0
votes
2
replies
557
views
DESeq2 Heatmap
heatmaps
updated 12 weeks ago by ★ 1.4k • written 12 weeks ago by • 0
0
votes
4
replies
1.1k
views
Biomart and ensembl not working?
ensembldb biomaRt
updated 12 weeks ago by 68k • written 12 weeks ago by • 0
0
votes
1
reply
176
views
Unknown gene transcripts after annotatr
annotatr
updated 12 weeks ago by 68k • written 12 weeks ago by • 0
0
votes
1
reply
169
views
Improve performance of qusage aggregateGeneSet
qusage
updated 12 weeks ago by 68k • written 12 weeks ago by • 0
0
votes
0
replies
154
views
gsameth GSA: probe annotation to multiple genes
missMethyl gsameth
12 weeks ago nurkenber • 0
0
votes
0
replies
190
views
Testing Differential Expression with Interaction Effect Between Categorical and Continuous Variable with Repeated (Paired) Measures using variancePar…
limma variancePartition
12 weeks ago GJ • 0
0
votes
1
reply
154
views
promoters_txdb <- promoters(txdb, upstream = 2000) is not 2000
TxDb.Hsapiens.UCSC.hg38.knownGene
updated 12 weeks ago by 68k • written 12 weeks ago by ▴ 20
0
votes
0
replies
189
views
News: Online course: Gene set enrichment analysis in R/Bioconductor
GSEABenchmarkeR
12 weeks ago info ▴ 10
0
votes
2
replies
483
views
Paired analysis in proteomics data for DE while interested in only a particular subset of the data
limma modelmatrix pairedanalysis Proteomics
written 3 months ago by ▴ 840
0
votes
2
replies
562
views
iam not able to do retrive data using GEOquery R package
HELP
updated 3 months ago by 68k • written 3 months ago by • 0
2
votes
5
replies
486
views
Differential variability modelling with vst() expression
limma DESeq2
written 3 months ago by • 0
0
votes
2
replies
269
views
Installation error for Rsamtools.
Rsamtools
updated 3 months ago by ★ 4.8k • written 3 months ago by • 0
3
votes
9
replies
1.0k
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 9 weeks ago by • 0 • written 3 months ago by • 0
0
votes
3
replies
618
views
DESeq2 analysis with transcript counts
Transcriptomics RNASeq DESeq2
written 3 months ago by • 0
0
votes
2
replies
595
views
Issue when attempting to use output from DECIPHER IDtaxa (pr2 V5) with dada2/phyloseq
DECIPHER taxonomyassignment phyloseq dada2 Pr2V5
updated 23 days ago by • 0 • written 3 months ago by • 0
2
votes
9
replies
1.2k
views
Why did PCA plots look exactly the same after adjusting for batch covariate in DESeq2 design?
DESeq2 BatchEffect
3 months ago • updated 11 weeks ago Quang NN ▴ 10
0
votes
5
replies
430
views
Diffbind interpretation of data - fold change
DiffBind
3 months ago Vera • 0
1
vote
1
reply
504
views
Considerations behind the choice of RNAseq Differential Expression Analysis Tools
fishpond DESeq2 rnaseqDTU
updated 3 months ago by 43k • written 3 months ago by • 0
0
votes
1
reply
277
views
No preprocessing allowed for EPICv2 with DMRcate
missMethyl DMRcate
updated 3 months ago by 68k • written 3 months ago by • 0
1
vote
2
replies
1.8k
views
Package `not available for Bioconductor version '3.20'` when it should be
consensusOV genefu
3 months ago Levi Waldron ★ 1.1k
0
votes
0
replies
144
views
Trouble with double delimiters in .fcs file (flowCore package)
flowCore FlowCytometry FlowCytometryData
3 months ago vpochic • 0
0
votes
4
replies
362
views
Newbie Question - adding metadata to an analysis
Biobase
3 months ago Bryan H • 0
0
votes
1
reply
232
views
Want numbers in DESeq to be seen as numerical, not categorical
DESeq2
updated 3 months ago by ★ 1.4k • written 3 months ago by • 0
0
votes
2
replies
381
views
MissMethyl failed to use gometh function for EPICv2
missMethyl EPICv2manifest
updated 3 months ago by 68k • written 3 months ago by • 0
0
votes
1
reply
238
views
Correlation between gene clusters
genomes RNASeqData
written 3 months ago by • 0
0
votes
2
replies
386
views
Mean variance curve troubleshoot filtering
limmavoom filtering edgeR RNASeqData meanvariancetrend
3 months ago gingergeiger22 • 0
0
votes
1
reply
431
views
Please, I desperately need help with DESeq2. Three groups of repeated measures with two timepoints... (plus an additional group)
edgeR DESeq2
updated 3 months ago by 43k • written 3 months ago by • 0
2
votes
1
reply
439
views
Is it possible to work with DESeq2 where data is not properly matched for sex and age
DESeq2 RNASeqData
updated 3 months ago by 43k • written 3 months ago by • 0
0
votes
1
reply
1.4k
views
How to increase font for gene name and increase arrow size for GVIZ's ( UcscTrack function ) track?
DMRcate Gviz
updated 3 months ago by • 0 • written 3.3 years ago by ▴ 60
6
votes
5
replies
740
views
How do I fix an odd voom plot in a combined dataset?
limma Normalization voom
updated 3 months ago by 68k • written 3 months ago by • 0
1
vote
8
replies
1.1k
views
Incorporating Salmon offset matrix into Wilcoxon DEG analysis
edgeR
3 months ago Andre • 0
0
votes
2
replies
457
views
DESeq error: counts matrix should be numeric, currently it has mode: character
DESeq2
3 months ago Kucsera • 0
0
votes
1
reply
287
views
combining raw counts and estimated counts
RNASeqData GEO TCGAbiolinks
updated 3 months ago by • 0 • written 3 months ago by • 0
0
votes
3
replies
1.3k
views
News: EuroBioC2023 abstract submission closing soon!
presentation EuroBioc2023 Conference community Bioconductor
written 24 months ago by ▴ 100
0
votes
5
replies
1.4k
views
News: EuroBioC2024 abstract submission is open!
Conference Bioconductor EuroBioC2024
updated 3 months ago by • 0 • written 14 months ago by ▴ 100
0
votes
2
replies
558
views
Cross-validation with multiple control subgroups in limma
limma multtest
3 months ago Ali Barry ▴ 40
1
vote
1
reply
452
views
Can DESeq2's design compensate for sequencing experimental design shortcomings?
DESeq2
updated 3 months ago by 43k • written 4 months ago by • 0
0
votes
1
reply
263
views
Job: Postdoctoral Researcher in Spatial Gene Regulatory Networks underlying Stomatal Patterning
JobPosting
updated 12 weeks ago by • 0 • written 3 months ago by ★ 2.0k
0
votes
1
reply
437
views
ChAMP.DMR error - Error in makeGenomicRatioSetFromMatrix
ChAMP
updated 3 months ago by • 0 • written 3 months ago by • 0
1
vote
9
replies
1.0k
views
Normalizing batch effects using technical replicates for DGE analysis between two conditions from 2 different runs
limma DESeq2 edgeR
written 3 months ago by ▴ 30
0
votes
2
replies
609
views
Error in get_anno_data(ontology) : ontology not supported yet...
EnrichDO
3 months ago GODseeker • 0
4
votes
2
replies
591
views
Standardization of rlog transformed counts before PCA
RNASeq DESeq2 Visualization
updated 3 months ago by ★ 4.8k • written 4 months ago by ▴ 10
0
votes
2
replies
396
views
Build error on kunpeng2 Linux aarch64
Bioconductor
updated 3 months ago by • 0 • written 3 months ago by • 0
0
votes
3
replies
1.4k
views
Limma - using both array and spot weights in lmFit
Genetics Genetics
written 18.0 years ago by ▴ 170
0
votes
2
replies
528
views
Margins for gene_set_enrichment_plot
spatialLIBD
updated 3 months ago by ★ 1.1k • written 4 months ago by • 0
0
votes
1
reply
221
views
Errors running learn.bn function from Pigengene in windows environment
Pigengene
written 3 months ago by • 0
0
votes
1
reply
420
views
Need new version : tx2gene.gencode.v47.csv
tximportData
updated 3 months ago by ★ 4.1k • written 4 months ago by • 0
1
vote
5
replies
706
views
Deseq2 Design
RNASeq DESeq2
updated 3 months ago by 68k • written 4 months ago by • 0
0
votes
5
replies
743
views
p value is 0, padj is 0
DESeq2
4 months ago Wirayatida • 0
0
votes
2
replies
1.1k
views
Cannot install GO.db and org.Hs.eg.db
Install
updated 4 months ago by 68k • written 4 months ago by • 0
46,451 results • Page 5 of 930
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Answer: WGCNA by ATpoint ★ 4.8k
> I would like to ask whether it would make sense to first normalize the count data using DESeq2 and VST before performing WGCNA. This …
Answer: cannot download atena annotation for human by Robert Castelo ★ 3.4k
Hi, sorry for the delay in getting back to you, probably by now you found the solution yourself, but just in case you didn't or anybody els…
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In general, using the entire dataset and then just comparing the subgroups you want within the whole dataset is preferable.
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If these are two different batches then they're fully confounded making it statistically invalid. Biologically, I find it at least question…
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Hi, please consider asking this at biostars.org as here we're mainly answering precise technical questions towards the packages. You are se…
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Answer: Origin of the labels for the SingleCellMultiModal dataset
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