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0
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28
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Source / binary version mismatch for rGADEM
rGADEM
1 day ago
Jay hesselberth
• 0
0
votes
9
replies
12k
views
Bioconductor version cannot be validated
BiocManager
Bioconductor
updated 1 day ago by
Hadi
• 0 • written 3.8 years ago by
charlotte
▴ 10
3
votes
1
reply
903
views
DESeq2 empirical bayes: variance of the prior for log fold changes (LFC)
DESeq2
updated 1 day ago by
Michael Love
43k • written 4 days ago by
Chenghao
▴ 10
0
votes
2
replies
920
views
Interaction in Design Experimental
rnaseqGene
4 days ago • updated 2 days ago
Ferdinand David
• 0
1
vote
1
reply
723
views
Deseq2 paired sample in the design is considered as "batch"?
DESeq2
updated 3 days ago by
ATpoint
★ 4.9k • written 3 days ago by
corranna98
• 0
3
votes
1
reply
948
views
Biological replicates consideration in DESeq2 design formula.
DESeq2
RNASeqData
RNASeq
updated 3 days ago by
ATpoint
★ 4.9k • written 3 days ago by
Christian
▴ 20
0
votes
0
replies
45
views
Job:
Lab Head positions at the WEHI, Melbourne, Australia
JobPosting
Bioconductor
4 days ago
Gordon Smyth
52k
1
vote
1
reply
787
views
Heatmap of the Count Matrix
rnaseqGene
updated 4 days ago by
ATpoint
★ 4.9k • written 4 days ago by
Ferdinand David
• 0
0
votes
1
reply
267
views
DESeq2 results
result
DESeq2
subsetting
updated 4 days ago by
ATpoint
★ 4.9k • written 4 days ago by
rajdeepboral00
• 0
0
votes
0
replies
33
views
DiffBind plot.profile error
BiocParallel
DiffBind
4 days ago
this_is_me_trying
• 0
0
votes
2
replies
7.6k
views
Bioconductor version cannot be validated
Bioconductor
Annotation
Ann
updated 1 day ago by
Hadi
• 0 • written 21 months ago by
Aytaç
• 0
0
votes
4
replies
634
views
Position of the legend object in complexHeatmap
ComplexHeatmap
5 days ago • updated 2 days ago
caroline.zanchi
▴ 10
0
votes
4
replies
2.9k
views
Drawing custom KEGG pathways
pathview
KEGG
written 4.0 years ago by
curiousmind007
▴ 10
1
vote
22
replies
6.5k
views
error in ChAMP loading file
ChAMP
written 2.6 years ago by
Giulia
• 0
0
votes
0
replies
41
views
Retrieve Salmon transcript quantification file from recount3
recount3
7 days ago
kyn
▴ 10
0
votes
3
replies
1.7k
views
How to left_join a tidySummarizedExperiment with a GRanges object by seqnames and start (tidyverse-style)?
GenomicRanges
tidySummarizedExperiment
tidyomics
updated 8 days ago by
Michael Love
43k • written 6 weeks ago by
Kateřina
• 0
2
votes
2
replies
1.9k
views
limma duplicateCorrelation appropriate where some blocks cross condition and some are in same condition?
limma
9 days ago • updated 6 days ago
Geoff
• 0
0
votes
1
reply
663
views
Workflow to Analyse DNA Sequence specify gene expression in a fungus under stress
rnaseqGene
updated 9 days ago by
Michael Love
43k • written 9 days ago by
Ferdinand David
• 0
0
votes
1
reply
206
views
Unclear DEseq2 replaceOutliers error message
DESeq2
updated 9 days ago by
Michael Love
43k • written 9 days ago by
Pak
• 0
0
votes
1
reply
271
views
lncRNA functional annotation package
RNAseq123
updated 10 days ago by
James W. MacDonald
68k • written 10 days ago by
tarek.mohamed
• 0
1
vote
1
reply
462
views
Biomart server error
biomaRt
BioMartGOGeneSets
updated 10 days ago by
James W. MacDonald
68k • written 11 days ago by
tarek.mohamed
• 0
0
votes
0
replies
8
views
Spam:
Best Piles Clinic in Hyderabad
cadd.v1.6.hg38
BestPilesClinicinHyderabad
hcg110.db
MethylSeekR
11 days ago
Laserqure03
0
0
votes
2
replies
1.6k
views
An ESR essay about software design, and how it applies to Bioconductor
GUI
GUI
written 21.3 years ago by
Ann Loraine
▴ 30
0
votes
1
reply
274
views
Difference in DESeq2 output and tidybulk DESeq2 method
DifferentialExpression
DESeq2
tidybulk
RNASeq
updated 12 days ago by
Michael Love
43k • written 27 days ago by
s.malik
• 0
3
votes
2
replies
1.8k
views
Deseq2 DE analysis of host-pathogen samples (model separately or jointly?)
DESeq2
26 days ago • updated 11 days ago
dudutchy
▴ 10
0
votes
8
replies
1.1k
views
ERCC Spike-In controls being discarded during Tximeta process:
@mikelove
tximeta
updated 10 days ago by
Michael Love
43k • written 16 days ago by
Gaurav
• 0
2
votes
4
replies
2.2k
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
13 days ago • updated 11 days ago
Maziya
• 0
4
votes
17
replies
4.9k
views
How to load scRNA-seq data from GEO
SingleCellExperiment
GEO
updated 4 days ago by
ATpoint
★ 4.9k • written 4 weeks ago by
petergrahamclark
▴ 10
2
votes
3
replies
1.0k
views
Differential gene expression analysis on haplotype-resolved diploid assembly
edgeR
DESeq2
haplotype
limma
16 days ago • updated 14 days ago
Paulito
• 0
0
votes
1
reply
382
views
Using EBI Image on Ranged Bar Chart
EBImage
written 16 days ago by
ekatcher
• 0
1
vote
3
replies
947
views
Possible issue following the logNormCounts(filtered) with resulted fit
single-cell
SingleCell
SingleCellExperiment
SingleCellWorkflow
SingleCellData
17 days ago • updated 11 days ago
Konstantinos Yeles
▴ 90
0
votes
2
replies
613
views
edgeR in DMR mode - replicates give batch effect - how to build design matrix with condition and replicate
edgeR
updated 13 days ago by
Paul Harrison
▴ 110 • written 18 days ago by
Francesco
• 0
0
votes
0
replies
113
views
GBCC2025: New Scholarship Opportunities Available!
Community
Conference
GBCC2025
Bioconductor
18 days ago
Maria Doyle
▴ 100
0
votes
0
replies
104
views
Blank gene_id in featureCounts
featureCounts
Rsubread
18 days ago
Meg
• 0
2
votes
5
replies
979
views
Heatmap of rnaseq data with z-score scale
heatmaps
RNASeq
updated 17 days ago by
Paul Harrison
▴ 110 • written 18 days ago by
giovanna
▴ 10
0
votes
1
reply
336
views
FCS 32 support going backwards?
flowCore
updated 11 days ago by
shosioness123q
• 0 • written 18 days ago by
Oliver
• 0
0
votes
1
reply
243
views
Typo in the help of lmFit()
limma
updated 19 days ago by
Gordon Smyth
52k • written 19 days ago by
Balazs
• 0
0
votes
2
replies
775
views
Memory issue while using "quickcluster" and "computeSumFactors" functions on single cell RNA seq dataset with 7-9 lac cells
scran
updated 17 days ago by
ATpoint
★ 4.9k • written 20 days ago by
amlanjyoti
• 0
4
votes
4
replies
1.7k
views
Adding gene names as row annotations to an RNAseq heatmap made with ComplexHeatmap
DESeq2
ComplexHeatmap
19 days ago • updated 13 days ago
caroline.zanchi
▴ 10
0
votes
2
replies
464
views
Limma suqeezeVar
limma
20 days ago • updated 18 days ago
Mengchun
• 0
0
votes
0
replies
112
views
What Input-type do I use in decouplR::run_viper?
decoupleR
viper
updated 12 days ago by
Michael Love
43k • written 20 days ago by
Julian
• 0
0
votes
2
replies
369
views
Limma trend with limpa
limpa
limma
trend
updated 10 days ago by
Gordon Smyth
52k • written 20 days ago by
Alejandro
• 0
0
votes
1
reply
218
views
DESeq2 from phyloseq error
DESeq2
phyloseq
20 days ago
asafpr
• 0
0
votes
0
replies
92
views
Combining COMBAT-seq result (raw count) with other raw count
rnaseq
combat-seq
sva
combat
bulk-rnaseq
20 days ago
dudwnsrla1
• 0
0
votes
1
reply
275
views
Can't install BioC packages (and manager) behind firewall
Install
updated 20 days ago by
Marcel Ramos
700 • written 23 days ago by
delphine
• 0
1
vote
2
replies
953
views
GSVA 1.52.2 (new API) nb of workers?
parallelize
workers
GSVA
written 12 months ago by
johanna.galvis
• 0
0
votes
2
replies
374
views
How to extract coordinates of mismatches from a BAM file lodaded in as a GAlignments?
GenomicAlignments
updated 25 days ago by
Hervé Pagès
16k • written 26 days ago by
Charles
• 0
4
votes
2
replies
1.1k
views
GAlignments Cigar to GRanges
GenomicRanges
cigarRangesAlongReferenceSpace
GenomicAlignments
Cigar
25 days ago • updated 24 days ago
pineiroalejandro
▴ 10
2
votes
3
replies
323
views
AnnotationHub/ExperimentHub resources backup
AnnotationHub
HubPub
ExperimentHub
updated 25 days ago by
James W. MacDonald
68k • written 25 days ago by
igor
▴ 50
6
votes
8
replies
5.2k
views
WGCNA coupled with differential expression analysis: question about baseline module detection
wgcna
WGCNA
written 5.1 years ago by
Colari19
▴ 60
46,531 results • Page
1 of 931
Recent ...
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Answer: Bioconductor version cannot be validated
by
Hadi
• 0
I found an answer that worked for me from https://2kk0d4cc31.proxynodejs.usequeue.com/tag/cannot-be-validated/ In brief: 1. Install BiocManager. install.pa…
Comment: Combining analysis of EPICv1 and EPICv2 using SeSAMe package
by
Mancy
• 0
@[block blast][1] Thank you for giving us that experience. We hope you will share more with us! [1]: https://rg8vp848lv.proxynodejs.usequeue.com/
Answer: DESeq2 empirical bayes: variance of the prior for log fold changes (LFC)
by
Michael Love
43k
> why the variance contributed by sampling distribution of LFC isn't separated out Good question, we say "though here we do not subtract t…
Comment: Interaction in Design Experimental
by
Ferdinand David
• 0
So, the design relies on what is my purpose, right? Not examine in all conditions like a regression model? In my understanding, I have in…
Comment: How to interpret MAST coefficients
by
Chenghao
▴ 10
Maybe you have solved those problems already, but just in case, I'd like to share my thoughts... 1. The model adjusts for some covariates …
Votes
Answer: DESeq2 empirical bayes: variance of the prior for log fold changes (LFC)
Answer: DESeq2 empirical bayes: variance of the prior for log fold changes (LFC)
Answer: Deseq2 paired sample in the design is considered as "batch"?
DESeq2 empirical bayes: variance of the prior for log fold changes (LFC)
Answer: Heatmap of the Count Matrix
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