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News:
Single-cell RNA-seq analysis with R/Bioconductor (online course)
SingleCellExperiment
SingleCell
14 months ago
info
▴ 10
4
votes
4
replies
833
views
How to conduct maSigPro analysis with only one condition?
maSigPro
masig
updated 14 months ago by
James W. MacDonald
68k • written 14 months ago by
Jiahao Tian
• 0
1
vote
4
replies
1.3k
views
Mostly increased counts in differentially accessible peaks using DESeq2
ATAC-seq
DESeq2
Oddresults
updated 14 months ago by
ATpoint
★ 5.0k • written 14 months ago by
Ricardo Iván
• 0
0
votes
1
reply
548
views
How to set filtering standard for low-expression genes in ImpulseDE2
DifferentialExpression
ImpulseDE2
DESeq2
updated 14 months ago by
Michael Love
43k • written 14 months ago by
Jiahao Tian
• 0
0
votes
0
replies
466
views
DMRcate pcutoff setting
EpicV2
DMRcate
14 months ago
kitzhu
• 0
2
votes
4
replies
942
views
RNASeq Time Course Question
DESeq2
RNASeq
TimeCourse
14 months ago
jihoon.kim.1495
▴ 10
0
votes
0
replies
463
views
[maser] Why does maser coverage filtering ignore skipping counts of an alt. splicing analysis?
rMATS
alternativesplicing
maser
R
14 months ago
Anke
• 0
0
votes
6
replies
1.4k
views
[DESeq2] Introduce a bias in DESeq2
DifferentialExpression
DESeq2
BatchEffect
updated 14 months ago by
Michael Love
43k • written 14 months ago by
CriticalPeriod
• 0
1
vote
1
reply
995
views
WGCNA
DEGselection
RNASeqData
WGCNA
updated 14 months ago by
Lluís Revilla Sancho
▴ 760 • written 14 months ago by
Nasim
• 0
5
votes
4
replies
1.1k
views
How to control batch effect if Group and batch are same?
limma
DESeq2
BatchEffect
updated 14 months ago by
ATpoint
★ 5.0k • written 14 months ago by
Bioinformagician
• 0
4
votes
1
reply
688
views
edgeR 4.2.1 compression bug: a minimally reproducible snippet
edger
edgeR
updated 14 months ago by
Gordon Smyth
53k • written 14 months ago by
Hongjian
• 0
2
votes
5
replies
1.1k
views
dmpFinder for other objects
methylset
minfi
dmpFinder
betaHMM
beta
updated 14 months ago by
James W. MacDonald
68k • written 14 months ago by
neyousha
• 0
0
votes
1
reply
481
views
Unevaluated error in ChIPQC combined with BiocParallel
BiocParallel
ChIPQC
written 14 months ago by
Young Boqin
• 0
0
votes
2
replies
723
views
RNA-Seq p value range variation
DESeq2
pvalue
RNA-Seq
14 months ago
paul.meraner
• 0
0
votes
0
replies
624
views
News:
RNAseq data analysis with Bioconductor (online course)
DESeq2
SummarizedExperiment
14 months ago • updated 13 months ago
info
▴ 10
2
votes
8
replies
1.9k
views
miRTarRnaseq library
miRNATarget
mirTarRnaSeq
updated 12 months ago by
mercedeh.movassagh
▴ 20 • written 21 months ago by
María Calvo
• 0
1
vote
6
replies
1.5k
views
heatmap with batch effect
DESeq2
BatchEffect
written 14 months ago by
tothuhien
• 0
0
votes
1
reply
576
views
how do I convert an Ilumn IDREF to a CPG loci
AnnotationDbi
Annotation
annotation
BiologicalQuestion
updated 14 months ago by
James W. MacDonald
68k • written 14 months ago by
Olajumoke
• 0
0
votes
1
reply
696
views
Setting ylims in bam coverage plot and assigning compound sashimi numbers to overlay plots
Coverage
Gviz
sashimi
updated 7 months ago by
macdonaldfrench7286566
• 0 • written 14 months ago by
Marco
• 0
0
votes
1
reply
940
views
Which input data is acceptable for MAST?
SCTransform
MAST
updated 14 months ago by
Andrew_McDavid
▴ 280 • written 14 months ago by
james.watson1
• 0
1
vote
1
reply
784
views
segfault when using singleR with Azimuth reference
SingleR
updated 14 months ago by
James W. MacDonald
68k • written 14 months ago by
Lluís Revilla Sancho
▴ 760
0
votes
1
reply
674
views
[BUG] featureCounts doesn't assign primary alignment of a multi-mapped read, even with `--primary` specified
featureCounts
Rsubread
14 months ago
isaac.vock
• 0
0
votes
2
replies
777
views
How can I obtain DEGs that are resulted from using salmon in alignment-based mode or mapping-based mode?
tximport
DESeq2
updated 14 months ago by
Michael Love
43k • written 14 months ago by
oguzhankaraosmanoglu
• 0
1
vote
1
reply
1.1k
views
Deseq2 sfType
Microbiome
DESeq2
RNASeq
updated 14 months ago by
James W. MacDonald
68k • written 14 months ago by
Caroline
• 0
1
vote
1
reply
717
views
Normalization RNA-seq for multiple plates
Normalization
DESeq2
RNASeqData
edgeR
updated 14 months ago by
ATpoint
★ 5.0k • written 14 months ago by
Pimpa
• 0
0
votes
1
reply
884
views
News:
Subject: Last 2 Seats Available for Metabolomics with R/Bioconductor Course (October 7-10)
Metabolomics
xcms
updated 14 months ago by
Harry
• 0 • written 14 months ago by
info
▴ 10
2
votes
2
replies
602
views
SAS token for Annotation package
AnnotationDbi
AnnotationForge
14 months ago
KABILAN
• 0
1
vote
1
reply
1.0k
views
Convert HGVS Representation back to Reference Genome Coordinates
GA4GHclient
updated 14 months ago by
Vince Schulz
▴ 160 • written 14 months ago by
Dario Strbenac
★ 1.6k
1
vote
1
reply
604
views
DEseq 2 LFC shrinkage with apeglm in single-cell pseudobulk: strange volcano plot results
DESeq2
updated 14 months ago by
ATpoint
★ 5.0k • written 14 months ago by
picasa1983
• 0
1
vote
2
replies
916
views
Poor dispersion fit in DESeq2
limma
DESeq2
RNASeq
edgeR
updated 15 months ago by
Michael Love
43k • written 15 months ago by
Ben
▴ 10
0
votes
2
replies
1.0k
views
DESeq2 analysis on 2 plant lines infected with virus, with 2 time points (days post infection)
DESeq2
updated 15 months ago by
Michael Love
43k • written 15 months ago by
duplessisantzel
• 0
1
vote
2
replies
1.0k
views
DESeq2 design and contrasts with 2 drug-treated and one control group
DESeq2
Bioconductor
updated 15 months ago by
Michael Love
43k • written 15 months ago by
JT
▴ 10
2
votes
4
replies
1.0k
views
Spectra and PSMatch- trouble in reducePSMs, joinSpectraData, or countIdentifications?
ProteomicsWorkflow
PSMatch
Spectra
RforProteomics
updated 14 months ago by
Laurent Gatto
1.6k • written 15 months ago by
Jane_Huang
• 0
0
votes
0
replies
487
views
Assistance with Bulk RNA-seq Data Analysis Including Random Effect (`duplicateCorrelation` from `limma`)
limma
RNAseq123
15 months ago
tim.meese
• 0
0
votes
1
reply
850
views
BiomaRt - improved access to Ensembl ?
biomaRt
updated 15 months ago by
Mike Smith
★ 6.6k • written 15 months ago by
Abiologist
• 0
0
votes
0
replies
19
views
Spam:
Online gaming
EWCE
games
15 months ago
Lisandro Hermoso
0
3
votes
3
replies
850
views
ISO a solution to rank-order introns by transcript
GenomicRanges
GenomicFeatures
15 months ago • updated 12 months ago
mat149
▴ 80
2
votes
2
replies
1.8k
views
Issues with retrieving Zea mays genes dataset: biomaRt error: looks like we're connecting to incompatible version of BioMart.
biomaRt
15 months ago
2044291597
• 0
0
votes
3
replies
1.2k
views
Meta-analysis on RNA-seq data sets
meta-analysis
sva
Combat_Seq
RNAseq
15 months ago
Travis
• 0
0
votes
0
replies
358
views
Deprecated Gates- tailgate
openCyto
15 months ago
ztflaten
• 0
0
votes
1
reply
410
views
Build error report
PLSDAbatch
updated 15 months ago by
shepherl
4.2k • written 15 months ago by
anjiwangyiwen
• 0
0
votes
0
replies
395
views
Getting error while running GenomicPlot
GenomicPlot
15 months ago
Lucky
• 0
0
votes
0
replies
531
views
News:
Opportunity for Carpentries Instructors to Teach Bioconductor in Africa
Carpentries
Community
Teaching
Bioconductor
15 months ago
Maria Doyle
▴ 110
1
vote
6
replies
1.9k
views
New to Deseq2 - DEG questions / MA plot
genomes
DESeq2
Transcriptomics
updated 14 months ago by
ATpoint
★ 5.0k • written 15 months ago by
Newbie
• 0
0
votes
2
replies
824
views
EdgeR - Apparent Wrong Direction of logFC with Low Count Data
limma
edgeR
updated 14 months ago by
Gordon Smyth
53k • written 15 months ago by
blmurphy
• 0
2
votes
2
replies
772
views
Batch adjustment for cohort based RNA seq data
RNASeqPower
removeBatchEffect
cpm
Batcheffect
15 months ago
sukeshinik5
▴ 20
2
votes
9
replies
1.8k
views
Can't post a question?
Bioconductor
updated 9 months ago by
DavideSant
• 0 • written 15 months ago by
blmurphy
• 0
0
votes
1
reply
1.6k
views
Job:
Research software engineer at UPF Barcelona
JobPosting
Devel
GSVA
Software
written 3.1 years ago by
Robert Castelo
★ 3.4k
0
votes
4
replies
931
views
rtracklayer accessing UCSC data table not working
UCSC
rtracklayer
getTable
15 months ago
Andreas.Herbst
• 0
0
votes
0
replies
622
views
WGCNA: Problem with selecting soft threshold
biologicalnetworkanalysis
genomes
RNA-Seq
co-expression
wgcna
15 months ago
Fernanda
• 0
1,000 results • Page
15 of 20
Recent ...
Replies
Answer: DESeq2 - how many surrogate variables from svaseq, use of lfcshrink
by
ATpoint
★ 5.0k
> and I first used the normalized counts You would not use these normalized counts for PCA as they're not on log2 scale. As such, the feat…
Comment: EuroBioC2026 abstract submission is open!
by
TikTsokaasocissalpc
• 0
Submitting abstracts for EuroBioC2026 can be exciting but organizing ideas is key. A Random Word Generator [visit][1] can help create uniqu…
Comment: DESeq2 on non-RNASeq counts data
by
TikTsokaasocissalpc
• 0
In data analysis, behavior differences based on data type are common. Similarly, Best EDI Software adapts to non-standard transaction volum…
Comment: blockwiseModule crashes in the end and doesn't generate modules
by
gexose2839
• 0
Sounds good. @[time][1] [1]: https://timeduration.github.io
Comment: PFAM formats changed - is it still possible to use this with ISA?
by
TikTsokaasocissalpc
• 0
For mobile gaming enthusiasts, 3 Patti Lucky offers a seamless experience, unlike the frustration Harris faced with incompatible PFAM resul…
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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