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News:
Ensembl 114 / Ensembl Genomes 61 has been released!
biomaRt
ensembldb
written 9 months ago by
Aleena_Ensembl
▴ 30
0
votes
0
replies
25
views
Spam:
wealthdt5
weaver
wealth
8 months ago
Enfurry
0
0
votes
0
replies
335
views
Y-axis break ihn Volcano Plot
EnhancedVolcano
Y-axis_break
Volcano_Plot
8 months ago
rajdeepboral00
• 0
0
votes
0
replies
318
views
getQC(RGset.raw) from IlluminaHumanMethylationMSAmanifest
getQC
hcg110.db
updated 8 months ago by
shepherl
4.3k • written 8 months ago by
zwang072005
• 0
3
votes
2
replies
1.6k
views
Biological replicates consideration in DESeq2 design formula.
DESeq2
RNASeqData
RNASeq
written 8 months ago by
Christian
▴ 20
1
vote
2
replies
2.8k
views
Deseq2 paired sample in the design is considered as "batch"?
DESeq2
written 8 months ago by
corranna98
• 0
0
votes
0
replies
344
views
Job:
Job: Ensembl Dataflow Coordinator
JobPosting
ensembldb
8 months ago
Aleena_Ensembl
▴ 30
0
votes
1
reply
1.5k
views
Retrieve Salmon transcript quantification file from recount3
recount3
updated 8 months ago by
Leonardo Collado Torres
★ 1.1k • written 8 months ago by
kyn
▴ 10
0
votes
1
reply
1.2k
views
error from library(IlluminaHumanMethylationMSAmanifest)
MSAarray25
hcg110.db
updated 8 months ago by
James W. MacDonald
68k • written 8 months ago by
zwang072005
• 0
0
votes
1
reply
942
views
Source / binary version mismatch for rGADEM
rGADEM
updated 8 months ago by
shepherl
4.3k • written 8 months ago by
Jay hesselberth
• 0
0
votes
9
replies
14k
views
Bioconductor version cannot be validated
BiocManager
Bioconductor
updated 8 months ago by
Hadi
• 0 • written 4.5 years ago by
charlotte
▴ 10
3
votes
1
reply
3.9k
views
DESeq2 empirical bayes: variance of the prior for log fold changes (LFC)
DESeq2
updated 8 months ago by
Michael Love
43k • written 8 months ago by
Chenghao
▴ 10
0
votes
2
replies
1.3k
views
Interaction in Design Experimental
rnaseqGene
8 months ago
Ferdinand David
• 0
0
votes
0
replies
399
views
Job:
Lab Head positions at the WEHI, Melbourne, Australia
JobPosting
Bioconductor
8 months ago
Gordon Smyth
53k
1
vote
4
replies
2.3k
views
Heatmap of the Count Matrix
rnaseqGene
updated 5 months ago by
ArnulfoByrd
• 0 • written 8 months ago by
Ferdinand David
• 0
0
votes
1
reply
685
views
DESeq2 results
result
DESeq2
subsetting
updated 8 months ago by
ATpoint
★ 5.0k • written 8 months ago by
rajdeepboral00
• 0
0
votes
1
reply
356
views
DiffBind plot.profile error
BiocParallel
DiffBind
written 8 months ago by
this_is_me_trying
• 0
0
votes
4
replies
9.4k
views
Bioconductor version cannot be validated
Bioconductor
Annotation
Ann
written 2.4 years ago by
Aytaç
• 0
0
votes
4
replies
1.2k
views
Position of the legend object in complexHeatmap
ComplexHeatmap
8 months ago
caroline.zanchi
▴ 10
0
votes
4
replies
3.4k
views
Drawing custom KEGG pathways
pathview
KEGG
written 4.7 years ago by
curiousmind007
▴ 10
1
vote
18
replies
7.6k
views
error in ChAMP loading file
ChAMP
updated 7 months ago by
josephasmith1310
• 0 • written 3.2 years ago by
Giulia
• 0
1
vote
4
replies
2.2k
views
How to left_join a tidySummarizedExperiment with a GRanges object by seqnames and start (tidyverse-style)?
GenomicRanges
tidySummarizedExperiment
tidyomics
9 months ago • updated 5 months ago
Kateřina
• 0
3
votes
2
replies
6.5k
views
limma duplicateCorrelation appropriate where some blocks cross condition and some are in same condition?
limma
8 months ago
Geoff
• 0
0
votes
1
reply
932
views
Workflow to Analyse DNA Sequence specify gene expression in a fungus under stress
rnaseqGene
updated 8 months ago by
Michael Love
43k • written 8 months ago by
Ferdinand David
• 0
0
votes
1
reply
503
views
Unclear DEseq2 replaceOutliers error message
DESeq2
updated 8 months ago by
Michael Love
43k • written 8 months ago by
Pak
• 0
0
votes
1
reply
573
views
lncRNA functional annotation package
RNAseq123
updated 8 months ago by
James W. MacDonald
68k • written 8 months ago by
tarek.mohamed
• 0
1
vote
1
reply
736
views
Biomart server error
biomaRt
BioMartGOGeneSets
updated 8 months ago by
James W. MacDonald
68k • written 8 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
8 months ago
Laserqure03
0
0
votes
2
replies
1.9k
views
An ESR essay about software design, and how it applies to Bioconductor
GUI
GUI
written 22.0 years ago by
Ann Loraine
▴ 30
0
votes
1
reply
673
views
Difference in DESeq2 output and tidybulk DESeq2 method
DifferentialExpression
DESeq2
tidybulk
RNASeq
updated 8 months ago by
Michael Love
43k • written 9 months ago by
s.malik
• 0
3
votes
3
replies
2.2k
views
Deseq2 DE analysis of host-pathogen samples (model separately or jointly?)
DESeq2
updated 2 days ago by
a2a2ddrhaa
• 0 • written 9 months ago by
dudutchy
▴ 10
0
votes
8
replies
1.7k
views
ERCC Spike-In controls being discarded during Tximeta process:
@mikelove
tximeta
updated 8 months ago by
Michael Love
43k • written 8 months ago by
Gaurav
• 0
2
votes
4
replies
2.8k
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
8 months ago
Maziya
• 0
4
votes
17
replies
6.6k
views
How to load scRNA-seq data from GEO
SingleCellExperiment
GEO
updated 8 months ago by
ATpoint
★ 5.0k • written 9 months ago by
petergrahamclark
▴ 10
2
votes
3
replies
1.7k
views
Differential gene expression analysis on haplotype-resolved diploid assembly
edgeR
DESeq2
haplotype
limma
8 months ago
Paulito
• 0
0
votes
1
reply
708
views
Using EBI Image on Ranged Bar Chart
EBImage
written 8 months ago by
ekatcher
• 0
1
vote
3
replies
1.3k
views
Possible issue following the logNormCounts(filtered) with resulted fit
single-cell
SingleCell
SingleCellExperiment
SingleCellWorkflow
SingleCellData
8 months ago
Konstantinos Yeles
▴ 90
0
votes
2
replies
995
views
edgeR in DMR mode - replicates give batch effect - how to build design matrix with condition and replicate
edgeR
updated 8 months ago by
Paul Harrison
▴ 110 • written 8 months ago by
Francesco
• 0
0
votes
2
replies
661
views
GBCC2025: New Scholarship Opportunities Available!
Community
Conference
GBCC2025
Bioconductor
updated 5 months ago by
Liona
• 0 • written 8 months ago by
Maria Doyle
▴ 110
0
votes
0
replies
349
views
Blank gene_id in featureCounts
featureCounts
Rsubread
8 months ago
Meg
• 0
2
votes
5
replies
1.9k
views
Heatmap of rnaseq data with z-score scale
heatmaps
RNASeq
updated 8 months ago by
Paul Harrison
▴ 110 • written 8 months ago by
giovanna
▴ 10
0
votes
1
reply
610
views
FCS 32 support going backwards?
flowCore
updated 8 months ago by
shosioness123q
• 0 • written 8 months ago by
Oliver
• 0
0
votes
1
reply
531
views
Typo in the help of lmFit()
limma
updated 8 months ago by
Gordon Smyth
53k • written 8 months ago by
Balazs
• 0
0
votes
2
replies
1.2k
views
Memory issue while using "quickcluster" and "computeSumFactors" functions on single cell RNA seq dataset with 7-9 lac cells
scran
updated 8 months ago by
ATpoint
★ 5.0k • written 9 months ago by
amlanjyoti
• 0
4
votes
4
replies
2.2k
views
Adding gene names as row annotations to an RNAseq heatmap made with ComplexHeatmap
DESeq2
ComplexHeatmap
8 months ago
caroline.zanchi
▴ 10
0
votes
2
replies
749
views
Limma suqeezeVar
limma
9 months ago • updated 8 months ago
Mengchun
• 0
0
votes
0
replies
422
views
What Input-type do I use in decouplR::run_viper?
decoupleR
viper
updated 8 months ago by
Michael Love
43k • written 9 months ago by
Julian
• 0
0
votes
2
replies
1.6k
views
Limma trend with limpa
limpa
limma
trend
updated 8 months ago by
Gordon Smyth
53k • written 9 months ago by
Alejandro
• 0
0
votes
1
reply
514
views
DESeq2 from phyloseq error
DESeq2
phyloseq
9 months ago
asafpr
• 0
0
votes
0
replies
392
views
Combining COMBAT-seq result (raw count) with other raw count
rnaseq
combat-seq
sva
combat
bulk-rnaseq
9 months ago
dudwnsrla1
• 0
46,753 results • Page
6 of 936
Recent ...
Replies
Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ?
by
Gordon Smyth
53k
I tend to use dpcCN(), because it more robust than dpc() to experiments with lots of samples and big differences between samples. You coul…
Answer: Which preprocessing steps are needed before running limpa?
by
Gordon Smyth
53k
Please see the example limpa analyses given at <http://github.com/smythlab/limpa>, especially the kidney cancer case study. limpa does not…
Comment: Why does IDTaxa trainingSet for SILVA contain "_2" suffixes in the taxonomy name
by
Korneel
• 0
Thanks for the quick reply! If I understand correctly, I think if I keep track of the full lineage, I shouldn't have any risk of collapsin…
Comment: Pathway abundance data from Curatedmetagenomics
by
yesquokkan
• 0
Hello, I was also wondering about the same issue. Did you figure it out?
Comment: [DESeq2] Changing dispersion estimates between runs of DESeq2
by
colinmccornack
• 0
FWIW: This seems to be due to architectural differences between two compute nodes I was running on, specifically with the DESeq2:::fitNbino…
Votes
Answer: Subsetting data verses contrasts [DESeq2]?
A: WGCNA differences two groups 10 replicates each group
A: WGCNA sample size minimum: why?
Comment: Why does IDTaxa trainingSet for SILVA contain "_2" suffixes in the taxonomy name
Answer: Can you colour dendrogram branch clusters in pheatmap?
Awards
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Popular Question
to
Peter Hickey
▴ 760
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to
Sean Davis
21k
Popular Question
to
James W. MacDonald
68k
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to
shepherl
4.3k
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to
Andreas Zankl
▴ 80
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17 minutes ago
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