0
votes
3
replies
10k
views
SingleR Label.Ont
SingleR
updated 11 days ago by • 0 • written 8 months ago by • 0
5
votes
8
replies
8.9k
views
Limma design with continuous and categorical covariates
limma batch effect covariates microarray
updated 29 days ago by • 0 • written 7.8 years ago by ▴ 30
8
votes
41
replies
5.9k
views
Ensembl plants at annotationHub?
ensembl ensembldb plant arabidopsis thaliana annotationhub
updated 1 day ago by • 0 • written 5.5 years ago by ★ 4.0k
0
votes
3
replies
3.7k
views
[Mfuzz] Error in cmeans(exprs(eset)
Mfuzz Mfuzz
updated 16 days ago by • 0 • written 13.2 years ago by ▴ 720
0
votes
44
replies
3.2k
views
How to use bootRanges to bootstrap small RNA loci (nullranges package)
bootRanges nullranges
updated 8 days ago by 42k • written 15 months ago by • 0
4
votes
9
replies
3.1k
views
Create protein sequences including variants from a VCF file
VariantAnnotation customProDB
updated 7 days ago by • 0 • written 5.2 years ago by ▴ 50
0
votes
5
replies
2.9k
views
DNAString: Standard checksum function?
Biostrings FASTA sequencing
8.2 years ago • updated 17 days ago Henrik Bengtsson ★ 2.4k
5
votes
6
replies
2.8k
views
Although I successfully installed the package "simpleaffy'' , I cannot library it. Why?
simpleaffy
updated 20 days ago by 66k • written 2.4 years ago by • 0
1
vote
3
replies
2.7k
views
WGNCA kME vs. kIM
WGCNA
updated 6 hours ago by • 0 • written 8.7 years ago by ▴ 30
6
votes
19
replies
2.6k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 22 days ago by • 0 • written 4.6 years ago by ▴ 10
0
votes
3
replies
2.1k
views
maSigPro genes from clusters
masigpro clustering
updated 5 days ago by • 0 • written 7.9 years ago by • 0
15
votes
23
replies
2.1k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
7 weeks ago • updated 22 days ago Chris ▴ 10
10
votes
11
replies
1.9k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq rnaseq
updated 16 hours ago by • 0 • written 6.8 years ago by ▴ 80
2
votes
4
replies
1.8k
views
slingshot: error with plot3d.SlingshotDataSet
slingshot plot3d.SlingshotDataSet
updated 6 hours ago by • 0 • written 23 months ago by ▴ 10
2
votes
3
replies
1.8k
views
ChipQC 'names' attribute [9] must be the same length as the vector [2]'
chipqc
updated 9 days ago by • 0 • written 3.6 years ago by ▴ 60
2
votes
4
replies
1.7k
views
EGSEA usage with microarray data (with vooma)?
EGSEA gene set testing vooma limma voom gsea
updated 14 days ago by ▴ 10 • written 7.4 years ago by ▴ 190
1
vote
5
replies
1.6k
views
Cannot connect to ExperimentHub server
ExperimentHub
updated 14 days ago by • 0 • written 5 months ago by • 0
0
votes
2
replies
1.5k
views
How to use spike-in information (sequences from another species) with DESeq2::DESeq()
DESeq2 SpikeIn Normalization
updated 12 days ago by • 0 • written 16 months ago by ▴ 10
0
votes
3
replies
1.5k
views
Limma, eBayes different sample size of groups and adjustment
limma limma
updated 22 days ago by • 0 • written 13.1 years ago by ▴ 10
3
votes
1
reply
1.5k
views
Limma without eBayes, is it indistunguishable from Ordinary Least Square?
Limma ebayes bayesian ls
updated 14 days ago by 50k • written 5.6 years ago by ▴ 10
0
votes
1
reply
1.4k
views
DSS CpG coverage threshold
DSS WGBS coverage
updated 13 days ago by • 0 • written 6.6 years ago by ▴ 30
15
votes
17
replies
1.3k
views
Why p value inconsistent when using different number of pathway score?
limma
4 weeks ago • updated 21 days ago Chris ▴ 10
0
votes
4
replies
1.2k
views
News: European Bioconductor Conference 2023 planning
Europe Conference EuroBioC Events News
updated 5 days ago by • 0 • written 19 months ago by ▴ 70
2
votes
2
replies
1.1k
views
limma for gene expression analysis with big and unbalanced sample size
limma microarray statistics
updated 22 days ago by • 0 • written 8.0 years ago by • 0
1
vote
2
replies
1.0k
views
DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE, : NA/NaN/Inf in foreign function call (arg 1)"
DMRcate Gviz
updated 29 days ago by ▴ 180 • written 14 months ago by ▴ 10
4
votes
3
replies
1.0k
views
BayesSpace parameters for DLPFC Visium data
BayesSpace
written 3.0 years ago by ▴ 30
0
votes
2
replies
962
views
using WGCNA, positive or negative corrlation between genes composing modules.
correlation wgcna network
updated 7 days ago by • 0 • written 18 months ago by • 0
1
vote
3
replies
900
views
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
clusterProfiler RNASeq
updated 28 days ago by ★ 1.2k • written 14 months ago by ▴ 10
1
vote
2
replies
763
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
5 weeks ago • updated 26 days ago Patadù ▴ 10
0
votes
7
replies
761
views
News: List of Deprecated Packages for Bioc3.19
Release Devel ExperimentData Software
11 weeks ago • updated 29 days ago shepherl 3.9k
0
votes
2
replies
759
views
Query regarding phyloseq object construct with QIIME output
phyloseq microbiome Metagenomics
updated 7 days ago by • 0 • written 11 months ago by • 0
0
votes
2
replies
749
views
Help with ENmix readidat
ENmix IlluminaHumanMethylationEPICmanifest
updated 2 days ago by 66k • written 2.0 years ago by • 0
0
votes
1
reply
729
views
How to arrange multiple plots into one page in NOISeq?
noiseq RNA-seq quality control
updated 1 day ago by • 0 • written 4.7 years ago by ▴ 80
7
votes
6
replies
659
views
Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it does not happen in Linux
GenomAutomorphism
written 17 days ago by • 0
4
votes
2
replies
646
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea edgeR
20 days ago • updated 16 days ago gene_bioconductor ▴ 10
0
votes
6
replies
587
views
Numerical differences in DESeq2 output depending on different design matrix construction
DESeq2
5 days ago • updated 2 days ago Ken C • 0
0
votes
8
replies
546
views
Can I trust the differential expression analysis when the two groups overlap on the PCA?
DESeq2 pcaExplorer
updated 8 days ago by ▴ 30 • written 9 days ago by • 0
1
vote
4
replies
536
views
DEseq2 coefficient
DESeq2 coefficient
12 weeks ago • updated 21 days ago JKim • 0
1
vote
5
replies
532
views
Can't post a question containing code?
Bioconductor
updated 12 days ago by • 0 • written 3 months ago by ▴ 10
2
votes
13
replies
517
views
Trying to use enrichGO
clusterProfiler GenomicDistributionsData KEGG
4 weeks ago • updated 28 days ago fernanda.backsouza ▴ 10
3
votes
10
replies
503
views
Extremely small p-values using Limma for proteomic data
Proteomics limma
updated 12 days ago by 66k • written 15 days ago by • 0
4
votes
9
replies
499
views
Memory errors using read.bismark?
dmrseq bsseq
5 weeks ago • updated 15 days ago Juan Higareda • 0
2
votes
7
replies
436
views
deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
14 days ago • updated 11 days ago sajadahmad41454 • 0
2
votes
9
replies
433
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 27 days ago by 66k • written 27 days ago by • 0
2
votes
2
replies
422
views
Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(paste("networks", net.suid, "tables", tbl, sep = "/"), : object 're…
RCy3
11 days ago • updated 6 days ago Matthew Thornton ▴ 360
1
vote
2
replies
411
views
limma Intercept vs No-intercept models completely changing DMR results?
limma DMRcate MethylationArray EPICV2
updated 19 days ago by 50k • written 19 days ago by • 0
0
votes
8
replies
405
views
DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 27 days ago by ★ 1.4k • written 29 days ago by • 0
1
vote
2
replies
397
views
CombineArrays for EPIC and EPIC V2
EPICV1 Methylation combineArrays minifi EPICv2manifest
7 weeks ago • updated 19 days ago Kim • 0
2
votes
4
replies
392
views
seqlevelsStyle() not working
ensembldb genomei GenomeInfoDb
written 3 months ago by ▴ 70
0
votes
4
replies
384
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
updated 11 days ago by • 0 • written 21 days ago by ▴ 70
180 results • Page 1 of 4
Recent ...
Replies
Comment: recount3 problem downloading data from source sra by Leonardo Collado Torres ★ 1.1k
Hi, What do you get if you run the following `httr::HEAD()` command? I noticed that you have `libcurl` version 8.3.0 from `curl::curl_vers…
Comment: Slightly different count plots from R and spreadsheet by boczniak767 ▴ 720
Thank you @mikelove for your patience and kind advice. So I assume the plots from R are valid. Best wishes.
Answer: Help with infinite recursion - non-zero exit status in installation of GenomeInf by James W. MacDonald 66k
Maybe just try again? ``` > install("GenomeInfoDbData", force = TRUE) 'getOption("repos")' replaces Bioconductor standard repositorie…
Comment: Help with infinite recursion - non-zero exit status in installation of GenomeInf by Brandon • 0
Hello, As an update, I am able to install and load GenomeInfoDb successfully in a fresh renv in my WSL distro. However, I'm not sure what …
Comment: slingshot: error with plot3d.SlingshotDataSet by Kelly Street • 0
This issue has been addressed [on GitHub][1]. [1]: https://github.com/kstreet13/slingshot/issues/249
Votes
Comment: recount3 problem downloading data from source sra
Answer: Slightly different count plots from R and spreadsheet
Including squared covariates to account for non-linear dependencies in differential gene expression analysis
DESeq2 DE gene expression of scRNA-seq pseudobulk
Answer: Multiple factor DSEq2 result generates weird volcano plot
Awards • All
Popular Question to Andrew Pattison • 0
Popular Question to pcantalupo ▴ 10
Scholar to Michael Love 42k
Popular Question to Jenny Drnevich ★ 2.0k
Centurion to boczniak767 ▴ 720
Locations • All
United States, 1 minute ago
Australia, 19 minutes ago
United States, 24 minutes ago
Seattle, WA, United States, 24 minutes ago
Australia, 47 minutes ago
Traffic: 564 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