[go: up one dir, main page]
0
votes
1
reply
39
views
Dealing with 0 miRNA counts in DESeq2 analysis and influence in adjusted p-value
microRNAome DESeq2
updated 9 hours ago by 42k • written 23 hours ago by • 0
0
votes
0
replies
48
views
How to read OSCA book?
BIOCON OSCA Bioconductor
1 day ago zr • 0
0
votes
1
reply
82
views
QSEA:Error in h(simpleError(msg, call))
qsea
2 days ago kf • 0
2
votes
1
reply
88
views
Question: How to Set Up Contrasts for Case-Control Analysis in Limma While Adjusting for Covariates?
MethylationArray EpigeneticsWorkflow limma Regression
updated 2 days ago by 67k • written 2 days ago by ▴ 10
1
vote
4
replies
536
views
clusterProfiler: BgRatio N value does not match the size of the gene universe that has GO annotations.
GO clusterProfiler enr
2 days ago • updated 1 day ago Fatima • 0
0
votes
9
replies
281
views
When doing differential methylation using the sesame package, seems to only go one way
methylation sesame methylationArrayAnalysis
2 days ago • updated 10 hours ago ramiro.barrantes ▴ 10
0
votes
0
replies
60
views
Mark seleced variables in the x-loading plot
OPLS genomes Proteomics
2 days ago Ragnhild • 0
0
votes
0
replies
55
views
News: Metabolomics with R/Bioconductor Online Course
metabomxtr MetaboCoreUtils metabolomicsWorkbenchR Metabolomics
3 days ago info ▴ 10
2
votes
1
reply
101
views
object 'hdac_targets' not found
TPP
updated 3 days ago by 67k • written 3 days ago by • 0
0
votes
1
reply
83
views
KEGGgraph result difference
igraph KEGGgraph RCy3 GraphNEL
updated 3 days ago by ▴ 20 • written 3 days ago by ▴ 80
0
votes
0
replies
61
views
Issue Installing Biostrings Package: gcc Compilation Errors
Biostrings packageinstallation
3 days ago semra • 0
1
vote
2
replies
195
views
In the sesame package, what does the estimate output mean from testEnrichment()
MethylationArray methylation sesame methylationArrayAnalysis
3 days ago • updated 2 days ago ramiro.barrantes ▴ 10
0
votes
1
reply
87
views
WGCNA Choosing soft threshold power below R^2 0.8
WGCNA
updated 3 days ago by ▴ 730 • written 3 days ago by • 0
1
vote
2
replies
138
views
WARNING: No Bioconductor dependencies detected.
Bioconductor Biocon
5 days ago • updated 3 days ago katja.danielzik • 0
0
votes
3
replies
227
views
Rsubread alignment crashes at 35%, valgrind indicates invalid writes
Rsubread
updated 2 days ago by ▴ 440 • written 4 days ago by • 0
0
votes
1
reply
88
views
Annotating DMRs
MethylationArray MethylationArrayData methylationArrayAnalysis
updated 4 days ago by 67k • written 4 days ago by ▴ 10
0
votes
2
replies
279
views
PCA analysis RNA-Seq QC looks strange?
DESeq2
updated 6 days ago by ★ 1.4k • written 11 days ago by • 0
0
votes
2
replies
181
views
concentration tables suitable as input for new packages?
Bioconductor
6 days ago • updated 5 days ago katja.danielzik • 0
2
votes
0
replies
134
views
News: Save the Date for EuroBioC2025 in Barcelona!
EuroBioC2025 Conference Bioconductor Community
6 days ago Maria Doyle ▴ 90
0
votes
1
reply
100
views
Ideal approach to adjust for covariates for WGCNA
WGCNA wgcna
updated 4 days ago by 67k • written 6 days ago by • 0
0
votes
5
replies
1.5k
views
DESeq2 Multi-factor design not full rank
RNASeq DESeq2
written 3.3 years ago by • 0
0
votes
4
replies
274
views
ı cant install clusterprofiler on my Ubuntu 20.04.6 LTS
Bioconductor clusterProfiler
updated 5 days ago by 67k • written 7 days ago by • 0
0
votes
0
replies
119
views
Job: Postdoctoral Research Associate in Computational Epigenomics
Phd SingleCell DNAMethylation Shanghai JobPosting
8 days ago xiaolong • 0
0
votes
1
reply
164
views
ensemblVEP deprecation and how to reproduce
VariantAnnotation
updated 9 days ago by 6.7k • written 9 days ago by • 0
0
votes
0
replies
138
views
News: Bioconductor 3.20 Release Schedule
software release Release
9 days ago shepherl 4.0k
1
vote
1
reply
250
views
Help with design matrix for RNA-seq data using edgeR
edgeR RNASeqData
updated 9 days ago by 51k • written 11 days ago by • 0
3
votes
6
replies
1.2k
views
[DESeq2] Normalization of External Test Dataset for Machine Learning (ML) Application
DESeq2
updated 7 days ago by 42k • written 10 days ago by • 0
0
votes
2
replies
254
views
tximport data import
tximport
updated 10 days ago by 42k • written 11 days ago by • 0
2
votes
1
reply
178
views
Should tSNE from biol. replicates look alike?
scRNAseq SingleCellExperiment batchelor
updated 10 days ago by 67k • written 10 days ago by ▴ 10
0
votes
0
replies
117
views
Problem merging metadata and feature-table before analysing LEfSe on R
microbiomeDataSets differential-abundance
10 days ago 샤니쿠마리 • 0
2
votes
2
replies
466
views
fgsea stuck in an infinite loop in the middle of the run
GSEABase fgsea msigdb GeneSetEnrichment
11 days ago • updated 10 days ago Assa Yeroslaviz ★ 1.5k
1
vote
1
reply
249
views
How to use compareCluster in ClusterProfiler?
RNASeqData GSEA clusterProfiler
updated 11 days ago by ★ 4.1k • written 12 days ago by • 0
0
votes
0
replies
142
views
News: Announcing GBCC 2025: The first-ever joint conference between Bioconductor and Galaxy!
Conference Bioconductor Community
12 days ago Maria Doyle ▴ 90
0
votes
1
reply
169
views
Unable to install/use limma
limma Bioconductor
updated 12 days ago by 67k • written 12 days ago by • 0
1
vote
3
replies
574
views
502 error biomaRt getLDS()
ensembldb biomaRt
updated 12 days ago by 67k • written 7 months ago by ▴ 10
1
vote
1
reply
236
views
Empty Results from champ.DMP Despite Expected Output
MethylationArray ChAMP R
updated 12 days ago by 67k • written 14 days ago by • 0
0
votes
1
reply
183
views
ReactomeGSA adjustment for confounding variables
BiologicalQuestion ReactomeGSA BatchEffect
updated 10 days ago by ▴ 20 • written 13 days ago by • 0
3
votes
6
replies
25k
views
Deseq: What does "BaseMean" mean?
deseq2
written 6.0 years ago by • 0
0
votes
1
reply
295
views
question about gseGO() in clusterprofiler package
clusterProfiler
updated 13 days ago by ★ 4.1k • written 15 days ago by • 0
0
votes
0
replies
221
views
Z-score Interpretation across components
MAST
16 days ago Greg • 0
0
votes
1
reply
245
views
error for the geneGOEnricher function of the NoRCE package
NoRCE
updated 16 days ago by 67k • written 16 days ago by • 0
0
votes
2
replies
677
views
Understanding Contrasts and Interaction in DESeq2 for 2 genotypes, 2 treatments
RNASeq DESeq2
updated 16 days ago by ★ 1.4k • written 17 days ago by • 0
1
vote
2
replies
266
views
BiomaRt Possible Ensembl SSL connectivity problems detected.
PureCN biomaRt
16 days ago • updated 13 days ago varga.luca • 0
1
vote
5
replies
550
views
Heatmap from the output of GSEA clusterProfiler?
clusterProfiler heatmaps
written 28 days ago by • 0
1
vote
2
replies
255
views
Review process for delivering R packages
Bioconductor
17 days ago XFWu • 0
4
votes
11
replies
588
views
Size factor normalized counts for between sample comparisons - correct?
DESeq2
18 days ago • updated 16 days ago boczniak767 ▴ 740
0
votes
2
replies
298
views
Open Sesame: in what genes are my differentially methylated probes!!
MethylationArray sesameData sesame
17 days ago ramiro.barrantes ▴ 10
0
votes
2
replies
253
views
DiffBind for MBD-seq
MBD-seq DiffBind
18 days ago Marianna ▴ 20
0
votes
0
replies
160
views
Job: Ensembl Job Vacancies
genomes Annotation GenomicVariation ensembldb
18 days ago Aleena ▴ 30
2
votes
9
replies
604
views
Seeking Advice on Using edgeR and variancePartition for RNA-seq Data from Multiple Tissues and Patients
edgeR variancePartition
updated 17 days ago by 51k • written 19 days ago by • 0
46,005 results • Page 1 of 921
Recent ...
Replies
Answer: Dealing with 0 miRNA counts in DESeq2 analysis and influence in adjusted p-value by Michael Love 42k
This is covered in the workflow (rnaseqGene). You can filter them, but no they will not negatively affect the multiple testing because o…
Comment: When doing differential methylation using the sesame package, seems to only go by ramiro.barrantes ▴ 10
Thank you, the strange thing is that I am only getting positive effect sizes. I [see two relevant definitions][1]: - Eff_* : The effect s…
Comment: When doing differential methylation using the sesame package, seems to only go by James W. MacDonald 67k
The odds ratio, not log FC. My bad.
Comment: When doing differential methylation using the sesame package, seems to only go by James W. MacDonald 67k
``` testResult$Eff_Condition > 0.1 ```
Comment: clusterProfiler: BgRatio N value does not match the size of the gene universe th by Fatima • 0
I identified 3804 genes with GO annotations. I put my liste of genes in this link [enter link description here][1] universe <- mapIds…
Votes
Answer: Question: How to Set Up Contrasts for Case-Control Analysis in Limma While Adjus
Answer: Question: How to Set Up Contrasts for Case-Control Analysis in Limma While Adjus
Answer: clusterProfiler: BgRatio N value does not match the size of the gene universe th
Answer: object 'hdac_targets' not found
Answer: object 'hdac_targets' not found
Awards • All
Popular Question to rae.alshammari ▴ 10
Popular Question to Mthabisi Moyo ▴ 40
Popular Question to peris_baba • 0
Popular Question to Aastha Kapoor • 0
Popular Question to kf • 0
Locations • All
WEHI, Melbourne, Australia, 10 minutes ago
France, 13 minutes ago
The city by the bay, 28 minutes ago
UPF, Barcelona, Spain, 1 hour ago
Türkiye, 1 hour ago
Traffic: 282 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