10
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7
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2.4k
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Why in Bioconductor community people rarely upvote questions?
bioconductor
updated 13 months ago by 4.2k • written 2.8 years ago by ▴ 50
5
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3
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29k
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DESeq2: thousands of NA for pvalues?
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written 6.9 years ago by ▴ 30
1
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3
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875
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makeContrastsDream for Interaction
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13 months ago • updated 12 months ago abadgerw • 0
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5
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Merge Replicates vs Mixed Model
limma DifferentialExpression variancePartition dream
13 months ago • updated 12 months ago abadgerw • 0
1
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6
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1.6k
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Volcano plot has many values around zero
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updated 13 months ago by 43k • written 13 months ago by ▴ 10
2
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4
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Differential Expression Analysis with unbalanced batches without replication between conditions
edgeR BatchEffect
updated 13 months ago by 53k • written 13 months ago by • 0
1
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8
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2.5k
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Combining RNAseq and microarray data using edgeR/limma-voom
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written 13 months ago by • 0
0
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2
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577
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DESeq2 interaction between cancer cells and microenvironment cells
DESeq2
written 13 months ago by • 0
2
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7
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4.0k
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Annotation for EPICv2
EpicV2 ChAMPdata
updated 13 months ago by • 0 • written 14 months ago by • 0
0
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0
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334
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ChIP peaks comparison
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13 months ago user_bioinfo • 0
0
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2
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986
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GOstats kegg analysis in wheat - help - none of the objects in the first column are legitimate kegg ids (but they are)
AnnotationDbi GOstats
13 months ago GV Yoshikawa • 0
1
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2
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1.4k
views
Consistent Decimals In Data After Antibody Array Background Correction Using Limma:nec Function
limma MicroarrayData Normalization
13 months ago Ai • 0
4
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5
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DESeq Input from Salmon + tximport/tximeta
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13 months ago LuciaNhu • 0
0
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0
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592
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Diffbind: Cut&Run: E-coli spike-in
Normalization DiffBind
13 months ago kim • 0
0
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0
replies
397
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Combining two closely related bacterial annotated genomes to analyze as one pooled group
genomes RNASeq
13 months ago brayas13 • 0
2
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3
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1.2k
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featureCounts segmentation fault with large chromosomes
Rsubread
13 months ago vkkodali ▴ 10
0
votes
1
reply
740
views
Average expression of genes across replicates
DESeq2
updated 13 months ago by ★ 5.0k • written 13 months ago by • 0
0
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1
reply
935
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Spike-in normalization method in ATACseq
sperm Drosophila_melanogaster ATACSeq Normalization SpikeIn
updated 13 months ago by ★ 5.0k • written 13 months ago by • 0
0
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1
reply
898
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single cell RNA seq pseudobulk batch correction
edgeR
updated 13 months ago by 68k • written 13 months ago by • 0
0
votes
1
reply
907
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Normalized counts to be used in decoupleR from deseq2 results
decoupleR
updated 13 months ago by 68k • written 13 months ago by • 0
2
votes
10
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2.7k
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incomplete official symbol mitochondrial genes in org.Hs.eg.db?
org.Hs.eg.db
updated 12 months ago by 68k • written 13 months ago by ★ 4.1k
0
votes
8
replies
946
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Why are internal functions in the package manual?
roxygen methyLImp2 manual
updated 13 months ago by 68k • written 13 months ago by • 0
0
votes
0
replies
324
views
export processed data from flowploidy
flowPloidy
13 months ago Zdenek Skala • 0
0
votes
1
reply
414
views
edit y axis scale in errBarchart?
ddCt
updated 13 months ago by 68k • written 13 months ago by • 0
2
votes
2
replies
1.0k
views
Error: 'term_similarity_from_KEGG' not found in simplifyEnrichment package
simplifyEnrichment
updated 13 months ago by 68k • written 13 months ago by • 0
1
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0
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1.3k
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News: Bioconductor 3.20 is Released!
Bioconductor Release Software
13 months ago shepherl 4.2k
0
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0
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418
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News: RNAseq data analysis with R/Bioconductor (4-15 November)
DESeq2 GenomicRanges
13 months ago info ▴ 10
0
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1
reply
667
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probe ID search for SNP (plink)
genomes
updated 13 months ago by 68k • written 13 months ago by • 0
2
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2
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905
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clusterProfiler enrichGO on only T-cell related GO terms
clusterProfiler
updated 13 months ago by ★ 1.2k • written 13 months ago by • 0
0
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11
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Question about using LRT test for time course experiments with DESeq2
DESeq2
updated 8 months ago by • 0 • written 13 months ago by • 0
2
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2
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1.6k
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Supercells with Basilisk fails for dtype('float64') to dtype('int64') conversion
basilisk
updated 13 months ago by ★ 5.0k • written 13 months ago by ▴ 40
4
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9
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2.9k
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biomaRt rnorvegicus_gene_ensembl not available anymore
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updated 11 months ago by 68k • written 13 months ago by ▴ 20
0
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0
replies
304
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Filtering Steps for proActiv Analysis
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13 months ago LuciaNhu • 0
2
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3
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Why `FoldEnrichment`,`RichFactor`and `zScore` are not in the ReactomePA::enrichPathway result
DOSE ReactomePA
13 months ago Yifeii.Ge • 0
0
votes
1
reply
561
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Deseq to output continous sequencing data
DESeq2
updated 13 months ago by 43k • written 14 months ago by • 0
1
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4
replies
1.4k
views
Adjusted p-values become NA when sub-setting samples
DESeq2
14 months ago • updated 13 months ago txema.heredia • 0
3
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3
replies
1.5k
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Robust way of dealing with low number of samples for Differential Gene Expression
limma edgeR DESeq2 MAST
written 13 months ago by • 0
0
votes
0
replies
389
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diffbind covariates
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updated 13 months ago by 43k • written 13 months ago by ▴ 220
0
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0
replies
320
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MOFA2: Confidence Intervals // Unvertainty estimates for MOFA model
MOFA2
13 months ago mario_de_manner • 0
5
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4
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2.7k
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GSVA ssGSEA vs. Broad implementation of ssGSEA
enrichment GSVA ssGSEA
updated 13 months ago by ▴ 10 • written 14 months ago by ▴ 30
0
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3
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1.0k
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Its possible to remove annotation names using anno_simple in ComplexHeatmap
ComplexHeatmap
updated 13 months ago by ▴ 10 • written 13 months ago by • 0
0
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4
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1.1k
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RNA-seq: samples form different experiments, how to do DGEs?
DGEs edgeR RNASeqData
13 months ago Philippine • 0
1
vote
4
replies
1.0k
views
Is there a way to allow elements with no IRanges when subsetting an IRangesList
IRanges Biostrings S4Vectors
written 13 months ago by • 0
2
votes
2
replies
639
views
Samples used for network inference in RegEnrich
RegEnrich
13 months ago A.Barden ▴ 10
0
votes
0
replies
556
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News: Announcing the GBCC2025 Logo Design Contest!
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13 months ago Maria Doyle ▴ 110
0
votes
3
replies
864
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qvalue density function error
qvalue
13 months ago Tim • 0
4
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3
replies
1.2k
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Analysis of 2*4 factorial design
limma
updated 13 months ago by 53k • written 13 months ago by • 0
2
votes
12
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2.7k
views
limma technical repeat correction
limma lmer duplicateCorrelation technicalrepeats
13 months ago • updated 12 months ago john • 0
0
votes
2
replies
794
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ESTMATE, MCPcounter, EPIC, xCell input
DESeq2 ESTIMATE RNASeqData MCPcounter
written 13 months ago by • 0
1
vote
3
replies
1.3k
views
Tutorial regarding metabolomics with R
Bioconductor Metabolomics xcms
updated 13 months ago by 68k • written 13 months ago by • 0
46,691 results • Page 13 of 934
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Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Answer: PTM analysis in LIMPA by Gordon Smyth 53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR by James W. MacDonald 68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Answer: Question about DESeq2 Design for Paired Treatment Study by ATpoint ★ 5.0k
It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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