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0
votes
0
replies
19
views
Getting way too many DEGs with LRT for time-series RNA-seq!
TimeCourse
DESeq2
1 day ago
Denise
• 0
0
votes
2
replies
88
views
Create consensusMatrix for codon bases
Biostrings
updated 3 days ago by
James W. MacDonald
68k • written 4 days ago by
Hassan
• 0
0
votes
0
replies
39
views
Memory error while running alignments
DECIPHER
Alignment
11 days ago
Mihir
• 0
0
votes
2
replies
153
views
BiocManager::install() doesn't work
Install
Biocond
updated 18 days ago by
Marcel Ramos
700 • written 19 days ago by
flying_breadman
• 0
0
votes
1
reply
134
views
Feedback needed on new user-friendly BED file tool
bedbaser
offtopic
updated 19 days ago by
James W. MacDonald
68k • written 19 days ago by
nadia
• 0
0
votes
0
replies
70
views
CRISPRSeek Question: changing weight and gRNA.size causes error
CRISPRseek
CRISPR
updated 23 days ago by
James W. MacDonald
68k • written 23 days ago by
Citrus
• 0
0
votes
0
replies
56
views
Empty boxes in treemap plot rrvgo package
rrvgo
24 days ago • updated 23 days ago
Asma
• 0
0
votes
0
replies
79
views
Results with PON give more variants
mutect2
variants
pon
25 days ago
ramiro.barrantes
▴ 10
0
votes
1
reply
146
views
ORFik: spliced 5utr regions
splicing
5utr
ORFik
updated 25 days ago by
James W. MacDonald
68k • written 26 days ago by
luna.picello
• 0
0
votes
0
replies
105
views
Guidance Requested on GCN Network Analysis and Module Enrichment in R
BioNERO
Bioconductor
Arabidopsis_thaliana_Data
updated 2 days ago by
Michael Love
43k • written 4 weeks ago by
Sabina
• 0
0
votes
2
replies
306
views
HMP_2019_t2d data origin
curatedMetagenomicData
4 weeks ago
Blan
• 0
0
votes
2
replies
837
views
Install old version of DESeq2
apeglm
Install
DESeq2
version
updated 5 weeks ago by
James W. MacDonald
68k • written 5 weeks ago by
Asma
• 0
0
votes
0
replies
103
views
Boolean Gate Combination for Any 2 Positive Events in flowWorkspace
flowWorkspace
FlowCytometry
5 weeks ago
Valeria
• 0
1
vote
3
replies
1.5k
views
How can I correctly use phyloseq with Docker?
phylo
phyloseq
Docker
written 3 months ago by
Franz Bachmann
• 0
0
votes
0
replies
178
views
Y-axis break ihn Volcano Plot
EnhancedVolcano
Y-axis_break
Volcano_Plot
9 weeks ago
rajdeepboral00
• 0
0
votes
0
replies
152
views
getQC(RGset.raw) from IlluminaHumanMethylationMSAmanifest
getQC
hcg110.db
updated 9 weeks ago by
shepherl
4.2k • written 9 weeks ago by
zwang072005
• 0
0
votes
0
replies
145
views
DiffBind plot.profile error
BiocParallel
DiffBind
10 weeks ago
this_is_me_trying
• 0
0
votes
1
reply
564
views
Using EBI Image on Ranged Bar Chart
EBImage
written 12 weeks ago by
ekatcher
• 0
1
vote
3
replies
1.1k
views
Possible issue following the logNormCounts(filtered) with resulted fit
single-cell
SingleCell
SingleCellExperiment
SingleCellWorkflow
SingleCellData
12 weeks ago • updated 11 weeks ago
Konstantinos Yeles
▴ 90
0
votes
1
reply
416
views
GBCC2025: New Scholarship Opportunities Available!
Community
Conference
GBCC2025
Bioconductor
updated 9 weeks ago by
Brian
• 0 • written 12 weeks ago by
Maria Doyle
▴ 100
0
votes
0
replies
193
views
Blank gene_id in featureCounts
featureCounts
Rsubread
12 weeks ago
Meg
• 0
0
votes
1
reply
449
views
FCS 32 support going backwards?
flowCore
updated 11 weeks ago by
shosioness123q
• 0 • written 12 weeks ago by
Oliver
• 0
0
votes
0
replies
225
views
What Input-type do I use in decouplR::run_viper?
decoupleR
viper
updated 11 weeks ago by
Michael Love
43k • written 3 months ago by
Julian
• 0
0
votes
0
replies
195
views
Combining COMBAT-seq result (raw count) with other raw count
rnaseq
combat-seq
sva
combat
bulk-rnaseq
3 months ago
dudwnsrla1
• 0
0
votes
1
reply
384
views
Can't install BioC packages (and manager) behind firewall
Install
updated 3 months ago by
Marcel Ramos
700 • written 3 months ago by
delphine
• 0
0
votes
0
replies
870
views
Diffbind Analysis gives error during profile plotting stage. Error in value[[3L]](cond) : profileplyr error: Error: BiocParallel errors 1 remote…
chipseq
profileplyr
DiffBind
3 months ago
Muhammad
• 0
0
votes
1
reply
586
views
Combat-seq usage
sva
3 months ago • updated 11 weeks ago
bbao
▴ 10
0
votes
1
reply
324
views
What happened to the Joost2016 dataset
org.Sc.sgd.db
updated 3 months ago by
shepherl
4.2k • written 3 months ago by
clementleong
• 0
0
votes
2
replies
540
views
FlowSOM is unable to create Output
FlowSOM
updated 12 weeks ago by
EvangelinePope
• 0 • written 3 months ago by
marco.klein1
• 0
0
votes
6
replies
1.6k
views
Discrepancies in normalised count data vs unnormalised
DESeq2
3 months ago • updated 11 weeks ago
AMgroup
• 0
0
votes
0
replies
364
views
Significant Probes and Genes differ in Probe and Region level Differential Methylation Analyses
limma
probe
DMRcate
GenomicRanges
DifferentialMethylation
3 months ago
jamiecatalano2
• 0
0
votes
0
replies
268
views
Batch correction for microarray
BatchEffect
sva
MicroarrayData
3 months ago
Shaimaa Gamal
• 0
0
votes
0
replies
174
views
GRaNIE with no internet
GRaNIE
4 months ago
maia.malonzo
• 0
0
votes
0
replies
206
views
Issue checking for convergence with the tutorial Dataset. EBseq 2.4.1
EBSeq
4 months ago
Javier
• 0
0
votes
0
replies
279
views
I want my overlapping peaks to stop merging by default doing read counting (using DiffBind in R-studio)
peakoverlap
mergingpeaks
ChIPseq
DiffBind
4 months ago
atlanta
• 0
1
vote
1
reply
1.2k
views
Differential expression analysis using two TCGA datasets
DifferentialExpression
TCGAbiolinks
RNASeq
updated 4 months ago by
ATpoint
★ 4.9k • written 4 months ago by
Shaimaa Gamal
• 0
1
vote
0
replies
507
views
Modelling gene program dynamics across time with {lemur}
lemur
4 months ago
BiotechPedro
▴ 10
0
votes
1
reply
485
views
Intepretation of results
AUCell
written 4 months ago by
jasperwong_123
• 0
0
votes
4
replies
2.2k
views
DiffBind can't find a DAR
dar
ATACSeq
DiffBind
4 months ago
Mengjun
• 0
1
vote
3
replies
945
views
DESeq - help with pair wise comparisons
DESeq2
4 months ago
bd2000
▴ 30
0
votes
0
replies
25
views
Spam:
Looking for Josey Wales Jacket?
MethylSeekR
4 months ago
Shoqz
0
0
votes
2
replies
445
views
Issue with Soft-Thresholding in WGCNA
WGCNA
updated 4 weeks ago by
conservativepaola
• 0 • written 4 months ago by
Μαρία
• 0
0
votes
0
replies
18
views
Spam:
Experience lasting confidence with Vidalista 40 mg
org.Sc.sgd.db
4 months ago
irenejoshi07
0
0
votes
4
replies
1.3k
views
Error in H5Dclose(h5dataset) when trying to read in kallisto h5 files
tximport
rhdf5
4 months ago
Sofia
• 0
1
vote
1
reply
931
views
ComBat with repeated measures
ComBat
sva
updated 4 months ago by
ATpoint
★ 4.9k • written 4 months ago by
s20
• 0
0
votes
0
replies
185
views
Correlation threshold
MethylationArray
methylationArrayAnalysis
StatisticalMethod
4 months ago
user_bioinfo
• 0
0
votes
5
replies
668
views
Bioconductor unable to update 'curl'
curl
HELP
4 months ago
kagodwi2
• 0
0
votes
4
replies
1.7k
views
Ensembl site unresponsive via biomaRt
biomaRt
updated 3 months ago by
darylruiz6545
• 0 • written 4 months ago by
hebda
• 0
0
votes
1
reply
412
views
GAGE kegg.gsets() self-signed certificate error
gageData
gage
5 months ago • updated 4 months ago
Lucas
• 0
0
votes
0
replies
167
views
DiffBind multi-tissue comparison
DiffBind
5 months ago
lryrainche
• 0
1,000 results • Page
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Comment: EuroBioC2024 abstract submission is open!
by
rajilrfaze
• 0
[Sportzfy smooth streaming APK][1] ensures zero buffering during your favorite games. [1]: https://sportzfytvapk.com.co/
Comment: p-adjusted values in multiple comparisons
by
ocanorocabayera
• 0
Thank you Gordon for your thorough reply. It seems when MDS-plotting the obtained object from 'voom', that the points do not cluster togeth…
Comment: Are voomByGroup and voomLmFit compatible?
by
Gordon Smyth
52k
Not sure what "points" you are referring to, or what you mean by them being "weighted".
Answer: p-adjusted values in multiple comparisons
by
Gordon Smyth
52k
If your data was completely random, with no truly differentially expressed (DE) genes, then you would expect to get nearly 5% of the p-valu…
Answer: Are voomByGroup and voomLmFit compatible?
by
Gordon Smyth
52k
voomByGroup isn't part of Bioconductor, so questions about it should be send to the voomByGroup issues page. I haven't brought voomByGroup…
Votes
Answer: p-adjusted values in multiple comparisons
Comment: Very different log2 Fold changes with DESeq2 and explict calculation
Answer: (Why) do limma's confidence intervals depend on topTable's p.value argument?
Answer: (Why) do limma's confidence intervals depend on topTable's p.value argument?
Answer: Very different log2 Fold changes with DESeq2 and explict calculation
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