1
vote
2
replies
995
views
Student
metaboliteIDmapping Metabolomics KEGG
updated 16 months ago by ▴ 60 • written 16 months ago by • 0
2
votes
5
replies
1.3k
views
Trying to convert ATACseq annotations of non-model species into human orthologs, but not sure of what to do.
genomes ATACSeq
16 months ago ronin • 0
0
votes
13
replies
2.4k
views
When doing differential methylation using the sesame package, seems to only go one way
methylation sesame methylationArrayAnalysis
updated 16 months ago by ▴ 20 • written 16 months ago by ▴ 10
17
votes
9
replies
8.5k
views
How to use removeBatchEffect for removing effect of multiple confounding variables
limma removebatcheffect deseq2
updated 16 months ago by 68k • written 9.7 years ago by ▴ 10
0
votes
0
replies
563
views
Trying to understand basic DiffBind usage
ChIPSeq DiffBind
16 months ago Alejandro • 0
0
votes
0
replies
1.0k
views
modelGeneVar in MulticoreParam: wrong args for environment subassignment
BiocParallel scran BiocParall
16 months ago Lluís Revilla Sancho ▴ 760
2
votes
2
replies
852
views
How to read OSCA book?
BIOCON OSCA Bioconductor
16 months ago zr • 0
0
votes
1
reply
683
views
Dealing with 0 miRNA counts in DESeq2 analysis and influence in adjusted p-value
microRNAome DESeq2
updated 16 months ago by 43k • written 16 months ago by • 0
0
votes
1
reply
699
views
QSEA:Error in h(simpleError(msg, call))
qsea
16 months ago kf • 0
2
votes
1
reply
884
views
Question: How to Set Up Contrasts for Case-Control Analysis in Limma While Adjusting for Covariates?
MethylationArray EpigeneticsWorkflow limma Regression
updated 16 months ago by 68k • written 16 months ago by ▴ 20
7
votes
9
replies
2.2k
views
clusterProfiler: BgRatio N value does not match the size of the gene universe that has GO annotations.
GO clusterProfiler enr
updated 16 months ago by ★ 4.1k • written 16 months ago by • 0
0
votes
0
replies
699
views
Mark seleced variables in the x-loading plot
OPLS genomes Proteomics
16 months ago Ragnhild • 0
0
votes
0
replies
777
views
News: Metabolomics with R/Bioconductor Online Course
metabomxtr MetaboCoreUtils metabolomicsWorkbenchR Metabolomics
16 months ago info ▴ 10
2
votes
1
reply
616
views
object 'hdac_targets' not found
TPP
updated 16 months ago by 68k • written 16 months ago by • 0
1
vote
2
replies
917
views
KEGGgraph result difference
igraph KEGGgraph RCy3 GraphNEL
16 months ago • updated 15 months ago Arindam ▴ 80
0
votes
1
reply
1.5k
views
Issue Installing Biostrings Package: gcc Compilation Errors
Biostrings packageinstallation
updated 16 months ago by ▴ 70 • written 16 months ago by • 0
1
vote
2
replies
1.3k
views
In the sesame package, what does the estimate output mean from testEnrichment()
MethylationArray methylation sesame methylationArrayAnalysis
16 months ago ramiro.barrantes ▴ 10
0
votes
1
reply
762
views
WGCNA Choosing soft threshold power below R^2 0.8
WGCNA
updated 16 months ago by ▴ 760 • written 16 months ago by • 0
1
vote
2
replies
893
views
WARNING: No Bioconductor dependencies detected.
Bioconductor Biocon
16 months ago katja.danielzik • 0
0
votes
5
replies
1.3k
views
Rsubread alignment crashes at 35%, valgrind indicates invalid writes
Rsubread
updated 16 months ago by ▴ 450 • written 16 months ago by • 0
0
votes
1
reply
762
views
Annotating DMRs
MethylationArray MethylationArrayData methylationArrayAnalysis
updated 16 months ago by 68k • written 16 months ago by ▴ 10
0
votes
2
replies
890
views
PCA analysis RNA-Seq QC looks strange?
DESeq2
updated 16 months ago by ★ 1.4k • written 17 months ago by • 0
0
votes
3
replies
907
views
concentration tables suitable as input for new packages?
Bioconductor
written 16 months ago by • 0
2
votes
0
replies
1.1k
views
News: Save the Date for EuroBioC2025 in Barcelona!
EuroBioC2025 Conference Bioconductor Community
16 months ago Maria Doyle ▴ 110
0
votes
1
reply
766
views
Ideal approach to adjust for covariates for WGCNA
WGCNA wgcna
updated 16 months ago by 68k • written 16 months ago by • 0
0
votes
5
replies
2.4k
views
DESeq2 Multi-factor design not full rank
RNASeq DESeq2
written 4.7 years ago by • 0
0
votes
5
replies
1.8k
views
ı cant install clusterprofiler on my Ubuntu 20.04.6 LTS
Bioconductor clusterProfiler
updated 16 months ago by ▴ 760 • written 16 months ago by • 0
0
votes
0
replies
788
views
Job: Postdoctoral Research Associate in Computational Epigenomics
Phd SingleCell DNAMethylation Shanghai JobPosting
17 months ago xiaolong • 0
0
votes
1
reply
715
views
ensemblVEP deprecation and how to reproduce
VariantAnnotation
updated 17 months ago by 6.7k • written 17 months ago by • 0
1
vote
1
reply
948
views
Help with design matrix for RNA-seq data using edgeR
edgeR RNASeqData
updated 17 months ago by 53k • written 17 months ago by • 0
3
votes
6
replies
2.1k
views
[DESeq2] Normalization of External Test Dataset for Machine Learning (ML) Application
DESeq2
updated 16 months ago by 43k • written 17 months ago by • 0
0
votes
2
replies
809
views
tximport data import
tximport
updated 17 months ago by 43k • written 17 months ago by • 0
2
votes
2
replies
936
views
Should tSNE from biol. replicates look alike?
scRNAseq SingleCellExperiment batchelor
written 17 months ago by ▴ 10
0
votes
0
replies
780
views
Problem merging metadata and feature-table before analysing LEfSe on R
microbiomeDataSets differential-abundance
17 months ago 샤니쿠마리 • 0
2
votes
2
replies
1.3k
views
fgsea stuck in an infinite loop in the middle of the run
GSEABase fgsea msigdb GeneSetEnrichment
17 months ago Assa Yeroslaviz ★ 1.5k
1
vote
2
replies
3.8k
views
How to use compareCluster in ClusterProfiler?
RNASeqData GSEA clusterProfiler
written 17 months ago by • 0
0
votes
4
replies
2.3k
views
News: Announcing GBCC 2025: The first-ever joint conference between Bioconductor and Galaxy!
Conference Bioconductor Community
updated 3 months ago by • 0 • written 17 months ago by ▴ 110
0
votes
1
reply
2.5k
views
Unable to install/use limma
limma Bioconductor
updated 17 months ago by 68k • written 17 months ago by • 0
1
vote
3
replies
2.0k
views
502 error biomaRt getLDS()
ensembldb biomaRt
updated 17 months ago by 68k • written 24 months ago by ▴ 10
1
vote
1
reply
917
views
Empty Results from champ.DMP Despite Expected Output
MethylationArray ChAMP R
updated 17 months ago by 68k • written 17 months ago by • 0
0
votes
2
replies
768
views
ReactomeGSA adjustment for confounding variables
BiologicalQuestion ReactomeGSA BatchEffect
written 17 months ago by • 0
3
votes
6
replies
32k
views
Deseq: What does "BaseMean" mean?
deseq2
written 7.4 years ago by • 0
0
votes
1
reply
1.8k
views
question about gseGO() in clusterprofiler package
clusterProfiler
updated 17 months ago by ★ 4.1k • written 17 months ago by • 0
0
votes
0
replies
518
views
Z-score Interpretation across components
MAST
17 months ago GJ • 0
0
votes
1
reply
614
views
error for the geneGOEnricher function of the NoRCE package
NoRCE
updated 17 months ago by 68k • written 17 months ago by • 0
0
votes
2
replies
1.8k
views
Understanding Contrasts and Interaction in DESeq2 for 2 genotypes, 2 treatments
RNASeq DESeq2
updated 17 months ago by ★ 1.4k • written 17 months ago by • 0
1
vote
4
replies
2.1k
views
BiomaRt Possible Ensembl SSL connectivity problems detected.
PureCN biomaRt
updated 14 months ago by • 0 • written 17 months ago by • 0
1
vote
5
replies
2.5k
views
Heatmap from the output of GSEA clusterProfiler?
clusterProfiler heatmaps
written 17 months ago by • 0
1
vote
2
replies
702
views
Review process for delivering R packages
Bioconductor
17 months ago XFWu • 0
4
votes
11
replies
1.9k
views
Size factor normalized counts for between sample comparisons - correct?
DESeq2
17 months ago boczniak767 ▴ 740
1,000 results • Page 17 of 20
Recent ...
Replies
Comment: msmsTests, inconsistent sign between lFC.Av and LogFC by Ben • 0
Continued here due to posting difficulties: Extract from the results table: ``` Inhibitor Vehicle lFC.Av LogFC ... F1 0.0 27…
Answer: DESeq2 for 16S rRNA Analysis by James W. MacDonald 68k
The Wald test is only meant for comparison of two groups at a time, so it depends on what you mean by 'analyze across multiple groups at a …
Comment: MetaDE.pvalue: Error in xj[i]: invalid subscript type 'list' by varying.mastodon.isyn • 0
Oh, that error! I remember wrestling with that one for hours when I was first learning Python. Turns out I was trying to use a list itself …
Comment: Confirm that OpenStats will not be archived (pryr dependency) by Marina • 0
Thank you!
Comment: AnnotationForge makeOrgPackage rsqlite_send_query error by ansley.r.burtch • 0
Hi! I am sure you are well into your career now and haven't worked on this for a while, but I wanted to let you know this is still helping …
Votes
A: DESeq2 - VST eliminates zero values
Comment: Normalise to a housekeeping gene in DESEq2
Comment: limpa analysis advice
C: AnnotationForge makeOrgPackage rsqlite_send_query error
Answer: Limpa Pipeline Order
Awards • All
Popular Question to James W. MacDonald 68k
Popular Question to James Aiden • 0
Popular Question to shepherl 4.3k
Popular Question to fl ▴ 20
Voter to SamGG ▴ 360
Locations • All
United States, 5 minutes ago
United States, 12 minutes ago
The city by the bay, 28 minutes ago
WEHI, Melbourne, Australia, 42 minutes ago
United States, 55 minutes ago
Traffic: 1620 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6