0
votes
0
replies
347
views
Combining two closely related bacterial annotated genomes to analyze as one pooled group
genomes RNASeq
10 months ago brayas13 • 0
2
votes
3
replies
1.2k
views
featureCounts segmentation fault with large chromosomes
Rsubread
11 months ago • updated 10 months ago vkkodali ▴ 10
0
votes
1
reply
699
views
Average expression of genes across replicates
DESeq2
updated 10 months ago by ★ 4.9k • written 10 months ago by • 0
0
votes
1
reply
854
views
Spike-in normalization method in ATACseq
sperm Drosophila_melanogaster ATACSeq Normalization SpikeIn
updated 10 months ago by ★ 4.9k • written 10 months ago by • 0
0
votes
1
reply
832
views
single cell RNA seq pseudobulk batch correction
edgeR
updated 10 months ago by 68k • written 10 months ago by • 0
0
votes
1
reply
855
views
Normalized counts to be used in decoupleR from deseq2 results
decoupleR
updated 10 months ago by 68k • written 10 months ago by • 0
2
votes
10
replies
2.4k
views
incomplete official symbol mitochondrial genes in org.Hs.eg.db?
org.Hs.eg.db
updated 10 months ago by 68k • written 10 months ago by ★ 4.1k
0
votes
8
replies
798
views
Why are internal functions in the package manual?
roxygen methyLImp2 manual
updated 10 months ago by 68k • written 10 months ago by • 0
0
votes
0
replies
280
views
export processed data from flowploidy
flowPloidy
10 months ago Zdenek Skala • 0
0
votes
1
reply
381
views
edit y axis scale in errBarchart?
ddCt
updated 10 months ago by 68k • written 10 months ago by • 0
2
votes
2
replies
939
views
Error: 'term_similarity_from_KEGG' not found in simplifyEnrichment package
simplifyEnrichment
updated 10 months ago by 68k • written 10 months ago by • 0
1
vote
0
replies
1.2k
views
News: Bioconductor 3.20 is Released!
Bioconductor Release Software
10 months ago shepherl 4.2k
0
votes
0
replies
371
views
News: RNAseq data analysis with R/Bioconductor (4-15 November)
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10 months ago info ▴ 10
0
votes
1
reply
450
views
probe ID search for SNP (plink)
genomes
updated 10 months ago by 68k • written 10 months ago by • 0
2
votes
2
replies
836
views
clusterProfiler enrichGO on only T-cell related GO terms
clusterProfiler
updated 10 months ago by ★ 1.2k • written 11 months ago by • 0
0
votes
11
replies
2.3k
views
Question about using LRT test for time course experiments with DESeq2
DESeq2
updated 5 months ago by • 0 • written 10 months ago by • 0
2
votes
2
replies
1.5k
views
Supercells with Basilisk fails for dtype('float64') to dtype('int64') conversion
basilisk
updated 10 months ago by ★ 4.9k • written 10 months ago by ▴ 40
4
votes
9
replies
2.7k
views
biomaRt rnorvegicus_gene_ensembl not available anymore
Rattus_norvegicus biomaRt
updated 9 months ago by 68k • written 10 months ago by ▴ 20
0
votes
0
replies
260
views
Filtering Steps for proActiv Analysis
Transcriptomics proActiv
10 months ago LuciaNhu • 0
2
votes
3
replies
1.6k
views
Why `FoldEnrichment`,`RichFactor`and `zScore` are not in the ReactomePA::enrichPathway result
DOSE ReactomePA
10 months ago Yifeii.Ge • 0
0
votes
1
reply
537
views
Deseq to output continous sequencing data
DESeq2
updated 10 months ago by 43k • written 11 months ago by • 0
1
vote
4
replies
1.3k
views
Adjusted p-values become NA when sub-setting samples
DESeq2
11 months ago • updated 10 months ago txema.heredia • 0
3
votes
3
replies
1.4k
views
Robust way of dealing with low number of samples for Differential Gene Expression
limma edgeR DESeq2 MAST
written 10 months ago by • 0
0
votes
0
replies
335
views
diffbind covariates
DiffBind ATACSeq
updated 10 months ago by 43k • written 10 months ago by ▴ 220
0
votes
0
replies
248
views
MOFA2: Confidence Intervals // Unvertainty estimates for MOFA model
MOFA2
10 months ago mario_de_manner • 0
5
votes
4
replies
2.4k
views
GSVA ssGSEA vs. Broad implementation of ssGSEA
enrichment GSVA ssGSEA
updated 10 months ago by ▴ 10 • written 11 months ago by ▴ 30
0
votes
3
replies
922
views
Its possible to remove annotation names using anno_simple in ComplexHeatmap
ComplexHeatmap
updated 10 months ago by ▴ 10 • written 11 months ago by • 0
0
votes
4
replies
974
views
RNA-seq: samples form different experiments, how to do DGEs?
DGEs edgeR RNASeqData
10 months ago Philippine • 0
1
vote
4
replies
943
views
Is there a way to allow elements with no IRanges when subsetting an IRangesList
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written 10 months ago by • 0
2
votes
2
replies
601
views
Samples used for network inference in RegEnrich
RegEnrich
10 months ago A.Barden ▴ 10
0
votes
0
replies
501
views
News: Announcing the GBCC2025 Logo Design Contest!
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10 months ago Maria Doyle ▴ 100
0
votes
3
replies
814
views
qvalue density function error
qvalue
10 months ago Tim • 0
4
votes
3
replies
1.1k
views
Analysis of 2*4 factorial design
limma
updated 10 months ago by 53k • written 10 months ago by • 0
2
votes
12
replies
2.5k
views
limma technical repeat correction
limma lmer duplicateCorrelation technicalrepeats
10 months ago john • 0
0
votes
2
replies
698
views
ESTMATE, MCPcounter, EPIC, xCell input
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written 11 months ago by • 0
1
vote
3
replies
1.1k
views
Tutorial regarding metabolomics with R
Bioconductor Metabolomics xcms
updated 11 months ago by 68k • written 11 months ago by • 0
1
vote
1
reply
610
views
DataFrame Character Truncation
S4Vectors
updated 11 months ago by 68k • written 11 months ago by ★ 1.6k
4
votes
6
replies
1.9k
views
LIMMA Differing P-Values for Treatment-Contrast Parameterization vs Group-Means Parameterization
limma
updated 11 months ago by 53k • written 11 months ago by • 0
5
votes
13
replies
2.3k
views
Installing annotation package in locally
AnnotationDbi AnnotationHub Annotation AnnotationForge
11 months ago KABILAN • 0
0
votes
2
replies
875
views
DiffBind dba.report discrepancy
DiffBind
11 months ago aelbassiouny • 0
1
vote
8
replies
1.5k
views
Suggestion for FGSEA and GSEA creation for C57BL/6J Mice
gsea mice org.Mm.eg.db
updated 11 months ago by 68k • written 11 months ago by • 0
0
votes
1
reply
468
views
Should zero counts in some replicates lead to inflated p-values?
DESeq2
updated 11 months ago by 43k • written 11 months ago by • 0
0
votes
2
replies
1.1k
views
Integration of Single Cell Experiments with batchelor::fastMNN
fastMNN SingleCellData BatchEffect batchelor
11 months ago José • 0
0
votes
0
replies
309
views
cbind for multiple SpatialExperiment takes so much time
SpatialExperiment SingleCellExperiment
11 months ago Ibrahim • 0
0
votes
1
reply
654
views
MethylKit CpG Island annotation for Hg38
methylKit
updated 11 months ago by 68k • written 11 months ago by • 0
0
votes
5
replies
1.1k
views
Need help converting vcf files to snp
VCFArray
11 months ago patrice.bridges457 • 0
0
votes
11
replies
2.3k
views
News: List of Deprecated Packages for Bioc3.19
Release Devel ExperimentData Software
18 months ago • updated 11 months ago shepherl 4.2k
4
votes
6
replies
1.7k
views
Zero intra-block correlation in RRBS analysis using voomLmFit with block
limma duplicateCorrelation edgeR modelMatrixMeth voomLmFit
11 months ago • updated 10 months ago altintas.ali • 0
2
votes
3
replies
1.3k
views
Analysis of large RNA-Seq Datasets
DESeq2
updated 11 months ago by 43k • written 11 months ago by • 0
0
votes
7
replies
1.4k
views
How should I know which platforms are available for TCGA methylation?
TCGAbiolinks
updated 10 months ago by 68k • written 11 months ago by • 0
46,630 results • Page 12 of 933
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Replies
Comment: GO.db and others package Download failure by James W. MacDonald 68k
Also, you never need to use anything but `BiocManager::install` to install any package, which has the beneficial side effect of ensuring th…
Comment: GO.db and others package Download failure by James W. MacDonald 68k
Yes. Your packages have odd Y version numbers (where the version is X.Y.Z). That means they are devel packages (release versions have even …
Comment: GO.db and others package Download failure by Skyler • 0
Am I using Bioc-devel?
Comment: GO.db and others package Download failure by James W. MacDonald 68k
Is there a reason to use Bioc-devel? If not, you should be using the release version (which I am, and which installs `GO.db` without compla…
Comment: GO.db and others package Download failure by Skyler • 0
Hi James, Below I have inserted all of my code. I have run r as an administrator and not as an administrator. I have changed my CRANmirror …
Votes
Comment: readDNAStringSet with non DNA characters
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
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