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Showing :
coexpression
•
reset
0
votes
0
replies
825
views
Sample size on Differential Network Analysis
coexpression
WGCNA
3.1 years ago
Hanna
▴ 10
15
votes
17
replies
23k
views
WGCNA: What is `soft thresholding`?
wgcna
network analysis
network
correlation
coexpression
updated 3.4 years ago by
Lluís Revilla Sancho
▴ 730 • written 7.6 years ago by
jol.espinoz
▴ 40
1
vote
1
reply
1.5k
views
WGCNA gene clusters vs eigengenes
wgcna
network
coexpression
eigengenes
updated 4.6 years ago by
Gordon Smyth
50k • written 4.6 years ago by
bioming
▴ 10
5
votes
3
replies
2.1k
views
Adjusting for known covariates before coexpression analysis with WGCNA
wgcna
coexpression
sva
updated 4.9 years ago by
Peter Langfelder
★ 3.0k • written 4.9 years ago by
mikhael.manurung
▴ 270
3
votes
7
replies
2.3k
views
novice: building gene co-expression network using RNA-Seq data
rna-seq
WGCNA
deseq
method
coexpression
updated 6.0 years ago by
Peter Langfelder
★ 3.0k • written 6.0 years ago by
7kemZmani
▴ 10
0
votes
0
replies
852
views
Principle in selecting the "appropriate" merging value for module generation
wgcna
module
mergecutheight
coexpression
6.1 years ago
tarun2
• 0
0
votes
1
reply
1.1k
views
Differential Coexpression Analysis
differential analysis
differential gene expression
coexpression
correlation
updated 6.1 years ago by
Peter Langfelder
★ 3.0k • written 6.1 years ago by
hkarakurt
▴ 20
0
votes
0
replies
1.7k
views
How to interpret WGCNA's modulePreservation output when comparing 2 networks?
wgcna
modules
coexpression
networks
6.1 years ago
jol.espinoz
▴ 40
0
votes
0
replies
724
views
correlation between PCGs and the neighboring lncRNAs using LINC
coexpression
linc
LINC package
6.2 years ago
edoardobertolini
• 0
2
votes
1
reply
1.4k
views
How to know which soft threshold to use for blockwise modules in WGCNA?
wgcna
coexpression
transcriptome
updated 6.2 years ago by
Peter Langfelder
★ 3.0k • written 6.2 years ago by
jol.espinoz
▴ 40
1
vote
1
reply
1.3k
views
Setting soft threshold when comparing 2 networks in WGCNA?
wgcna
coexpression
cooccurrence
coabundance
network
updated 6.5 years ago by
Lluís Revilla Sancho
▴ 730 • written 6.6 years ago by
jol.espinoz
▴ 40
0
votes
2
replies
1.8k
views
Cutoff for coexpressed gene pairs using Pearson/Spearman correlation
microarray
pearsoncorrelation
coexpression
spearman
updated 7.1 years ago by
James W. MacDonald
65k • written 7.2 years ago by
juls
• 0
1
vote
0
replies
1.3k
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
8.0 years ago
m.fletcher
▴ 20
3
votes
2
replies
2.5k
views
Finding nearest neighbors of given hub gene in a co-expression network module
wgcna
rbgl
graph
coexpression
hub genes
updated 8.1 years ago by
Peter Langfelder
★ 3.0k • written 8.1 years ago by
Alan Smith
▴ 150
2
votes
7
replies
4.6k
views
How to create "trait data" file for WGCNA
wgcna
coexpression
correlation
microarray
updated 8.2 years ago by
Peter Langfelder
★ 3.0k • written 8.2 years ago by
shalinisonar13
▴ 20
0
votes
1
reply
2.7k
views
WGCNA data format?
WGCNA
coexpression
microarray
updated 8.4 years ago by
Peter Langfelder
★ 3.0k • written 8.4 years ago by
michael.ridley6
• 0
13
votes
1
reply
4.6k
views
WGCNA - Compare module preservation between class
WGCNA
coexpression
updated 8.7 years ago by
Peter Langfelder
★ 3.0k • written 8.7 years ago by
abellonau
▴ 60
4
votes
5
replies
6.2k
views
WGCNA Tutorial Selection
wgcna
coexpression
updated 8.8 years ago by
Dan Tenenbaum
★ 8.2k • written 8.9 years ago by
ctruongctruong
▴ 10
18 results • Page
1 of 1
Recent ...
Replies
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
Alexandre
• 0
Hello James, Thank you for your answer and precise exemple ! It is disappointing but makes sense. Best, Alexandre
Comment: How to retrieve gene ontology GO class from gene list?
by
James W. MacDonald
65k
Yes. The `keys` argument to both `select` and `mapIds` will accept a vector (see `?select` for more information). Also, the [vignette][1] f…
Comment: How to retrieve gene ontology GO class from gene list?
by
bandconductor
• 0
Thanks, this is potentially a much faster way than parsing BiomRt. However, it is only returning one GO term right now (biomaRt returns a f…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
James W. MacDonald
65k
Both `RUVseq` and `sva` are meant to be used to remove technical variability. The problem is the identification of variability that is tech…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
Alexandre
• 0
Hello James, Thank you very much for your answer and taking the time to read my post. I understand your remark, but isn't the approach o…
Votes
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
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