by
Alan Smith
▴ 150
2
votes
7
replies
5.0k
views
How to create "trait data" file for WGCNA
wgcna
coexpression
correlation
microarray
updated 8.8 years ago by
Peter Langfelder
★ 3.0k • written 8.8 years ago by
shalinisonar13
▴ 20
0
votes
1
reply
2.9k
views
WGCNA data format?
WGCNA
coexpression
microarray
updated 9.0 years ago by
Peter Langfelder
★ 3.0k • written 9.0 years ago by
michael.ridley6
• 0
13
votes
1
reply
5.1k
views
WGCNA - Compare module preservation between class
WGCNA
coexpression
updated 9.3 years ago by
Peter Langfelder
★ 3.0k • written 9.3 years ago by
abellonau
▴ 60
4
votes
5
replies
6.7k
views
WGCNA Tutorial Selection
wgcna
coexpression
updated 9.5 years ago by
Dan Tenenbaum
★ 8.2k • written 9.5 years ago by
ctruongctruong
▴ 10
18 results • Page
1 of 1
Recent ...
Replies
Answer: scuttle::perFeatureQCMetrics runs very slow for big scRNA-seq data
by
Aaron Lun
★ 28k
You don't mention how your matrix data is being represented, but if it's a file-backed matrix (e.g., `HDF5Matrix` or one of its variants, b…
Comment: contrast matrix design for a continuous variable
by
dtzhu337
• 0
Thank you, Gordon. X is time splines for time point, and yes, it's needed. However, I was also thinking to incorporate time point with se…
Answer: contrast matrix design for a continuous variable
by
Gordon Smyth
52k
Yes, the design and contrasts are correct. Your analysis is also adjusted for covariates defined by X, which I assume is what you want to …
Comment: fail to use addPerROIQC in Rmd
by
liu.n
• 0
That's odd. So it can run successfully within markdown but would be failed when knitting?
Comment: fail to use addPerROIQC in Rmd
by
joseph.joonsang
• 0
> dim(spe) [1] 19962 425
Votes
Answer: contrast matrix design for a continuous variable
A: What's the difference between p.adjust and qvalue?
Answer: DESeq2- merging technical vs biological replicates
Comment: What type of counts data to import for performing Isoform analysis in edgeR
Answer: What type of counts data to import for performing Isoform analysis in edgeR
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