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4
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How to left_join a tidySummarizedExperiment with a GRanges object by seqnames and start (tidyverse-style)?
GenomicRanges
tidySummarizedExperiment
tidyomics
7 months ago • updated 12 weeks ago
Kateřina
• 0
3
votes
2
replies
6.4k
views
limma duplicateCorrelation appropriate where some blocks cross condition and some are in same condition?
limma
6 months ago
Geoff
• 0
0
votes
1
reply
858
views
Workflow to Analyse DNA Sequence specify gene expression in a fungus under stress
rnaseqGene
updated 6 months ago by
Michael Love
43k • written 6 months ago by
Ferdinand David
• 0
0
votes
1
reply
429
views
Unclear DEseq2 replaceOutliers error message
DESeq2
updated 6 months ago by
Michael Love
43k • written 6 months ago by
Pak
• 0
0
votes
1
reply
467
views
lncRNA functional annotation package
RNAseq123
updated 6 months ago by
James W. MacDonald
68k • written 6 months ago by
tarek.mohamed
• 0
1
vote
1
reply
676
views
Biomart server error
biomaRt
BioMartGOGeneSets
updated 6 months ago by
James W. MacDonald
68k • written 6 months ago by
tarek.mohamed
• 0
0
votes
0
replies
9
views
Spam:
Best Piles Clinic in Hyderabad
cadd.v1.6.hg38
BestPilesClinicinHyderabad
hcg110.db
MethylSeekR
6 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 21.8 years ago by
Ann Loraine
▴ 30
0
votes
1
reply
584
views
Difference in DESeq2 output and tidybulk DESeq2 method
DifferentialExpression
DESeq2
tidybulk
RNASeq
updated 6 months ago by
Michael Love
43k • written 7 months ago by
s.malik
• 0
3
votes
2
replies
2.1k
views
Deseq2 DE analysis of host-pathogen samples (model separately or jointly?)
DESeq2
7 months ago • updated 6 months ago
dudutchy
▴ 10
0
votes
8
replies
1.5k
views
ERCC Spike-In controls being discarded during Tximeta process:
@mikelove
tximeta
updated 6 months ago by
Michael Love
43k • written 6 months ago by
Gaurav
• 0
2
votes
4
replies
2.7k
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
6 months ago
Maziya
• 0
4
votes
17
replies
5.8k
views
How to load scRNA-seq data from GEO
SingleCellExperiment
GEO
updated 6 months ago by
ATpoint
★ 5.0k • written 7 months ago by
petergrahamclark
▴ 10
2
votes
3
replies
1.5k
views
Differential gene expression analysis on haplotype-resolved diploid assembly
edgeR
DESeq2
haplotype
limma
6 months ago
Paulito
• 0
0
votes
1
reply
641
views
Using EBI Image on Ranged Bar Chart
EBImage
written 6 months ago by
ekatcher
• 0
1
vote
3
replies
1.2k
views
Possible issue following the logNormCounts(filtered) with resulted fit
single-cell
SingleCell
SingleCellExperiment
SingleCellWorkflow
SingleCellData
6 months ago
Konstantinos Yeles
▴ 90
0
votes
2
replies
887
views
edgeR in DMR mode - replicates give batch effect - how to build design matrix with condition and replicate
edgeR
updated 6 months ago by
Paul Harrison
▴ 110 • written 6 months ago by
Francesco
• 0
0
votes
2
replies
573
views
GBCC2025: New Scholarship Opportunities Available!
Community
Conference
GBCC2025
Bioconductor
updated 3 months ago by
Liona
• 0 • written 6 months ago by
Maria Doyle
▴ 110
0
votes
0
replies
294
views
Blank gene_id in featureCounts
featureCounts
Rsubread
6 months ago
Meg
• 0
2
votes
5
replies
1.3k
views
Heatmap of rnaseq data with z-score scale
heatmaps
RNASeq
updated 6 months ago by
Paul Harrison
▴ 110 • written 6 months ago by
giovanna
▴ 10
0
votes
1
reply
549
views
FCS 32 support going backwards?
flowCore
updated 6 months ago by
shosioness123q
• 0 • written 6 months ago by
Oliver
• 0
0
votes
1
reply
488
views
Typo in the help of lmFit()
limma
updated 6 months ago by
Gordon Smyth
53k • written 6 months ago by
Balazs
• 0
0
votes
2
replies
1.1k
views
Memory issue while using "quickcluster" and "computeSumFactors" functions on single cell RNA seq dataset with 7-9 lac cells
scran
updated 6 months ago by
ATpoint
★ 5.0k • written 6 months ago by
amlanjyoti
• 0
4
votes
4
replies
2.1k
views
Adding gene names as row annotations to an RNAseq heatmap made with ComplexHeatmap
DESeq2
ComplexHeatmap
6 months ago
caroline.zanchi
▴ 10
0
votes
2
replies
671
views
Limma suqeezeVar
limma
6 months ago
Mengchun
• 0
0
votes
0
replies
350
views
What Input-type do I use in decouplR::run_viper?
decoupleR
viper
updated 6 months ago by
Michael Love
43k • written 6 months ago by
Julian
• 0
0
votes
2
replies
1.3k
views
Limma trend with limpa
limpa
limma
trend
updated 6 months ago by
Gordon Smyth
53k • written 6 months ago by
Alejandro
• 0
0
votes
1
reply
430
views
DESeq2 from phyloseq error
DESeq2
phyloseq
6 months ago
asafpr
• 0
0
votes
0
replies
323
views
Combining COMBAT-seq result (raw count) with other raw count
rnaseq
combat-seq
sva
combat
bulk-rnaseq
6 months ago
dudwnsrla1
• 0
0
votes
1
reply
528
views
Can't install BioC packages (and manager) behind firewall
Install
updated 6 months ago by
Marcel Ramos
700 • written 6 months ago by
delphine
• 0
1
vote
2
replies
1.4k
views
GSVA 1.52.2 (new API) nb of workers?
parallelize
workers
GSVA
written 18 months ago by
johanna.galvis
• 0
0
votes
2
replies
557
views
How to extract coordinates of mismatches from a BAM file lodaded in as a GAlignments?
GenomicAlignments
updated 7 months ago by
Hervé Pagès
16k • written 7 months ago by
Charles
• 0
4
votes
2
replies
1.4k
views
GAlignments Cigar to GRanges
GenomicRanges
cigarRangesAlongReferenceSpace
GenomicAlignments
Cigar
7 months ago
pineiroalejandro
▴ 10
3
votes
3
replies
648
views
AnnotationHub/ExperimentHub resources backup
AnnotationHub
HubPub
ExperimentHub
updated 7 months ago by
James W. MacDonald
68k • written 7 months ago by
igor
▴ 50
6
votes
8
replies
5.7k
views
WGCNA coupled with differential expression analysis: question about baseline module detection
wgcna
WGCNA
written 5.7 years ago by
Colari19
▴ 60
0
votes
2
replies
5.2k
views
blockwiseModule crashes in the end and doesn't generate modules
WGCNA
updated 4 months ago by
quordle
• 0 • written 2.7 years ago by
mauricio.microbiol
• 0
3
votes
1
reply
650
views
DESeq2 Apeglm Coefficient Reordering / Log2FoldChange Comparison Change
DESeq2
apeglm
updated 7 months ago by
James W. MacDonald
68k • written 7 months ago by
sk
• 0
0
votes
0
replies
1.1k
views
Diffbind Analysis gives error during profile plotting stage. Error in value[[3L]](cond) : profileplyr error: Error: BiocParallel errors 1 remote…
chipseq
profileplyr
DiffBind
7 months ago
Muhammad
• 0
0
votes
0
replies
11
views
Spam:
County Group Wave City Ghaziabad
ri16cod.db
ncdfFlow
7 months ago
countywavecityghaziabad
0
1
vote
5
replies
1.5k
views
Heatmap of a transformed deseq object with pheatmap
DESeq2
heatmaps
updated 7 months ago by
James W. MacDonald
68k • written 7 months ago by
caroline.zanchi
▴ 10
0
votes
1
reply
404
views
Error in readCodelinkSet function
error
codelink
updated 7 months ago by
James W. MacDonald
68k • written 7 months ago by
nazaninhoseinkhan
• 0
0
votes
1
reply
694
views
Combat-seq usage
sva
7 months ago • updated 6 months ago
bbao
▴ 10
0
votes
1
reply
469
views
Best tximport quant.genes.sf
tximport
tximeta
Bioconductor
updated 7 months ago by
ATpoint
★ 5.0k • written 7 months ago by
yob4003
• 0
0
votes
1
reply
409
views
What happened to the Joost2016 dataset
org.Sc.sgd.db
updated 7 months ago by
shepherl
4.2k • written 7 months ago by
clementleong
• 0
2
votes
5
replies
1.3k
views
Dealing with heteroscedascity in limma
limma
splines
Proteomics
written 7 months ago by
Thomas
• 0
0
votes
3
replies
53k
views
SingleR Label.Ont
SingleR
written 2.2 years ago by
saeed.khalili
• 0
5
votes
7
replies
3.4k
views
limma correction for tumor purity
limma
7 months ago
gabriella.jacobson-eisenberg
▴ 20
0
votes
1
reply
483
views
Filtering out non-variable probes from EPICv2 matrix
DMRcate
EPICv2manifest
updated 7 months ago by
James W. MacDonald
68k • written 7 months ago by
Sasha
• 0
0
votes
2
replies
669
views
FlowSOM is unable to create Output
FlowSOM
updated 6 months ago by
EvangelinePope
• 0 • written 7 months ago by
marco.klein1
• 0
8
votes
3
replies
3.1k
views
DESeq2 class error: superclass "ExpData" not defined in the environment of the object's class
DESeq2
updated 6 months ago by
Michael Love
43k • written 7 months ago by
Cassia
▴ 40
46,693 results • Page
5 of 934
Recent ...
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Comment: p.adjust BH Question
by
TikTsoksocissalpc
• 0
Thanks for sharing your question about RMA limma analysis While working on your experiment, it s always helpful to have some background mu…
Answer: NUPOP usage
by
shepherl
4.2k
You should read the documentation in the package especially the package vignette https://bioconductor.org/packages/release/bioc/html/NuPoP.…
Comment: How can I correctly use phyloseq with Docker?
by
fnfgame
• 0
In a rocker image, this error usually means the Bioconductor install happened as root but the runtime library paths used by the shiny user …
Comment: DECIPHER DesignProbes unable to design FISH-probes
by
Erik Wright
▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
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.
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
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