0
votes
1
reply
214
views
I am having issues with bowtie2_build
genomes bowtiew Index
updated 9 weeks ago by 68k • written 9 weeks ago by • 0
0
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1
reply
244
views
DEG analysis across multiple timepoints, treatments and tissues
DifferentialExpression RNASeq DESeq2
updated 9 weeks ago by 43k • written 9 weeks ago by • 0
0
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0
replies
118
views
My DEXSeqDataSetFromSE is returning an Error, but all of my checks to seem to indicate that this error is not present
DifferentialSplicing RNASeqData DEXSeq
9 weeks ago cftattersfield • 0
1
vote
0
replies
241
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News: Bioconductor Course, Kenya 2025: Applications Open!
Events Community Training Africa Bioconductor
9 weeks ago Maria Doyle ▴ 100
0
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2
replies
564
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How to visualize these pathways using pathview
Salmo_salar RNASeq KEGG pathview
9 weeks ago • updated 7 weeks ago ingrid.h • 0
2
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2
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477
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Selection of correct coefficients or contrasts in DESeq2
DESeq2
updated 9 weeks ago by ★ 1.4k • written 10 weeks ago by • 0
9
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3
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2.0k
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Job: Postdoc/RA position: Software Engineer For R and High-Performance Computing
JobPosting CuratedAtlasQueryR tidySpatialExperiment tidyomics tidySingleCellExperiment
written 9 months ago by ▴ 40
0
votes
4
replies
998
views
Why select top highly expressed genes based on normalized counts, but then plot VST-transformed values in DESeq2 pheatmap?
RNASeq DESeq2
9 weeks ago Quang NN ▴ 10
1
vote
3
replies
755
views
Csaw normalization strategies - general inquiry
ChIPSeq csaw
updated 9 weeks ago by • 0 • written 9 weeks ago by • 0
4
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9
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2.3k
views
Issues with seqlevelsStyle when making custom txdb objects for genomes/annotations from ToxoDB
txdbmaker GenomeInfoDb GenomicFeatures Biostrings gDNAx
updated 9 weeks ago by ★ 3.4k • written 3 months ago by ▴ 20
0
votes
1
reply
229
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WGCNA sample-data preprocessing order
Microarray WGCNA GeneExpression
updated 10 weeks ago by ★ 4.8k • written 10 weeks ago by • 0
0
votes
2
replies
238
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WGCNA: Can we use high power (26) for signed network?
Networkanalysis RNA-seqdata Powerselection WGCNA
10 weeks ago Vinesh • 0
0
votes
1
reply
148
views
Ph.D. scholar
WGCNA DataNormalization MicroarrayData
updated 10 weeks ago by ★ 4.8k • written 10 weeks ago by • 0
0
votes
1
reply
200
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Unable to find sample sheet file for ChAMP methylation data analysis
MethylationArray MethylationArrayData methylationArrayAnalysis
updated 10 weeks ago by 68k • written 10 weeks ago by • 0
0
votes
2
replies
629
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How to generate circular cnetplot and color nodes and edges in the same plot ?
cnetplot DESeq2
10 weeks ago Blandine • 0
0
votes
5
replies
385
views
Is there a way to do DEG analysis across two batches sharing one sample only?
DESeq2 DifferentialExpression RNASeqData BatchEffect
written 10 weeks ago by • 0
0
votes
1
reply
177
views
affymetrix
genomes Annotation
updated 10 weeks ago by 68k • written 10 weeks ago by • 0
0
votes
1
reply
725
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Problems with GSEA
GSEABase
updated 10 weeks ago by ★ 4.1k • written 10 weeks ago by • 0
0
votes
1
reply
275
views
Error compiling Rbowtie2 in R-4.4 (Bioconductor 3.20 and probably 3.19)
Rbowtie
11 weeks ago • updated 10 weeks ago ja.garcia • 0
0
votes
4
replies
575
views
How to sort negative log2FC or FC in RNAseq for GSEA?
DESeq2 GSEA clusterProfiler
10 weeks ago Quang NN ▴ 10
2
votes
4
replies
587
views
EdgeR Biological CVs
edgeR
written 10 weeks ago by • 0
0
votes
1
reply
326
views
Curiously shaped volcano plot with using oarfish + swish to do differential gene expression on long-read RNA-seq
fishpond fish
updated 10 weeks ago by 43k • written 11 weeks ago by • 0
0
votes
0
replies
90
views
Problem with PCAtool as dependencie
COTAN PCAtools
10 weeks ago Silvia • 0
1
vote
2
replies
294
views
Detecting genomic signatures of drug resistance breast cancer in transcriptomic data
TransOmicsData signatureSearchData StatisticalMethod
written 4 months ago by • 0
0
votes
2
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49k
views
SingleR Label.Ont
SingleR
written 18 months ago by • 0
0
votes
0
replies
107
views
cnvEQTL : Error in cpm.default(y, lib.size = lib.size) : NA counts not allowed
CNVRanger
11 weeks ago xiaofeiwang18266 ▴ 60
3
votes
5
replies
1.3k
views
Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
limma edgeR biomaRt
updated 11 weeks ago by 68k • written 11 weeks ago by ▴ 10
0
votes
1
reply
187
views
XCMS Data Processing
r xcms metabolomi NTA Metabolomics
updated 11 weeks ago by 68k • written 11 weeks ago by • 0
0
votes
2
replies
872
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Error using useMart or useEnsembl
biomaRt
updated 11 weeks ago by 68k • written 11 weeks ago by • 0
2
votes
1
reply
605
views
Error in download.file for TCGAutils::symbolsToRanges
TCGAutils
updated 11 weeks ago by 68k • written 11 weeks ago by ▴ 60
0
votes
11
replies
835
views
Problems with oarfish + tximport + swish
fishpond tximport tximeta
updated 10 weeks ago by • 0 • written 11 weeks ago by • 0
0
votes
2
replies
536
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DESeq2 Heatmap
heatmaps
updated 11 weeks ago by ★ 1.4k • written 11 weeks ago by • 0
0
votes
4
replies
995
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Biomart and ensembl not working?
ensembldb biomaRt
updated 11 weeks ago by 68k • written 11 weeks ago by • 0
0
votes
1
reply
171
views
Unknown gene transcripts after annotatr
annotatr
updated 11 weeks ago by 68k • written 11 weeks ago by • 0
0
votes
1
reply
168
views
Improve performance of qusage aggregateGeneSet
qusage
updated 11 weeks ago by 68k • written 11 weeks ago by • 0
0
votes
0
replies
146
views
gsameth GSA: probe annotation to multiple genes
missMethyl gsameth
11 weeks ago nurkenber • 0
0
votes
0
replies
183
views
Testing Differential Expression with Interaction Effect Between Categorical and Continuous Variable with Repeated (Paired) Measures using variancePar…
limma variancePartition
11 weeks ago GJ • 0
0
votes
1
reply
146
views
promoters_txdb <- promoters(txdb, upstream = 2000) is not 2000
TxDb.Hsapiens.UCSC.hg38.knownGene
updated 11 weeks ago by 68k • written 11 weeks ago by ▴ 20
0
votes
0
replies
176
views
News: Online course: Gene set enrichment analysis in R/Bioconductor
GSEABenchmarkeR
11 weeks ago info ▴ 10
0
votes
2
replies
463
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Paired analysis in proteomics data for DE while interested in only a particular subset of the data
limma modelmatrix pairedanalysis Proteomics
written 12 weeks ago by ▴ 840
0
votes
2
replies
523
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iam not able to do retrive data using GEOquery R package
HELP
updated 12 weeks ago by 68k • written 12 weeks ago by • 0
2
votes
5
replies
465
views
Differential variability modelling with vst() expression
limma DESeq2
written 12 weeks ago by • 0
0
votes
2
replies
244
views
Installation error for Rsamtools.
Rsamtools
updated 12 weeks ago by ★ 4.8k • written 12 weeks ago by • 0
3
votes
9
replies
971
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 8 weeks ago by • 0 • written 12 weeks ago by • 0
0
votes
3
replies
600
views
DESeq2 analysis with transcript counts
Transcriptomics RNASeq DESeq2
written 12 weeks ago by • 0
0
votes
2
replies
581
views
Issue when attempting to use output from DECIPHER IDtaxa (pr2 V5) with dada2/phyloseq
DECIPHER taxonomyassignment phyloseq dada2 Pr2V5
updated 16 days ago by • 0 • written 12 weeks ago by • 0
2
votes
9
replies
1.1k
views
Why did PCA plots look exactly the same after adjusting for batch covariate in DESeq2 design?
DESeq2 BatchEffect
12 weeks ago • updated 10 weeks ago Quang NN ▴ 10
0
votes
5
replies
394
views
Diffbind interpretation of data - fold change
DiffBind
12 weeks ago Vera • 0
1
vote
1
reply
480
views
Considerations behind the choice of RNAseq Differential Expression Analysis Tools
fishpond DESeq2 rnaseqDTU
updated 12 weeks ago by 43k • written 12 weeks ago by • 0
0
votes
1
reply
267
views
No preprocessing allowed for EPICv2 with DMRcate
missMethyl DMRcate
updated 12 weeks ago by 68k • written 12 weeks ago by • 0
46,434 results • Page 4 of 929
Recent ...
Replies
Comment: DESeq2 - human data, weird results, troubleshooting by bd2000 ▴ 30
I didn't include all of my code the post would be too long. Here's a link to my GitHub if anyone would like to see the full code: [Full Rst…
Answer: DESeq: Gene is not flagged as differentially expressed despite count data showin by James W. MacDonald 68k
The simple answer is that the within-group variability is much higher for the first gene as compared to the second. The Wald statistic is j…
Comment: DESeq: Gene is not flagged as differentially expressed despite count data showin by ATpoint ★ 4.8k
> since there doesn't seem to be as much count variability, No? Your CD45 samples range on normalized scale from 2 to 3255. That's 3 orde…
Comment: Ensembl site unresponsive via biomaRt by darylruiz6545 • 0
Thank you so much for sharing the link.
Comment: compute_fasta_digest does not match Salmon index hash by Alex • 0
I use the `fastaDigest` tool from [COMBINE-lab/fastaDigest](https://github.com/COMBINE-lab/FastaDigest/), which has the function `compute_f…
Votes
Answer: DESeq: Gene is not flagged as differentially expressed despite count data showin
Two EPIC Methylation Array Analysis Questions
How to get DMR for Infinium methylation EPIC v2
A: GEOquery Fails to Download Series Matrix File
Comment: Gene IDs conversion between Ensembl and NCBI nomenclature for non-model species
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