3
votes
1
reply
3.7k
views
DESeq2 empirical bayes: variance of the prior for log fold changes (LFC)
DESeq2
updated 4 months ago by 43k • written 4 months ago by ▴ 10
0
votes
2
replies
1.2k
views
Interaction in Design Experimental
rnaseqGene
4 months ago Ferdinand David • 0
0
votes
0
replies
311
views
Job: Lab Head positions at the WEHI, Melbourne, Australia
JobPosting Bioconductor
4 months ago Gordon Smyth 53k
1
vote
4
replies
2.2k
views
Heatmap of the Count Matrix
rnaseqGene
updated 6 weeks ago by • 0 • written 4 months ago by • 0
0
votes
1
reply
489
views
DESeq2 results
result DESeq2 subsetting
updated 4 months ago by ★ 5.0k • written 4 months ago by • 0
0
votes
0
replies
209
views
DiffBind plot.profile error
BiocParallel DiffBind
4 months ago this_is_me_trying • 0
0
votes
4
replies
8.7k
views
Bioconductor version cannot be validated
Bioconductor Annotation Ann
written 2.1 years ago by • 0
0
votes
4
replies
889
views
Position of the legend object in complexHeatmap
ComplexHeatmap
4 months ago caroline.zanchi ▴ 10
0
votes
4
replies
3.1k
views
Drawing custom KEGG pathways
pathview KEGG
written 4.4 years ago by ▴ 10
1
vote
18
replies
7.3k
views
error in ChAMP loading file
ChAMP
updated 4 months ago by • 0 • written 3.0 years ago by • 0
1
vote
4
replies
2.0k
views
How to left_join a tidySummarizedExperiment with a GRanges object by seqnames and start (tidyverse-style)?
GenomicRanges tidySummarizedExperiment tidyomics
6 months ago • updated 6 weeks ago Kateřina • 0
3
votes
2
replies
6.3k
views
limma duplicateCorrelation appropriate where some blocks cross condition and some are in same condition?
limma
5 months ago Geoff • 0
0
votes
1
reply
835
views
Workflow to Analyse DNA Sequence specify gene expression in a fungus under stress
rnaseqGene
updated 5 months ago by 43k • written 5 months ago by • 0
0
votes
1
reply
395
views
Unclear DEseq2 replaceOutliers error message
DESeq2
updated 5 months ago by 43k • written 5 months ago by • 0
0
votes
1
reply
438
views
lncRNA functional annotation package
RNAseq123
updated 5 months ago by 68k • written 5 months ago by • 0
1
vote
1
reply
634
views
Biomart server error
biomaRt BioMartGOGeneSets
updated 5 months ago by 68k • written 5 months ago by • 0
0
votes
0
replies
9
views
Spam: Best Piles Clinic in Hyderabad
cadd.v1.6.hg38 BestPilesClinicinHyderabad hcg110.db MethylSeekR
5 months ago Laserqure03 0
0
votes
2
replies
1.8k
views
An ESR essay about software design, and how it applies to Bioconductor
GUI GUI
written 21.7 years ago by ▴ 30
0
votes
1
reply
518
views
Difference in DESeq2 output and tidybulk DESeq2 method
DifferentialExpression DESeq2 tidybulk RNASeq
updated 5 months ago by 43k • written 5 months ago by • 0
3
votes
2
replies
2.0k
views
Deseq2 DE analysis of host-pathogen samples (model separately or jointly?)
DESeq2
5 months ago dudutchy ▴ 10
0
votes
8
replies
1.5k
views
ERCC Spike-In controls being discarded during Tximeta process:
@mikelove tximeta
updated 5 months ago by 43k • written 5 months ago by • 0
2
votes
4
replies
2.6k
views
Altered (negative or positive) logFC values for same gene from two intitial count matrices, one being a subset of the other
Transcriptomics edgeR DEG
5 months ago Maziya • 0
4
votes
17
replies
5.6k
views
How to load scRNA-seq data from GEO
SingleCellExperiment GEO
updated 4 months ago by ★ 5.0k • written 5 months ago by ▴ 10
2
votes
3
replies
1.4k
views
Differential gene expression analysis on haplotype-resolved diploid assembly
edgeR DESeq2 haplotype limma
5 months ago Paulito • 0
0
votes
1
reply
613
views
Using EBI Image on Ranged Bar Chart
EBImage
written 5 months ago by • 0
1
vote
3
replies
1.1k
views
Possible issue following the logNormCounts(filtered) with resulted fit
single-cell SingleCell SingleCellExperiment SingleCellWorkflow SingleCellData
5 months ago Konstantinos Yeles ▴ 90
0
votes
2
replies
842
views
edgeR in DMR mode - replicates give batch effect - how to build design matrix with condition and replicate
edgeR
updated 5 months ago by ▴ 110 • written 5 months ago by • 0
0
votes
2
replies
509
views
GBCC2025: New Scholarship Opportunities Available!
Community Conference GBCC2025 Bioconductor
updated 10 weeks ago by • 0 • written 5 months ago by ▴ 100
0
votes
0
replies
246
views
Blank gene_id in featureCounts
featureCounts Rsubread
5 months ago Meg • 0
2
votes
5
replies
1.3k
views
Heatmap of rnaseq data with z-score scale
heatmaps RNASeq
updated 5 months ago by ▴ 110 • written 5 months ago by ▴ 10
0
votes
1
reply
507
views
FCS 32 support going backwards?
flowCore
updated 5 months ago by • 0 • written 5 months ago by • 0
0
votes
1
reply
454
views
Typo in the help of lmFit()
limma
updated 5 months ago by 53k • written 5 months ago by • 0
0
votes
2
replies
993
views
Memory issue while using "quickcluster" and "computeSumFactors" functions on single cell RNA seq dataset with 7-9 lac cells
scran
updated 5 months ago by ★ 5.0k • written 5 months ago by • 0
4
votes
4
replies
2.0k
views
Adding gene names as row annotations to an RNAseq heatmap made with ComplexHeatmap
DESeq2 ComplexHeatmap
5 months ago caroline.zanchi ▴ 10
0
votes
2
replies
639
views
Limma suqeezeVar
limma
5 months ago Mengchun • 0
0
votes
0
replies
290
views
What Input-type do I use in decouplR::run_viper?
decoupleR viper
updated 5 months ago by 43k • written 5 months ago by • 0
0
votes
2
replies
648
views
Limma trend with limpa
limpa limma trend
updated 5 months ago by 53k • written 5 months ago by • 0
0
votes
1
reply
385
views
DESeq2 from phyloseq error
DESeq2 phyloseq
5 months ago asafpr • 0
0
votes
0
replies
276
views
Combining COMBAT-seq result (raw count) with other raw count
rnaseq combat-seq sva combat bulk-rnaseq
5 months ago dudwnsrla1 • 0
0
votes
1
reply
473
views
Can't install BioC packages (and manager) behind firewall
Install
updated 5 months ago by 700 • written 5 months ago by • 0
1
vote
2
replies
1.2k
views
GSVA 1.52.2 (new API) nb of workers?
parallelize workers GSVA
written 16 months ago by • 0
0
votes
2
replies
529
views
How to extract coordinates of mismatches from a BAM file lodaded in as a GAlignments?
GenomicAlignments
updated 5 months ago by 16k • written 5 months ago by • 0
4
votes
2
replies
1.3k
views
GAlignments Cigar to GRanges
GenomicRanges cigarRangesAlongReferenceSpace GenomicAlignments Cigar
5 months ago pineiroalejandro ▴ 10
3
votes
3
replies
589
views
AnnotationHub/ExperimentHub resources backup
AnnotationHub HubPub ExperimentHub
updated 5 months ago by 68k • written 5 months ago by ▴ 50
6
votes
8
replies
5.5k
views
WGCNA coupled with differential expression analysis: question about baseline module detection
wgcna WGCNA
written 5.5 years ago by ▴ 60
0
votes
2
replies
5.1k
views
blockwiseModule crashes in the end and doesn't generate modules
WGCNA
updated 3 months ago by • 0 • written 2.6 years ago by • 0
3
votes
1
reply
603
views
DESeq2 Apeglm Coefficient Reordering / Log2FoldChange Comparison Change
DESeq2 apeglm
updated 5 months ago by 68k • written 5 months ago by • 0
0
votes
0
replies
1.0k
views
Diffbind Analysis gives error during profile plotting stage. Error in value[[3L]](cond) : profileplyr error: Error: BiocParallel errors 1 remote…
chipseq profileplyr DiffBind
5 months ago Muhammad • 0
0
votes
0
replies
11
views
Spam: County Group Wave City Ghaziabad
ri16cod.db ncdfFlow
5 months ago countywavecityghaziabad 0
1
vote
5
replies
1.3k
views
Heatmap of a transformed deseq object with pheatmap
DESeq2 heatmaps
updated 5 months ago by 68k • written 5 months ago by ▴ 10
46,655 results • Page 4 of 934
Recent ...
Replies
Comment: "Watched Tags" are being erased rather than updated by shepherl 4.2k
I can reproduce this and have opened an issue on the code base https://github.com/Bioconductor/support.bioconductor.org/issues/112
Comment: "Watched Tags" are being erased rather than updated by shepherl 4.2k
we can investigate this issue. thank you for bringing it to our attention
Comment: deseq2 filter the low counts by Michael Love 43k
> But within each comparison (contrast), if I trace some DEGs back to the original salmon merged gene counts (or even to normalised counts)…
Comment: deseq2 filter the low counts by empty_mt • 0
Thank you for you suggestion to look at the pre-filtering section in the DESeq2 vignettes - am I missing something? I have 6 treatments, …
Comment: deseq2 filter the low counts by Michael Love 43k
Have you seen this part: https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#pre-filtering
Votes
Comment: "Watched Tags" are being erased rather than updated
Comment: deseq2 filter the low counts
Answer: DESeq2 interactions
Answer: Important: Bioconductor Release 3.22 Delayed
A: Multi-level experiments in Limma
Awards • All
Popular Question to shepherl 4.2k
Popular Question to Hervé Pagès 16k
Popular Question to Ou, Jianhong ★ 1.3k
Popular Question to Maria Doyle ▴ 100
Popular Question to Gordon Smyth 53k
Locations • All
Pakistan, just now
United States, 14 minutes ago
United Kingdom, 33 minutes ago
United States, 43 minutes ago
United States, 49 minutes ago
Traffic: 1710 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