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coexpression
•
reset
0
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0
replies
1.2k
views
Sample size on Differential Network Analysis
coexpression
WGCNA
4.6 years ago
Hanna
▴ 10
15
votes
17
replies
30k
views
WGCNA: What is `soft thresholding`?
wgcna
network analysis
network
correlation
coexpression
updated 4.8 years ago by
Lluís Revilla Sancho
▴ 760 • written 9.1 years ago by
jol.espinoz
▴ 40
1
vote
1
reply
2.4k
views
WGCNA gene clusters vs eigengenes
wgcna
network
coexpression
eigengenes
updated 6.1 years ago by
Gordon Smyth
53k • written 6.1 years ago by
bioming
▴ 10
5
votes
3
replies
3.1k
views
Adjusting for known covariates before coexpression analysis with WGCNA
wgcna
coexpression
sva
updated 6.4 years ago by
Peter Langfelder
★ 3.0k • written 6.4 years ago by
mikhael.manurung
▴ 280
3
votes
7
replies
3.3k
views
novice: building gene co-expression network using RNA-Seq data
rna-seq
WGCNA
deseq
method
coexpression
updated 7.5 years ago by
Peter Langfelder
★ 3.0k • written 7.5 years ago by
7kemZmani
▴ 10
0
votes
0
replies
1.2k
views
Principle in selecting the "appropriate" merging value for module generation
wgcna
module
mergecutheight
coexpression
7.5 years ago
tarun2
• 0
0
votes
1
reply
1.5k
views
Differential Coexpression Analysis
differential analysis
differential gene expression
coexpression
correlation
updated 7.6 years ago by
Peter Langfelder
★ 3.0k • written 7.6 years ago by
hkarakurt
▴ 20
0
votes
0
replies
2.3k
views
How to interpret WGCNA's modulePreservation output when comparing 2 networks?
wgcna
modules
coexpression
networks
7.6 years ago
jol.espinoz
▴ 40
0
votes
0
replies
985
views
correlation between PCGs and the neighboring lncRNAs using LINC
coexpression
linc
LINC package
7.6 years ago
edoardobertolini
• 0
2
votes
1
reply
2.0k
views
How to know which soft threshold to use for blockwise modules in WGCNA?
wgcna
coexpression
transcriptome
updated 7.7 years ago by
Peter Langfelder
★ 3.0k • written 7.7 years ago by
jol.espinoz
▴ 40
1
vote
1
reply
1.8k
views
Setting soft threshold when comparing 2 networks in WGCNA?
wgcna
coexpression
cooccurrence
coabundance
network
updated 8.0 years ago by
Lluís Revilla Sancho
▴ 760 • written 8.0 years ago by
jol.espinoz
▴ 40
0
votes
2
replies
2.4k
views
Cutoff for coexpressed gene pairs using Pearson/Spearman correlation
microarray
pearsoncorrelation
coexpression
spearman
updated 8.6 years ago by
James W. MacDonald
68k • written 8.6 years ago by
juls
• 0
1
vote
0
replies
1.8k
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
9.5 years ago
m.fletcher
▴ 20
3
votes
2
replies
3.0k
views
Finding nearest neighbors of given hub gene in a co-expression network module
wgcna
rbgl
graph
coexpression
hub genes
updated 9.5 years ago by
Peter Langfelder
★ 3.0k • written 9.5 years ago by
Alan Smith
▴ 150
2
votes
7
replies
5.6k
views
How to create "trait data" file for WGCNA
wgcna
coexpression
correlation
microarray
updated 9.6 years ago by
Peter Langfelder
★ 3.0k • written 9.7 years ago by
shalinisonar13
▴ 20
0
votes
1
reply
3.2k
views
WGCNA data format?
WGCNA
coexpression
microarray
updated 9.8 years ago by
Peter Langfelder
★ 3.0k • written 9.8 years ago by
michael.ridley6
• 0
13
votes
1
reply
5.8k
views
WGCNA - Compare module preservation between class
WGCNA
coexpression
updated 10.2 years ago by
Peter Langfelder
★ 3.0k • written 10.2 years ago by
abellonau
▴ 60
4
votes
5
replies
7.3k
views
WGCNA Tutorial Selection
wgcna
coexpression
updated 10.3 years ago by
Dan Tenenbaum
★ 8.2k • written 10.3 years ago by
ctruongctruong
▴ 10
18 results • Page
1 of 1
Recent ...
Replies
Comment: Help with defining groups
by
Phinney, Brett
▴ 10
I got it working , thank you!!!
Comment: Check removeBatchEffect effectiveness
by
massimo
• 0
I would kindly ask for additional support. When not including the design_timepoint argument in removeBatchEffect and thus keeping the inter…
Comment: Error Loading Experiment from SimBenchData Package
by
ksankaran
• 0
Aha, that was it! The object was class Seurat, but I didn't have it installed. After installing, everything works as expected.
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset?
by
ATpoint
★ 5.0k
Is a method that is so computationally expensive really beneficial and necessary? You seem to have biological replication, don't you, so ps…
Answer: NA values for DESeq2 p-values and adjusted p-values using large sample sizes
by
ATpoint
★ 5.0k
Outliers without replacement, independent filtering or all-zero counts for that gene. That's the three options that trigger NAs https://bio…
Votes
Comment: Check removeBatchEffect effectiveness
Gene expression associated with continuous (quantitative) traits (Limma/edgeR/correlation)
Answer: Error Loading Experiment from SimBenchData Package
Comment: incomplete imputation of missing values with LEA impute() function
Answer: Expected memory usage for analyzing large single-cell seq datasets (> 450,000 ce
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