0
votes
1
reply
85
views
How to generate circular cnetplot and color nodes and edges in the same plot ?
cnetplot DESeq2
updated 7 hours ago by ★ 4.1k • written 23 hours ago by • 0
0
votes
0
replies
18
views
Unable to find sample sheet file for ChAMP methylation data analysis
MethylationArray MethylationArrayData methylationArrayAnalysis
11 hours ago Anki • 0
0
votes
4
replies
154
views
Is there a way to do DEG analysis across two batches sharing one sample only?
DESeq2 DifferentialExpression RNASeqData BatchEffect
1 day ago georgeyu703 • 0
0
votes
1
reply
84
views
affymetrix
genomes Annotation
updated 2 days ago by 67k • written 2 days ago by • 0
0
votes
1
reply
102
views
Problems with GSEA
GSEABase
updated 2 days ago by ★ 4.1k • written 2 days ago by • 0
0
votes
1
reply
123
views
Error compiling Rbowtie2 in R-4.4 (Bioconductor 3.20 and probably 3.19)
Rbowtie
6 days ago • updated 2 days ago ja.garcia • 0
0
votes
0
replies
30
views
WGCNA: Can we use high power (26) for signed network?
Networkanalysis RNA-seqdata Powerselection WGCNA
2 days ago Vinesh • 0
1
vote
1
reply
123
views
SingleCellExperiment convenience function for metadata+expression?
SpatialExperiment SingleCellExperiment SpatialFeatureExperiment
updated 2 days ago by ▴ 750 • written 6 days ago by • 0
0
votes
4
replies
318
views
How to sort negative log2FC or FC in RNAseq for GSEA?
DESeq2 GSEA clusterProfiler
3 days ago • updated 1 day ago Quang NN ▴ 10
2
votes
4
replies
307
views
EdgeR Biological CVs
edgeR
updated 4 hours ago by 52k • written 3 days ago by • 0
0
votes
0
replies
40
views
WGCNA sample-data preprocessing order
Microarray WGCNA GeneExpression
3 days ago Reuben • 0
0
votes
1
reply
212
views
Curiously shaped volcano plot with using oarfish + swish to do differential gene expression on long-read RNA-seq
fishpond fish
updated 4 days ago by 43k • written 6 days ago by • 0
0
votes
0
replies
27
views
Problem with PCAtool as dependencie
COTAN PCAtools
4 days ago Silvia • 0
1
vote
2
replies
211
views
Detecting genomic signatures of drug resistance breast cancer in transcriptomic data
TransOmicsData signatureSearchData StatisticalMethod
written 8 weeks ago by • 0
0
votes
2
replies
46k
views
SingleR Label.Ont
SingleR
written 16 months ago by • 0
0
votes
0
replies
33
views
cnvEQTL : Error in cpm.default(y, lib.size = lib.size) : NA counts not allowed
CNVRanger
6 days ago xiaofeiwang18266 ▴ 50
2
votes
5
replies
697
views
Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
limma edgeR biomaRt
updated 6 days ago by 67k • written 6 days ago by ▴ 10
0
votes
1
reply
96
views
XCMS Data Processing
r xcms metabolomi NTA Metabolomics
updated 6 days ago by 67k • written 8 days ago by • 0
0
votes
2
replies
175
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Error using useMart or useEnsembl
biomaRt
updated 7 days ago by 67k • written 7 days ago by • 0
2
votes
1
reply
459
views
Error in download.file for TCGAutils::symbolsToRanges
TCGAutils
updated 7 days ago by 67k • written 7 days ago by ▴ 50
0
votes
11
replies
610
views
Problems with oarfish + tximport + swish
fishpond tximport tximeta
updated 3 days ago by • 0 • written 7 days ago by • 0
0
votes
2
replies
225
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DESeq2 Heatmap
heatmaps
updated 7 days ago by ★ 1.4k • written 8 days ago by • 0
0
votes
4
replies
261
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Biomart and ensembl not working?
ensembldb biomaRt
updated 8 days ago by 67k • written 8 days ago by • 0
0
votes
1
reply
95
views
Unknown gene transcripts after annotatr
annotatr
updated 8 days ago by 67k • written 8 days ago by • 0
0
votes
1
reply
88
views
Improve performance of qusage aggregateGeneSet
qusage
updated 8 days ago by 67k • written 8 days ago by • 0
0
votes
0
replies
71
views
gsameth GSA: probe annotation to multiple genes
missMethyl gsameth
9 days ago nurkenber • 0
0
votes
0
replies
78
views
Testing Differential Expression with Interaction Effect Between Categorical and Continuous Variable with Repeated (Paired) Measures using variancePar…
limma variancePartition
9 days ago GJ • 0
0
votes
1
reply
78
views
promoters_txdb <- promoters(txdb, upstream = 2000) is not 2000
TxDb.Hsapiens.UCSC.hg38.knownGene
updated 9 days ago by 67k • written 10 days ago by ▴ 20
0
votes
0
replies
58
views
News: Online course: Gene set enrichment analysis in R/Bioconductor
GSEABenchmarkeR
11 days ago info ▴ 10
0
votes
1
reply
142
views
org.Hs.eg.db issue
org.Hs.eg.db
updated 9 days ago by 4.1k • written 11 days ago by • 0
0
votes
2
replies
357
views
Paired analysis in proteomics data for DE while interested in only a particular subset of the data
limma modelmatrix pairedanalysis Proteomics
written 12 days ago by ▴ 840
0
votes
2
replies
224
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iam not able to do retrive data using GEOquery R package
HELP
updated 13 days ago by 67k • written 13 days ago by • 0
2
votes
5
replies
291
views
Differential variability modelling with vst() expression
limma DESeq2
written 13 days ago by • 0
0
votes
2
replies
130
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Installation error for Rsamtools.
Rsamtools
updated 13 days ago by ★ 4.6k • written 13 days ago by • 0
2
votes
8
replies
526
views
Different annotation packages (org.Mm.eg.db, EnsDb.Mmusculus.v79, BiomaRt) returning drastically different numbers of transcripts
AnnotationDbi EnsDb.Mmusculus.v79 biomaRt org.Mm.eg.db
updated 13 days ago by 67k • written 14 days ago by • 0
0
votes
2
replies
355
views
DESeq2 analysis with transcript counts
Transcriptomics RNASeq DESeq2
14 days ago • updated 12 days ago sindhuri • 0
0
votes
0
replies
59
views
Issue when attempting to use output from DECIPHER IDtaxa (pr2 V5) with dada2/phyloseq
DECIPHER taxonomyassignment phyloseq dada2 Pr2V5
14 days ago Maggie • 0
2
votes
9
replies
729
views
Why did PCA plots look exactly the same after adjusting for batch covariate in DESeq2 design?
DESeq2 BatchEffect
15 days ago • updated 3 days ago Quang NN ▴ 10
0
votes
5
replies
234
views
Diffbind interpretation of data - fold change
DiffBind
15 days ago Vera • 0
1
vote
1
reply
282
views
Considerations behind the choice of RNAseq Differential Expression Analysis Tools
fishpond DESeq2 rnaseqDTU
updated 15 days ago by 43k • written 16 days ago by • 0
0
votes
1
reply
86
views
No preprocessing allowed for EPICv2 with DMRcate
missMethyl DMRcate
updated 15 days ago by 67k • written 16 days ago by • 0
1
vote
2
replies
407
views
Package `not available for Bioconductor version '3.20'` when it should be
consensusOV genefu
16 days ago Levi Waldron ★ 1.1k
0
votes
0
replies
52
views
Trouble with double delimiters in .fcs file (flowCore package)
flowCore FlowCytometry FlowCytometryData
16 days ago vpochic • 0
0
votes
4
replies
225
views
Newbie Question - adding metadata to an analysis
Biobase
16 days ago • updated 15 days ago Bryan H • 0
0
votes
1
reply
157
views
Want numbers in DESeq to be seen as numerical, not categorical
DESeq2
updated 16 days ago by ★ 1.4k • written 16 days ago by • 0
0
votes
2
replies
258
views
MissMethyl failed to use gometh function for EPICv2
missMethyl EPICv2manifest
updated 17 days ago by 67k • written 17 days ago by • 0
0
votes
1
reply
110
views
Correlation between gene clusters
genomes RNASeqData
written 17 days ago by • 0
0
votes
2
replies
235
views
Mean variance curve troubleshoot filtering
limmavoom filtering edgeR RNASeqData meanvariancetrend
18 days ago • updated 16 days ago gingergeiger22 • 0
0
votes
0
replies
73
views
Error ("could not find function "EM_estimate"") when running ENmix mpreprocess() on Microsoft Azure
Preprocessing ENmix
19 days ago balf0020 • 0
0
votes
1
reply
344
views
Please, I desperately need help with DESeq2. Three groups of repeated measures with two timepoints... (plus an additional group)
edgeR DESeq2
updated 19 days ago by 43k • written 4 weeks ago by • 0
46,293 results • Page 1 of 926
Recent ...
Replies
Comment: Rain error: invalid annotation of time points by Dominik • 0
Hi, I kept running into the same issue until I double checked their help and understood, that columns and rows have to be designed in anoth…
Answer: How to generate circular cnetplot and color nodes and edges in the same plot ? by Guido Hooiveld ★ 4.1k
Since the release of `enrichplot` of October 2024, the code of the function `cnetplot` has been completely rewritten by Guangchuang in orde…
Comment: CUT&Tag differential peak analysis using Diffbind, with pre-calculated normaliza by mec25 • 0
I am unable to find the math behind the dba.normalize(), for instance when the E-coli fraction is used is the signal mutliplied by the fact…
Comment: How to sort negative log2FC or FC in RNAseq for GSEA? by Quang NN ▴ 10
Thank you so much for taking time to provide this clarification!
Comment: How can I generate a heatmap and clustering of differentially expressed genes in by Renuka • 0
Thanks Kelvin i had same doubt .Do i need to do log2 (FPKMcounts) for this
Votes
Answer: DESeq2- merging technical vs biological replicates
Answer: SingleCellExperiment convenience function for metadata+expression?
How to correct for tumor purity using DESeq2 to analyze TCGA tumor sample expression.
Answer: EdgeR Biological CVs
Answer: Error in download.file for TCGAutils::symbolsToRanges
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