Showing : wgcna • reset
15
votes
17
replies
23k
views
WGCNA: What is `soft thresholding`?
wgcna network analysis network correlation coexpression
updated 3.4 years ago by ▴ 730 • written 7.6 years ago by ▴ 40
14
votes
4
replies
14k
views
WGCNA Hub Gene Selection Method
WGCNA Hub Genes KmE Intramodular Connectivity
updated 8.8 years ago by ★ 3.0k • written 8.8 years ago by ▴ 150
13
votes
1
reply
4.6k
views
WGCNA - Compare module preservation between class
WGCNA coexpression
updated 8.7 years ago by ★ 3.0k • written 8.7 years ago by ▴ 60
12
votes
4
replies
3.8k
views
WGCNA following salmon/DESeq2
deseq2 wgcna salmon
updated 5.4 years ago by ★ 3.0k • written 5.4 years ago by ▴ 30
11
votes
5
replies
7.3k
views
Theoretical WGCNA Question
WGCNA Theory Scale-Free Topology
updated 1 day ago by • 0 • written 9.1 years ago by ▴ 150
11
votes
3
replies
4.9k
views
WGCNA - Signed vs signed hybrid networks
wgcna
updated 7.8 years ago by ★ 3.0k • written 7.8 years ago by ▴ 20
11
votes
8
replies
8.5k
views
Pre-processing of RNA-Seq data for WGCNA and DGE
WGCNA RNA-Seq DESeq2 voom removebatcheffect()
updated 7.6 years ago by ★ 3.0k • written 7.6 years ago by ▴ 70
11
votes
5
replies
3.1k
views
WGCNA with paired samples
wgcna paired samples exercise
updated 7.7 years ago by ★ 3.0k • written 7.7 years ago by ▴ 60
10
votes
1
reply
3.6k
views
WGCNA: Module preservation vs consensus analysis
WGCNA wgcna
updated 3.1 years ago by ▴ 70 • written 3.2 years ago by ▴ 60
9
votes
2
replies
4.2k
views
Filtering low variance genes for WGCNA
deseq2 WGCNA
updated 4.2 years ago by ★ 3.0k • written 4.2 years ago by ▴ 30
9
votes
7
replies
4.1k
views
WGCNA: relate modules to binary trait
WGCNA module eigengene binary trait R
updated 5.3 years ago by ▴ 30 • written 5.3 years ago by ▴ 50
8
votes
6
replies
4.4k
views
Subset WGCNA results for export to Cytoscape
wgcna
updated 4.5 years ago by ★ 3.0k • written 4.6 years ago by ▴ 160
8
votes
17
replies
14k
views
WGCNA for RNA-Seq Sample Set, Outliers, and Spearman correlation
WGCNA Sample Size Outliers
updated 8.6 years ago by • 0 • written 9.2 years ago by ▴ 150
8
votes
4
replies
6.9k
views
WGCNA: overlapping colors in plotDendroAndColors?
wgcna plotDendroAndColors Network
updated 9.6 years ago by ★ 3.0k • written 9.6 years ago by ▴ 180
7
votes
3
replies
5.4k
views
WGCNA sample size minimum: why?
wgcna
updated 3.1 years ago by • 0 • written 4.8 years ago by ▴ 160
7
votes
4
replies
2.7k
views
Minimum number of samples per treatment/group for WGCNA analysis
WGCNA RNA-seq GCN gene coexpression network
updated 4.9 years ago by ▴ 20 • written 5.0 years ago by ▴ 50
7
votes
9
replies
3.6k
views
WGCNA - networking RNA seq gives only one module!
WGCNA R network co-expression
updated 15 months ago by ★ 3.0k • written 5.0 years ago by ▴ 10
7
votes
9
replies
1.3k
views
Unclear of calculating correlations with case+control samples together
WGCNA wgcna
7.5 years ago mocharrout ▴ 20
6
votes
2
replies
4.5k
views
WGCNA: how to change module color
wgcna
updated 5.5 years ago by ★ 3.0k • written 5.5 years ago by ▴ 20
6
votes
8
replies
8.2k
views
WGCNA export to cytoscape
wgcna cytoscape
updated 6.3 years ago by ▴ 60 • written 6.9 years ago by ▴ 60
6
votes
6
replies
2.7k
views
WGCNA coupled with differential expression analysis: question about baseline module detection
wgcna WGCNA
written 4.0 years ago by ▴ 60
5
votes
3
replies
934
views
Steep dendrograms and few modules. WGCNA on RNA seq data
RNA seq wgcna
updated 4.9 years ago by ★ 3.0k • written 4.9 years ago by ▴ 20
5
votes
3
replies
2.4k
views
Analyzing RNA-seq data by WGCNA
wgcna rna-seq
updated 7.6 years ago by ★ 3.0k • written 7.6 years ago by ▴ 20
5
votes
6
replies
6.6k
views
WGCNA - module membership via max kME?
wgcna modules
updated 6.5 years ago by ★ 3.0k • written 6.5 years ago by ▴ 10
5
votes
8
replies
3.9k
views
Problem about picking soft threshold power in WGCNA software
wgcna rnaseq
written 7.1 years ago by ▴ 40
5
votes
7
replies
2.7k
views
problem for Using RNA-seq data-set in WGCNA
WGCNA RNA-seq
updated 5.8 years ago by ★ 3.0k • written 5.8 years ago by ▴ 10
5
votes
1
reply
1.8k
views
WGCNA - looking for over-representation of DEGs within gene networks
wgcna r differential gene expression bioconductor
updated 8.3 years ago by ★ 3.0k • written 8.3 years ago by ▴ 30
5
votes
2
replies
4.1k
views
[WGCNA]How to visualize network of genes in one module
WGCNA network
updated 4.2 years ago by ★ 3.9k • written 4.2 years ago by ▴ 30
5
votes
8
replies
4.4k
views
WGCNA tutorial II
WGCNA female and male datasets
updated 2.1 years ago by • 0 • written 4.0 years ago by ▴ 60
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 ★ 3.0k • written 4.9 years ago by ▴ 270
4
votes
6
replies
5.5k
views
WGCNA automatic vs manual network creation
WGCNA
updated 8.5 years ago by ★ 3.0k • written 8.5 years ago by ▴ 30
4
votes
6
replies
1.1k
views
WGCNA: consensusTOM() doesn't save TOMs & returns setNames error (but sets are named)
WGCNA
updated 5.2 years ago by ★ 3.0k • written 5.2 years ago by ▴ 20
4
votes
3
replies
898
views
WGCNA from different lengths RNAseq read
wgcna network co-expression rnaseq
updated 5.0 years ago by ★ 3.0k • written 5.0 years ago by ▴ 80
4
votes
3
replies
827
views
WGCNA documentation not available
WGCNA
written 4 months ago by ▴ 10
4
votes
5
replies
2.2k
views
WGCNA network visualisation in RCyjs
WGCNA rcytoscape network analysis
updated 7.9 years ago by ▴ 470 • written 7.9 years ago by ▴ 20
4
votes
9
replies
3.3k
views
WGCNA | pickSoftThreshold.fromSimilarity not working for input similarity matrix
WGCNA similarity correlation bioconductor rnaseq
updated 7.2 years ago by ★ 3.0k • written 7.2 years ago by ▴ 40
4
votes
2
replies
2.8k
views
WGCNA blockwiseModules parallelisation question
wgcna rnaseq
updated 7.7 years ago by ★ 3.0k • written 7.7 years ago by ▴ 10
4
votes
2
replies
4.0k
views
Selecting genes based on expressional variance
geneexpression wgcna rnaseq
updated 9.6 years ago by 1.6k • written 9.6 years ago by ▴ 250
4
votes
1
reply
1.8k
views
WGCNA always requires trait data?
wgcna rnaseq
updated 6.9 years ago by ★ 13k • written 6.9 years ago by ▴ 20
4
votes
2
replies
1.8k
views
The Mac version of R always reports an error when installing WGCNA
software error WGCNA mac
updated 4.0 years ago by 65k • written 4.0 years ago by • 0
4
votes
5
replies
6.1k
views
WGCNA Tutorial Selection
wgcna coexpression
updated 8.8 years ago by ★ 8.2k • written 8.8 years ago by ▴ 10
4
votes
2
replies
3.4k
views
WGCNA: Relating Modules to Categorical External Traits
WGCNA BetweenGroupComparison
8.4 years ago mjc5038 ▴ 30
3
votes
6
replies
4.5k
views
WGCNA gene significance and module membership
WGCNA R
updated 17 months ago by ★ 3.0k • written 4.4 years ago by • 0
3
votes
3
replies
2.5k
views
WGCNA module colors not displaying correctly
WGCNA
updated 4.2 years ago by ★ 3.0k • written 4.2 years ago by ▴ 30
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 ★ 3.0k • written 6.0 years ago by ▴ 10
3
votes
1
reply
1.7k
views
Consensus modules preservation WGCNA
WGCNA Networks
updated 5.1 years ago by ★ 3.0k • written 5.1 years ago by ▴ 20
3
votes
4
replies
3.4k
views
interactive networks from WGCNA clusters
wgcna rcytoscape
updated 7.8 years ago by ▴ 120 • written 7.8 years ago by ▴ 20
3
votes
9
replies
2.2k
views
problem for finding soft thresholding in WGCNA algorithm
wgcna abline function Scale independence diagram
5.5 years ago modarzi ▴ 10
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 ★ 3.0k • written 8.1 years ago by ▴ 150
3
votes
1
reply
2.9k
views
WGCNA: single channel microarray, one categorical covariate, how to apply it?
wgcna twochannel onechannel
updated 9.4 years ago by ★ 3.0k • written 9.4 years ago by ▴ 20
50 results • Page 1 of 1
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Answer: Cannabis and KEGGgraph by deeenes ▴ 30
Hello, I'm a developer of the `OmnipathR` package, and I wrote [a function][1] to access certain KEGG data: library(OmnipathR) cs…
Answer: RNAseq:Technical replicates from different batches by Gordon Smyth 50k
I am not entirely clear what you mean by "technical" replicates in this case. Are they resequencing of the same RNA samples or are they fre…
Comment: DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, param by russ.bainer ▴ 10
Hi, I'm hitting this too. As far as I can tell my DataTrack is fine, but perhaps I am missing something. Notably the same code works on o…
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions by Chris • 0
Hi Robert, If I don't want to use all pathway in c2 gene set but only a few pathways of interested, how can I do that? So we try to get a …
Comment: How to retrieve detailed regression results from deseq2 by Weiqian ▴ 10
Hi Michael, thanks for the answer! I'll have a look : )
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Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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