Showing : WGCNA • reset
0
votes
1
reply
147
views
WGCNA with TPM tables
RNASeq WGCNA ComparativeGenomics
updated 28 days ago by ★ 4.6k • written 28 days ago by • 0
6
votes
6
replies
3.9k
views
WGCNA coupled with differential expression analysis: question about baseline module detection
wgcna WGCNA
written 4.7 years ago by ▴ 60
0
votes
0
replies
120
views
WGCNA module preservation using only adjacency matrix
WGCNA
5 weeks ago yang1641 • 0
3
votes
4
replies
488
views
What should be the normalization protocol for RNA seq data for WGCNA?
RNA_seqdata Normalization_method WGCNA
9 weeks ago sukeshinik5 ▴ 20
1
vote
1
reply
341
views
WGCNA
DEGselection RNASeqData WGCNA
updated 10 weeks ago by ▴ 760 • written 10 weeks ago by • 0
0
votes
0
replies
210
views
WGCNA: Problem with selecting soft threshold
biologicalnetworkanalysis genomes RNA-Seq co-expression wgcna
3 months ago Fernanda • 0
0
votes
1
reply
302
views
WGCNA Choosing soft threshold power below R^2 0.8
WGCNA
updated 3 months ago by ▴ 760 • written 3 months ago by • 0
0
votes
1
reply
311
views
Ideal approach to adjust for covariates for WGCNA
WGCNA wgcna
updated 3 months ago by 67k • written 3 months ago by • 0
0
votes
6
replies
2.7k
views
blockwiseModule crashes in the end and doesn't generate modules
WGCNA
written 20 months ago by • 0
1
vote
3
replies
3.5k
views
WGNCA kME vs. kIM
WGCNA
updated 7 months ago by • 0 • written 9.3 years ago by ▴ 30
0
votes
0
replies
262
views
query regarding how to apply WGCNA on replicates
replicatesRNAseq WGCNA
7 months ago k200987 • 0
0
votes
2
replies
493
views
voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom Limma WGCNA
8 months ago Gimena • 0
0
votes
2
replies
561
views
WGCNA: analysis of complex trait associations with regressions
Regression WGCNA
8 months ago w.cookson • 0
0
votes
1
reply
424
views
problem with ClusterRepro function
WGCNA
updated 9 months ago by 67k • written 9 months ago by • 0
0
votes
1
reply
816
views
WGCNA | plotDendroAndColors ERROR
plotDendroAndColor WGCNA
updated 10 months ago by ★ 4.6k • written 10 months ago by • 0
0
votes
2
replies
1.1k
views
Trouble generating a dendrogram with colored gene modules using WGCNA for large RNA-seq experiment
WGCNA
written 12 months ago by • 0
4
votes
3
replies
2.0k
views
WGCNA documentation not available
WGCNA
written 12 months ago by ▴ 10
0
votes
2
replies
1.6k
views
using WGCNA, positive or negative corrlation between genes composing modules.
correlation wgcna network
updated 7 months ago by • 0 • written 2.1 years ago by • 0
0
votes
1
reply
1.3k
views
WGCNA correlation sign differences between eigen genes/ hub genes and clinical traits
hub correlation eigen WGCNA
updated 12 months ago by • 0 • written 3.0 years ago by • 0
1
vote
2
replies
1.2k
views
Different results from blockwiseModules and blockwiseConsensusModules individual TOM
RNASeqData WGCNA consensusnetworks
12 months ago Levi • 0
0
votes
2
replies
532
views
WGCNA less samples
RNA-Seq WGCNA Worms
13 months ago davca • 0
0
votes
1
reply
762
views
WGCNA tutorial docs needed: Horvath Lab site down
WGCNA
updated 13 months ago by ★ 4.6k • written 13 months ago by • 0
1
vote
1
reply
705
views
How do I select a subset of genes for functional enrichment(GO/KEGG) analysis from WGCNA results?
WGCNA
updated 14 months ago by ▴ 200 • written 14 months ago by ▴ 10
0
votes
1
reply
592
views
TOMsimilarityFromExpr the returned matrix has NaN values except for diagonal 1
TOMsimilarityFromExpr WGCNA
updated 16 months ago by ★ 4.6k • written 16 months ago by • 0
0
votes
1
reply
4.4k
views
Is it proper to compare two WGCNA matrixes if they were raised to different power (soft threshold)?
Network cluster WGCNA RNASeq
updated 17 months ago by 67k • written 17 months ago by • 0
1
vote
1
reply
700
views
WGCNA Cluster batch effect
BatchEffect TCGA WGCNA
updated 18 months ago by ★ 4.6k • written 18 months ago by • 0
0
votes
1
reply
969
views
Hub genes selection in WGCNA
wgcna WGCNA hubgene
updated 18 months ago by ★ 4.6k • written 18 months ago by ▴ 20
2
votes
5
replies
1.7k
views
DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 8 months ago by • 0 • written 18 months ago by • 0
3
votes
6
replies
1.2k
views
Question on constructing design matrix and defining contrasts for analysis
wgcna DESeq2 edgeR limma design
updated 18 months ago by 52k • written 19 months ago by ▴ 10
1
vote
0
replies
735
views
WGCNA of two different cohorts study
DifferentialExpression WGCNA
updated 18 months ago by 43k • written 19 months ago by ▴ 20
2
votes
1
reply
818
views
WGCNA: many over and under-expressed features in modules of a signed network
WGCNA wgcna_package
updated 18 months ago by ▴ 50 • written 19 months ago by ▴ 10
0
votes
0
replies
588
views
blockwiseConsensusModules won't save individualTOM data?
blockwiseconsensusModules WGCNA consensus
19 months ago Levi • 0
3
votes
7
replies
1.8k
views
"Degree values are the same for all nodes in a network imported from WGCNA to Cytoscape using RCy3. Seeking insights and potential causes."
Cytoscape RCy3 Networkvisualization WGCNA
19 months ago Ortega-C ▴ 10
0
votes
1
reply
693
views
WGCNA for one perturbation time series (pooled from two independent replicates)?
WGCNA
updated 19 months ago by ★ 4.6k • written 19 months ago by • 0
0
votes
0
replies
729
views
Problems with the input (from TPM) - How to remove isoforms in WGCNA
Arabidopsis_thaliana removeisoforms WGCNA
20 months ago Ortega-C ▴ 10
0
votes
2
replies
820
views
WGCNA problem
WGCNA
updated 20 months ago by ▴ 10 • written 20 months ago by • 0
0
votes
0
replies
740
views
WGCNA approach on multiregional brain transcriptomes
Neurotranscriptome RNAseq WGCNA
20 months ago Levi • 0
0
votes
0
replies
611
views
Module Trait Corelation
WGCNA
21 months ago allanokwaro • 0
2
votes
3
replies
1.3k
views
Batch correction and Deseq2
DESeq2 WGCNA Normalization NormalyzerDE BatchEffect
updated 21 months ago by ★ 4.6k • written 21 months ago by ▴ 20
0
votes
0
replies
655
views
How to draw module significance barplot?
module_significance barplot WGCNA
22 months ago Sooni ▴ 10
0
votes
0
replies
673
views
Multiple way network preservation
wgcna
22 months ago madzayasodara • 0
0
votes
0
replies
747
views
WGCNA TOM file empty
WGCNA TOM
22 months ago gianni.drm • 0
0
votes
0
replies
1.2k
views
WGCNA Heatmap and Export to Cytoscape Not Working
Cytoscape Heatmap heatmaps WGCNA
22 months ago gianni.drm • 0
0
votes
1
reply
1.3k
views
WGCNA soft thresholding suggesting a power of 1
independence thresholding WGCNA connectivity scale
updated 9 months ago by ▴ 740 • written 22 months ago by • 0
0
votes
1
reply
672
views
In WGCNA which is the matrix on which the eigen decomposition is run to get the module eigen gene
WGCNA
updated 23 months ago by ▴ 50 • written 23 months ago by • 0
0
votes
0
replies
804
views
Does verboseScatterplot in WGCNA package allow for highlighting a subset of genes
WGCNA
23 months ago S • 0
0
votes
0
replies
796
views
Problems running WGCNA
WGCNA
2.0 years ago S • 0
0
votes
0
replies
670
views
coexpression networks
WGCNA igraph
2.1 years ago María José • 0
0
votes
0
replies
725
views
A question about GWENA R/Bioconductor package
proteomics GWENA Proteomics WGCNA
2.1 years ago Abdullah • 0
0
votes
0
replies
1.1k
views
WGCNA: minModuleSize is not responding correctly
Network minModuleSize WGCNA wgcna
2.1 years ago • updated 12 weeks ago bioinformaticssrm2011 • 0
50 results • Page 1 of 1
Recent ...
Replies
Answer: Cross-validation with multiple control subgroups in limma by Gordon Smyth 52k
limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Robert Castelo ★ 3.4k
Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS by Aidan ▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings? by Michael Love 43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by xiaofeiwang198266 • 0
Thanks for your reply!
Votes
C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
A: Expected counts from RSEM in DESeq2
A: Using RSEM reads for DESeq2
Awards • All
Popular Question to Ali Barry ▴ 40
Popular Question to gabriel.hoffman ▴ 170
Popular Question to Jenny Drnevich ★ 2.0k
Popular Question to martin.grigorov ▴ 10
Scholar to James W. MacDonald 67k
Locations • All
France, 2 minutes ago
United States, 31 minutes ago
United Kingdom, 35 minutes ago
WEHI, Melbourne, Australia, 3 hours ago
30 N Gould St STE 39034 Sheridan, WY, 3 hours ago
Traffic: 547 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6