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coexpression
•
reset
0
votes
0
replies
784
views
Sample size on Differential Network Analysis
coexpression
WGCNA
3.0 years ago
Hanna
▴ 10
15
votes
17
replies
22k
views
WGCNA: What is `soft thresholding`?
wgcna
network analysis
network
correlation
coexpression
updated 3.3 years ago by
Lluís Revilla Sancho
▴ 730 • written 7.5 years ago by
jol.espinoz
▴ 40
1
vote
1
reply
1.4k
views
WGCNA gene clusters vs eigengenes
wgcna
network
coexpression
eigengenes
updated 4.5 years ago by
Gordon Smyth
50k • written 4.5 years ago by
bioming
▴ 10
5
votes
3
replies
2.0k
views
Adjusting for known covariates before coexpression analysis with WGCNA
wgcna
coexpression
sva
updated 4.8 years ago by
Peter Langfelder
★ 2.9k • written 4.8 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 5.9 years ago by
Peter Langfelder
★ 2.9k • written 5.9 years ago by
7kemZmani
▴ 10
0
votes
0
replies
828
views
Principle in selecting the "appropriate" merging value for module generation
wgcna
module
mergecutheight
coexpression
6.0 years ago
tarun2
• 0
0
votes
1
reply
1.0k
views
Differential Coexpression Analysis
differential analysis
differential gene expression
coexpression
correlation
updated 6.0 years ago by
Peter Langfelder
★ 2.9k • written 6.0 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
6.0 years ago
jol.espinoz
▴ 40
0
votes
0
replies
704
views
correlation between PCGs and the neighboring lncRNAs using LINC
coexpression
linc
LINC package
6.1 years ago • updated 6.0 years ago
edoardobertolini
• 0
2
votes
1
reply
1.3k
views
How to know which soft threshold to use for blockwise modules in WGCNA?
wgcna
coexpression
transcriptome
updated 6.1 years ago by
Peter Langfelder
★ 2.9k • written 6.1 years ago by
jol.espinoz
▴ 40
1
vote
1
reply
1.2k
views
Setting soft threshold when comparing 2 networks in WGCNA?
wgcna
coexpression
cooccurrence
coabundance
network
updated 6.4 years ago by
Lluís Revilla Sancho
▴ 730 • written 6.5 years ago by
jol.espinoz
▴ 40
0
votes
2
replies
1.7k
views
Cutoff for coexpressed gene pairs using Pearson/Spearman correlation
microarray
pearsoncorrelation
coexpression
spearman
updated 7.0 years ago by
James W. MacDonald
65k • written 7.0 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
7.9 years ago
m.fletcher
▴ 20
3
votes
2
replies
2.4k
views
Finding nearest neighbors of given hub gene in a co-expression network module
wgcna
rbgl
graph
coexpression
hub genes
updated 8.0 years ago by
Peter Langfelder
★ 2.9k • written 8.0 years ago by
Alan Smith
▴ 150
2
votes
7
replies
4.5k
views
How to create "trait data" file for WGCNA
wgcna
coexpression
correlation
microarray
updated 8.1 years ago by
Peter Langfelder
★ 2.9k • written 8.1 years ago by
shalinisonar13
▴ 20
0
votes
1
reply
2.7k
views
WGCNA data format?
WGCNA
coexpression
microarray
updated 8.3 years ago by
Peter Langfelder
★ 2.9k • written 8.3 years ago by
michael.ridley6
• 0
13
votes
1
reply
4.5k
views
WGCNA - Compare module preservation between class
WGCNA
coexpression
updated 8.6 years ago by
Peter Langfelder
★ 2.9k • written 8.6 years ago by
abellonau
▴ 60
4
votes
5
replies
6.0k
views
WGCNA Tutorial Selection
wgcna
coexpression
updated 8.7 years ago by
Dan Tenenbaum
★ 8.2k • written 8.8 years ago by
ctruongctruong
▴ 10
18 results • Page
1 of 1
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Replies
Comment: DEG Filtering
by
Gordon Smyth
50k
RMA normalization is good but batch correction using NOISeq isn't right. Data shouldn't be batch corrected before the limma analysis and NO…
Answer: maftools: Error in validateMaf(maf = maf, isTCGA = isTCGA, rdup = removeDuplicat
by
snijesh
▴ 20
You can try: using `read.delim` or `fread`. ``` my_maf = data.table::fread("path/to/maf/sample.maf") my_maf = read.maf(maf = my_maf) …
Comment: DEG Filtering
by
Amit
• 0
Hi Gordon, Thank you for your response and advice. I want to analyze Dataset GSE18090 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi) whic…
Comment: edgeR, 3 x 2 design with a batch effect and contrasts
by
Gordon Smyth
50k
Yes, that is a quote from [A guide to creating design matrices for gene expression experiments](https://bioconductor.org/packages/release/w…
Comment: edgeR, 3 x 2 design with a batch effect and contrasts
by
JKim
• 0
Thank you. I think I found why the order matters. > Although an intercept-free design matrix has been coded using the 0+ notation, the in…
Votes
C: How to check that the reads in two fastq files are in the same order
Answer: edgeR, 3 x 2 design with a batch effect and contrasts
Answer: Need help with creating and plotting temporal clustering analysis of DEGs
Answer: Problem converting msigdb Human symbols to Zebrafish in gmt format
Answer: Problem converting msigdb Human symbols to Zebrafish in gmt format
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