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How to compute the "completeness" of a KEGG module using a set of KEGG orthologs? (Module Completion Ratio)
KEGG KEGGREST keggorthology Metagenomics
3.8 years ago jol.espinoz ▴ 40
0
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0
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1.4k
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Why is `scale-free topology` estimated as -sign(slope) * (R^2) in WGCNA?
Network StatisticalMethod WGCNA ExpressionData
4.0 years ago jol.espinoz ▴ 40
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1.6k
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Comment: Comment: P adjusted values in Deseq2
4.0 years ago jol.espinoz ▴ 40
15
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17
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26k
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WGCNA: What is `soft thresholding`?
wgcna network analysis network correlation coexpression
updated 4.1 years ago by ▴ 760 • written 8.3 years ago by ▴ 40
1
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1
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1.3k
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How to use ENCprime via coRdon with a custom background sequence set?
software codon usage bias dna
updated 5.1 years ago by ▴ 10 • written 5.1 years ago by ▴ 40
1
vote
0
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1.4k
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dynamicTreeCut and WGCNA show clusters overlapping. Why is this?
dynamictreecut wgcna hierarchical clustering
6.3 years ago jol.espinoz ▴ 40
0
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0
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1.7k
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Comment: C: [metagenomeSeq] "Error: Warning sample with one or zero features" from cumNormSt
6.6 years ago jol.espinoz ▴ 40
0
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1
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1.7k
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[metagenomeSeq] "Error: Warning sample with one or zero features" from cumNormStatFast
metagenomeseq cumNormStatFast features error
6.6 years ago jol.espinoz ▴ 40
0
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0
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2.0k
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How to interpret WGCNA's modulePreservation output when comparing 2 networks?
wgcna modules coexpression networks
6.8 years ago jol.espinoz ▴ 40
1
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1
reply
3.6k
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Cannot use Bioconductor with new conda R installation?
bioconductor biocinstaller installation conda
6.9 years ago jol.espinoz ▴ 40
1
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0
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3.6k
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Answer: A: Cannot use Bioconductor with new conda R installation?
6.9 years ago jol.espinoz ▴ 40
2
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1
reply
1.7k
views
How to know which soft threshold to use for blockwise modules in WGCNA?
wgcna coexpression transcriptome
updated 6.9 years ago by ★ 3.0k • written 6.9 years ago by ▴ 40
0
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0
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1.5k
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What is the recommended method for running WGCNA on large metatranscriptomic dataset?
wgcna transcriptome big data metagenomics gene expression
6.9 years ago jol.espinoz ▴ 40
1
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1
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1.6k
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Setting soft threshold when comparing 2 networks in WGCNA?
wgcna coexpression cooccurrence coabundance network
updated 7.2 years ago by ▴ 760 • written 7.2 years ago by ▴ 40
0
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0
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12k
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Comment: C: RNA-Seq, generate batch-free count matrix
7.5 years ago jol.espinoz ▴ 40
0
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1
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3.4k
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Comment: C: Can edgeR TMM normalization be used for other count data?
7.7 years ago jol.espinoz ▴ 40
6
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4
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3.4k
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Can edgeR TMM normalization be used for other count data?
edgeR tmm normalization counts
updated 7.7 years ago by 67k • written 7.7 years ago by ▴ 40
0
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0
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1.8k
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Comment: C: pvclust and distance matrices
7.9 years ago jol.espinoz ▴ 40
0
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0
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3.8k
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Comment: C: WGCNA | pickSoftThreshold.fromSimilarity not working for input similarity matrix
7.9 years ago jol.espinoz ▴ 40
4
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9
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3.8k
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WGCNA | pickSoftThreshold.fromSimilarity not working for input similarity matrix
WGCNA similarity correlation bioconductor rnaseq
updated 7.9 years ago by ★ 3.0k • written 7.9 years ago by ▴ 40
0
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0
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2.2k
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Comment: C: WGCNA | Which module is reserved for outliers/unclustered genes?
7.9 years ago jol.espinoz ▴ 40
0
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0
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3.8k
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Comment: C: WGCNA | pickSoftThreshold.fromSimilarity not working for input similarity matrix
7.9 years ago jol.espinoz ▴ 40
0
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1
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3.8k
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Comment: C: WGCNA | pickSoftThreshold.fromSimilarity not working for input similarity matrix
7.9 years ago jol.espinoz ▴ 40
1
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2
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2.2k
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WGCNA | Which module is reserved for outliers/unclustered genes?
wgcna
updated 7.9 years ago by ▴ 760 • written 7.9 years ago by ▴ 40
0
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0
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3.8k
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Comment: C: WGCNA | pickSoftThreshold.fromSimilarity not working for input similarity matrix
7.9 years ago jol.espinoz ▴ 40
0
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1
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3.8k
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Comment: C: WGCNA | pickSoftThreshold.fromSimilarity not working for input similarity matrix
7.9 years ago jol.espinoz ▴ 40
2
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2
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8.5k
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edgeR: How is FDR calculated for logFC? (False Discovery Rate)
edgeR bioconductor fdr statistics differential gene expression
8.1 years ago jol.espinoz ▴ 40
0
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0
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8.5k
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Comment: C: edgeR: How is FDR calculated for logFC? (False Discovery Rate)
8.1 years ago jol.espinoz ▴ 40
0
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0
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26k
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Comment: C: WGCNA: What is `soft thresholding`?
8.3 years ago jol.espinoz ▴ 40
0
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2
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26k
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Comment: C: WGCNA: What is `soft thresholding`?
8.3 years ago jol.espinoz ▴ 40
0
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1
reply
26k
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Comment: C: WGCNA: What is `soft thresholding`?
8.3 years ago jol.espinoz ▴ 40
0
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1
reply
26k
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Comment: C: WGCNA: What is `soft thresholding`?
8.3 years ago jol.espinoz ▴ 40
0
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0
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26k
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Comment: C: WGCNA: What is `soft thresholding`?
8.3 years ago jol.espinoz ▴ 40
0
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2
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26k
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Comment: C: WGCNA: What is `soft thresholding`?
8.3 years ago jol.espinoz ▴ 40
0
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1
reply
4.2k
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Comment: C: source(biocLite.R) leads to this error >>> Peer certificate cannot be authentica
8.4 years ago jol.espinoz ▴ 40
0
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2
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4.2k
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Comment: C: source(biocLite.R) leads to this error >>> Peer certificate cannot be authentica
8.4 years ago jol.espinoz ▴ 40
0
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5
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4.2k
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source(biocLite.R) leads to this error >>> Peer certificate cannot be authenticated with given CA certificates
biocinstaller installation install source conda
updated 8.4 years ago by 25k • written 8.4 years ago by ▴ 40
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