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0
votes
0
replies
28
views
PFAM formats changed - is it still possible to use this with ISA?
IsoformSwitchAnalyzeR
1 day ago
bolusharris
• 0
0
votes
0
replies
26
views
DECIPHER DesignProbes unable to design FISH-probes
decipher
FISH
DECIPHER
FISH-probe
probe-design
2 days ago
vreinmuth
• 0
3
votes
5
replies
193
views
upstream git branches of bioc-release
Bioconductor
updated 1 day ago by
TrentonCollier99
• 0 • written 3 days ago by
Jeroen
▴ 10
0
votes
2
replies
98
views
APAlyzer
APAlyzer
updated 8 days ago by
Kevin Blighe
★ 4.0k • written 10 days ago by
anjanaram1
▴ 10
0
votes
1
reply
1.9k
views
Co-occurrence Network Analysis between Algae and Bacteria
igraph
networkanalysis
Phylogenetics
phyloseq
updated 8 days ago by
Stefano Mangiola
▴ 40 • written 4.9 years ago by
Chantel
• 0
0
votes
0
replies
7
views
Spam:
Best Rehab Center In India | Luxury, Alcohol & Mental Health Care
COSMIC.67
10 weeks ago
Best Rehab Center
0
0
votes
0
replies
5
views
Spam:
Exploring Robotic Hair Restoration Procedure
COSMIC.67
3 months ago
paseje6172
0
0
votes
0
replies
265
views
Y-axis break ihn Volcano Plot
EnhancedVolcano
Y-axis_break
Volcano_Plot
5 months ago
rajdeepboral00
• 0
0
votes
0
replies
245
views
getQC(RGset.raw) from IlluminaHumanMethylationMSAmanifest
getQC
hcg110.db
updated 5 months ago by
shepherl
4.2k • written 5 months ago by
zwang072005
• 0
0
votes
0
replies
244
views
DiffBind plot.profile error
BiocParallel
DiffBind
5 months ago
this_is_me_trying
• 0
0
votes
1
reply
629
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
546
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
282
views
Blank gene_id in featureCounts
featureCounts
Rsubread
6 months ago
Meg
• 0
0
votes
1
reply
533
views
FCS 32 support going backwards?
flowCore
updated 6 months ago by
shosioness123q
• 0 • written 6 months ago by
Oliver
• 0
0
votes
0
replies
335
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
0
replies
307
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
510
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
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
6 months ago
Muhammad
• 0
0
votes
1
reply
675
views
Combat-seq usage
sva
6 months ago
bbao
▴ 10
0
votes
1
reply
398
views
What happened to the Joost2016 dataset
org.Sc.sgd.db
updated 6 months ago by
shepherl
4.2k • written 6 months ago by
clementleong
• 0
0
votes
2
replies
653
views
FlowSOM is unable to create Output
FlowSOM
updated 6 months ago by
EvangelinePope
• 0 • written 6 months ago by
marco.klein1
• 0
0
votes
6
replies
1.8k
views
Discrepancies in normalised count data vs unnormalised
DESeq2
7 months ago • updated 6 months ago
AMgroup
• 0
0
votes
0
replies
449
views
Significant Probes and Genes differ in Probe and Region level Differential Methylation Analyses
limma
probe
DMRcate
GenomicRanges
DifferentialMethylation
7 months ago
jamiecatalano2
• 0
0
votes
0
replies
351
views
Batch correction for microarray
BatchEffect
sva
MicroarrayData
7 months ago
Shaimaa Gamal
• 0
0
votes
0
replies
204
views
GRaNIE with no internet
GRaNIE
7 months ago
maia.malonzo
• 0
0
votes
0
replies
246
views
Issue checking for convergence with the tutorial Dataset. EBseq 2.4.1
EBSeq
7 months ago
Javier
• 0
0
votes
0
replies
349
views
I want my overlapping peaks to stop merging by default doing read counting (using DiffBind in R-studio)
peakoverlap
mergingpeaks
ChIPseq
DiffBind
7 months ago
atlanta
• 0
1
vote
1
reply
1.3k
views
Differential expression analysis using two TCGA datasets
DifferentialExpression
TCGAbiolinks
RNASeq
updated 7 months ago by
ATpoint
★ 5.0k • written 7 months ago by
Shaimaa Gamal
• 0
1
vote
0
replies
544
views
Modelling gene program dynamics across time with {lemur}
lemur
7 months ago
BiotechPedro
▴ 10
0
votes
1
reply
563
views
Intepretation of results
AUCell
written 7 months ago by
jasperwong_123
• 0
0
votes
4
replies
2.3k
views
DiffBind can't find a DAR
dar
ATACSeq
DiffBind
7 months ago
Mengjun
• 0
1
vote
3
replies
1.0k
views
DESeq - help with pair wise comparisons
DESeq2
7 months ago
bd2000
▴ 30
0
votes
0
replies
26
views
Spam:
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MethylSeekR
7 months ago
Shoqz
0
0
votes
0
replies
18
views
Spam:
Experience lasting confidence with Vidalista 40 mg
org.Sc.sgd.db
8 months ago
irenejoshi07
0
0
votes
4
replies
1.5k
views
Error in H5Dclose(h5dataset) when trying to read in kallisto h5 files
tximport
rhdf5
8 months ago
Sofia
• 0
1
vote
1
reply
1.0k
views
ComBat with repeated measures
ComBat
sva
updated 8 months ago by
ATpoint
★ 5.0k • written 8 months ago by
s20
• 0
0
votes
0
replies
229
views
Correlation threshold
MethylationArray
methylationArrayAnalysis
StatisticalMethod
8 months ago
user_bioinfo
• 0
0
votes
5
replies
840
views
Bioconductor unable to update 'curl'
curl
HELP
8 months ago
kagodwi2
• 0
0
votes
4
replies
2.3k
views
Ensembl site unresponsive via biomaRt
biomaRt
updated 7 months ago by
darylruiz6545
• 0 • written 8 months ago by
hebda
• 0
0
votes
1
reply
480
views
GAGE kegg.gsets() self-signed certificate error
gageData
gage
8 months ago
Lucas
• 0
0
votes
0
replies
245
views
DiffBind multi-tissue comparison
DiffBind
8 months ago
lryrainche
• 0
0
votes
0
replies
458
views
fgsea: ranking genes using log2FC and pvalues derived from spline model
fgsea
GeneSetEnrichment
splines
RNASeq
8 months ago
GT
• 0
0
votes
1
reply
472
views
Discrepancy between Excel TPP-TR reported values and the Melt Curve reported values
TPP
updated 8 months ago by
James W. MacDonald
68k • written 8 months ago by
flowreen.shikwana
• 0
0
votes
1
reply
426
views
Transcript ID Mismatch in riboWaltz Annotation Table
RiboProfiling
RiboSeq
updated 8 months ago by
shepherl
4.2k • written 8 months ago by
ramya2kumar0
• 0
0
votes
0
replies
282
views
Simple confidence intervall Gviz
Gviz
8 months ago
William
• 0
0
votes
2
replies
733
views
Removing UTR from GTF for gene quantification
edgeR
DESeq2
updated 8 months ago by
Michael Love
43k • written 8 months ago by
rohitsatyam102
▴ 20
0
votes
0
replies
361
views
DiffBind recommendation on using IgG bams
peakcalling
DiffBind
8 months ago
Harish
• 0
0
votes
1
reply
364
views
DepMap data mismatch
depmap
updated 8 months ago by
Laurent Gatto
1.6k • written 8 months ago by
Mikhail Dozmorov
▴ 30
0
votes
2
replies
514
views
graper 1.22 Build is Broken
bug
graper
offtopic
updated 9 months ago by
shepherl
4.2k • written 9 months ago by
Bjarne
• 0
1,000 results • Page
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Replies
Comment: upstream git branches of bioc-release
by
TrentonCollier99
• 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments. https://bioc-release.r-univ…
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
by
Ahmed Salah
• 0
Thank you very much! will take that into consideration
Comment: Large logFC but somewhat high FDR
by
JKim
• 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments.
Comment: upstream git branches of bioc-release
by
Jeroen
▴ 10
OK I have updated https://bioc-release.r-universe.dev accordingly. Let me know if you find version differences when mirroring binaries.
Comment: Large logFC but somewhat high FDR
by
Gordon Smyth
53k
I don't know what `tp1` is. The relevant histogram would be: ``` hist(fit2$p.value[,"KO_vs_WT"]) ```
Votes
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
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
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