1
vote
1
reply
983
views
WGCNA
DEGselection RNASeqData WGCNA
updated 14 months ago by ▴ 760 • written 14 months ago by • 0
5
votes
4
replies
1.0k
views
How to control batch effect if Group and batch are same?
limma DESeq2 BatchEffect
updated 14 months ago by ★ 5.0k • written 14 months ago by • 0
4
votes
1
reply
675
views
edgeR 4.2.1 compression bug: a minimally reproducible snippet
edger edgeR
updated 14 months ago by 53k • written 14 months ago by • 0
2
votes
5
replies
1.1k
views
dmpFinder for other objects
methylset minfi dmpFinder betaHMM beta
updated 14 months ago by 68k • written 14 months ago by • 0
0
votes
1
reply
466
views
Unevaluated error in ChIPQC combined with BiocParallel
BiocParallel ChIPQC
written 14 months ago by • 0
0
votes
2
replies
695
views
RNA-Seq p value range variation
DESeq2 pvalue RNA-Seq
14 months ago paul.meraner • 0
0
votes
0
replies
607
views
News: RNAseq data analysis with Bioconductor (online course)
DESeq2 SummarizedExperiment
14 months ago • updated 13 months ago info ▴ 10
2
votes
8
replies
1.9k
views
miRTarRnaseq library
miRNATarget mirTarRnaSeq
updated 11 months ago by ▴ 20 • written 20 months ago by • 0
1
vote
6
replies
1.5k
views
heatmap with batch effect
DESeq2 BatchEffect
written 14 months ago by • 0
0
votes
1
reply
561
views
how do I convert an Ilumn IDREF to a CPG loci
AnnotationDbi Annotation annotation BiologicalQuestion
updated 14 months ago by 68k • written 14 months ago by • 0
0
votes
1
reply
672
views
Setting ylims in bam coverage plot and assigning compound sashimi numbers to overlay plots
Coverage Gviz sashimi
updated 6 months ago by • 0 • written 14 months ago by • 0
0
votes
1
reply
912
views
Which input data is acceptable for MAST?
SCTransform MAST
updated 14 months ago by ▴ 280 • written 14 months ago by • 0
1
vote
1
reply
764
views
segfault when using singleR with Azimuth reference
SingleR
updated 14 months ago by 68k • written 14 months ago by ▴ 760
0
votes
1
reply
640
views
[BUG] featureCounts doesn't assign primary alignment of a multi-mapped read, even with `--primary` specified
featureCounts Rsubread
14 months ago isaac.vock • 0
0
votes
2
replies
758
views
How can I obtain DEGs that are resulted from using salmon in alignment-based mode or mapping-based mode?
tximport DESeq2
updated 14 months ago by 43k • written 14 months ago by • 0
1
vote
1
reply
1.0k
views
Deseq2 sfType
Microbiome DESeq2 RNASeq
updated 14 months ago by 68k • written 14 months ago by • 0
1
vote
1
reply
696
views
Normalization RNA-seq for multiple plates
Normalization DESeq2 RNASeqData edgeR
updated 14 months ago by ★ 5.0k • written 14 months ago by • 0
0
votes
1
reply
859
views
News: Subject: Last 2 Seats Available for Metabolomics with R/Bioconductor Course (October 7-10)
Metabolomics xcms
updated 14 months ago by • 0 • written 14 months ago by ▴ 10
2
votes
2
replies
581
views
SAS token for Annotation package
AnnotationDbi AnnotationForge
14 months ago KABILAN • 0
1
vote
1
reply
992
views
Convert HGVS Representation back to Reference Genome Coordinates
GA4GHclient
updated 14 months ago by ▴ 160 • written 14 months ago by ★ 1.6k
1
vote
1
reply
598
views
DEseq 2 LFC shrinkage with apeglm in single-cell pseudobulk: strange volcano plot results
DESeq2
updated 14 months ago by ★ 5.0k • written 14 months ago by • 0
1
vote
2
replies
894
views
Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 14 months ago by 43k • written 14 months ago by ▴ 10
0
votes
2
replies
1.0k
views
DESeq2 analysis on 2 plant lines infected with virus, with 2 time points (days post infection)
DESeq2
updated 14 months ago by 43k • written 14 months ago by • 0
1
vote
2
replies
1.0k
views
DESeq2 design and contrasts with 2 drug-treated and one control group
DESeq2 Bioconductor
updated 14 months ago by 43k • written 14 months ago by ▴ 10
2
votes
4
replies
1.0k
views
Spectra and PSMatch- trouble in reducePSMs, joinSpectraData, or countIdentifications?
ProteomicsWorkflow PSMatch Spectra RforProteomics
updated 14 months ago by 1.6k • written 14 months ago by • 0
0
votes
0
replies
473
views
Assistance with Bulk RNA-seq Data Analysis Including Random Effect (`duplicateCorrelation` from `limma`)
limma RNAseq123
14 months ago tim.meese • 0
0
votes
1
reply
819
views
BiomaRt - improved access to Ensembl ?
biomaRt
updated 14 months ago by ★ 6.6k • written 14 months ago by • 0
0
votes
0
replies
19
views
Spam: Online gaming
EWCE games
14 months ago Lisandro Hermoso 0
3
votes
3
replies
826
views
ISO a solution to rank-order introns by transcript
GenomicRanges GenomicFeatures
14 months ago • updated 11 months ago mat149 ▴ 80
2
votes
2
replies
1.7k
views
Issues with retrieving Zea mays genes dataset: biomaRt error: looks like we're connecting to incompatible version of BioMart.
biomaRt
14 months ago 2044291597 • 0
0
votes
3
replies
1.1k
views
Meta-analysis on RNA-seq data sets
meta-analysis sva Combat_Seq RNAseq
14 months ago Travis • 0
0
votes
0
replies
350
views
Deprecated Gates- tailgate
openCyto
14 months ago ztflaten • 0
0
votes
1
reply
399
views
Build error report
PLSDAbatch
updated 14 months ago by 4.2k • written 14 months ago by • 0
0
votes
0
replies
385
views
Getting error while running GenomicPlot
GenomicPlot
14 months ago Lucky • 0
0
votes
0
replies
517
views
News: Opportunity for Carpentries Instructors to Teach Bioconductor in Africa
Carpentries Community Teaching Bioconductor
14 months ago Maria Doyle ▴ 110
1
vote
6
replies
1.8k
views
New to Deseq2 - DEG questions / MA plot
genomes DESeq2 Transcriptomics
updated 13 months ago by ★ 5.0k • written 14 months ago by • 0
0
votes
2
replies
807
views
EdgeR - Apparent Wrong Direction of logFC with Low Count Data
limma edgeR
updated 14 months ago by 53k • written 14 months ago by • 0
2
votes
2
replies
751
views
Batch adjustment for cohort based RNA seq data
RNASeqPower removeBatchEffect cpm Batcheffect
14 months ago sukeshinik5 ▴ 20
2
votes
9
replies
1.8k
views
Can't post a question?
Bioconductor
updated 8 months ago by • 0 • written 14 months ago by • 0
0
votes
1
reply
1.6k
views
Job: Research software engineer at UPF Barcelona
JobPosting Devel GSVA Software
written 3.0 years ago by ★ 3.4k
0
votes
4
replies
898
views
rtracklayer accessing UCSC data table not working
UCSC rtracklayer getTable
14 months ago Andreas.Herbst • 0
0
votes
0
replies
602
views
WGCNA: Problem with selecting soft threshold
biologicalnetworkanalysis genomes RNA-Seq co-expression wgcna
14 months ago Fernanda • 0
0
votes
0
replies
438
views
package rpx, unable to download any dataset (PRIDE, MassIVE, iProX)
rpx PXDataset RforProteomics
14 months ago Jane_Huang • 0
0
votes
2
replies
712
views
Question on performing ANOVA-like analysis using limma
limma
updated 14 months ago by 53k • written 14 months ago by • 0
0
votes
1
reply
497
views
For feline genome
genomes Analysisoffelinegenome
updated 14 months ago by 68k • written 14 months ago by • 0
0
votes
1
reply
469
views
Many DEGs (Is a high percentage of DEGs acceptable in DESeq2)?
DESeq2
updated 14 months ago by 43k • written 14 months ago by • 0
0
votes
1
reply
642
views
Rstudio died when put more than three letters in subseting a SummarizedExperiment object
SummarizedExperiment
14 months ago Shuo GG • 0
0
votes
0
replies
678
views
Generating Boxplots for Gene Expression by CellType in NanoStringGeoMXSet
GeomxTools SpatialDecon GeoMxWorkflows
14 months ago Cinque • 0
0
votes
2
replies
1.0k
views
Harmonizing RNA-seq data of different sourceS(cell vs. tissue) to further conduct unsupervised clustering analysis?
HarmonizedTCGAData
written 14 months ago by • 0
1
vote
2
replies
700
views
Inconsistent result in edgeR
edgeR
14 months ago hiroko.ohmiya • 0
46,691 results • Page 15 of 934
Recent ...
Replies
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
Awards • All
Commentator to sina.nassiri ▴ 130
Popular Question to Hervé Pagès 16k
Popular Question to jared.andrews07 ▴ 30
Popular Question to James W. MacDonald 68k
Popular Question to shepherl 4.2k
Locations • All
United States, 27 minutes ago
The city by the bay, 41 minutes ago
Finland, 1 hour ago
The Netherlands, 5 hours ago
United Kingdom, 5 hours ago
Traffic: 723 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