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2
votes
4
replies
1.3k
views
DESeq normalized counts vs CQN and statistics
DESeq2
cqn
written 18 months ago by
emlucero
• 0
1
vote
4
replies
2.8k
views
Should I perform batch correction of normalized RNA-seq counts prior to GSVA?
GSVA
GSVAdata
RNAseq
18 months ago • updated 17 months ago
Lucy
▴ 60
0
votes
2
replies
1.5k
views
Installing Bioconductor
Bioconductor
updated 17 months ago by
Lluís Revilla Sancho
▴ 760 • written 18 months ago by
mariyahgeorge14
• 0
0
votes
1
reply
621
views
featureCounts from Rsubread
Rsubread
updated 18 months ago by
Gordon Smyth
53k • written 18 months ago by
Emiliano
• 0
0
votes
0
replies
639
views
News:
EuroBioC2024 Carpentries workshops Sep 2-3
Community
Workshop
Bioconductor
EuroBioC2024
18 months ago
Maria Doyle
▴ 110
0
votes
1
reply
1.1k
views
Problem with spike-ins (ERCC) in DESeq2 analysis after doing RUVg!
SpikeIn
RUVSeq
DESeq2
RUV
updated 18 months ago by
Michael Love
43k • written 18 months ago by
Ειρήνη
• 0
5
votes
9
replies
2.9k
views
Inconsistent nullp and goseq enrichment results across operating systems
goseq
written 18 months ago by
Danielle
• 0
0
votes
4
replies
1.1k
views
DE analysis in EdgeR /Can any one please help me.
RNASeqData
DEGraph
RNASeq
edgeR
DegNorm
written 18 months ago by
Shaozhen
• 0
0
votes
4
replies
1.5k
views
Generating Gene Expression Levels from TSV files on GEO
GEOquery
GEO
TSV
updated 18 months ago by
Sean Davis
21k • written 18 months ago by
gallantk5
• 0
0
votes
0
replies
837
views
Linear Mixed Model for Differential Gene Expression in Single-Cell RNAseq with Batch Effects
lmer
MAST
DifferentialExpression
18 months ago
nhaus
▴ 70
3
votes
4
replies
1.3k
views
Differences in Limma and Dreamlet random effects from confounded dataset
limma
dreamlet
18 months ago
jcollier
• 0
0
votes
1
reply
968
views
ChAMP analysis Error: Meth Matrix and UnMeth Matrix seems not paried correctly AND incomplete final line
MethylationArray
methylationArrayAnalysis
ChAMP
updated 13 months ago by
nereaherrera23
• 0 • written 18 months ago by
Mathu
• 0
1
vote
0
replies
637
views
RUVg spike-in assumption global expression
RUVSeq
RUVnormalize
18 months ago
Erdi
▴ 10
0
votes
0
replies
5
views
Spam:
Ground Handling Companies in Maldives
alabaster.schemas
db0
18 months ago
vvipflight01
0
0
votes
2
replies
1.3k
views
Fail to install hgu133plus2.db
org.Hs.eg.db
hgu133plus2
updated 18 months ago by
James W. MacDonald
68k • written 18 months ago by
yu
• 0
0
votes
0
replies
11
views
Spam:
How do professional SEO services enhance user experience on my website?
metaMSdata
18 months ago
Steven
0
0
votes
0
replies
485
views
How to perform a methylation analyisis from beta values matrix and pd.csv
minfiDataEPIC
18 months ago
yemeijie123
• 0
0
votes
1
reply
1.4k
views
XCMS2 of orbitrap data
metabolite data
xcms2
updated 18 months ago by
Elodie
• 0 • written 9.0 years ago by
Yashwant
▴ 10
0
votes
0
replies
642
views
News:
BioC2024 in-person registration closes soon (July 10)
BioC2024
Conference
Bioconductor
Community
18 months ago
Maria Doyle
▴ 110
0
votes
1
reply
663
views
unreal negative log2fc values
DESeq2
des
updated 18 months ago by
James W. MacDonald
68k • written 18 months ago by
Atul K.
• 0
0
votes
0
replies
440
views
Error in bam loading in getUniqueCleavageEvents() in GUIDEseq package
GUIDEseq
18 months ago
StayM
• 0
0
votes
0
replies
1.6k
views
Job:
Toxicogenomics Statistician
JobPosting
updated 18 months ago by
shepherl
4.2k • written 21.7 years ago by
Warnes, Gregory R
▴ 460
0
votes
0
replies
41
views
Spam:
GenOMICC DNA biobank
alabaster.schemas
db0
18 months ago
Jolka
0
0
votes
1
reply
716
views
Create a Graph w/ Only the Genes Interaction
EnrichedPathways
GeneInteractionGraph
graph
18 months ago
Antonio
• 0
0
votes
0
replies
532
views
EPIC v2 annotation and BigWig
EPICv2manifest
IlluminaHumanMethylationEPICv2anno.20a1.hg38
18 months ago
MajaVu
• 0
0
votes
1
reply
576
views
LRT test for different timepoints (one tissue types vs. many tissue types)
DESeq2
updated 18 months ago by
Michael Love
43k • written 18 months ago by
K
• 0
0
votes
0
replies
778
views
Improving Gene Matching for CIBERSORT Deconvolution with Monaco Reference Matrix in Bulk RNA-Seq
DeconRNASeq
AnnotationDbi
org.Hs.eg.db
18 months ago
chunglee13
• 0
0
votes
4
replies
1.9k
views
Trouble Installing DADA2 (warning: R new user)
dada2
updated 18 months ago by
shepherl
4.2k • written 18 months ago by
schott01
• 0
0
votes
0
replies
773
views
Difference in Predictive component of PLS and OPLS Model
Metabolomics
plotGrouper
Bioconductor
ropls
PLSDAbatch
18 months ago
devarti.mahakalkar
• 0
0
votes
0
replies
753
views
Problem with MethylAid ("Cannot get Manifest object for an 'Unknown' array") and Epicv2
minfi
EPICv2manifest
MethylAid
18 months ago
pcibin
• 0
0
votes
4
replies
9.3k
views
Any tools to convert .gff to .gtf format
AnnotationData
CrispRdesignR
BSgenome
updated 12 months ago by
ControlF5
• 0 • written 3.4 years ago by
Manoj Kumar R
• 0
0
votes
3
replies
1.0k
views
Conumee with EPICv2 Segment function
Conu
conumee
updated 9 months ago by
zpingfeng
• 0 • written 18 months ago by
idatta1
• 0
0
votes
0
replies
893
views
Job:
Postdoc Opportunity in Bioinformatics at Northwestern University (Research on Human Pregnancy and Autoimmunity)
Bioinformatics
scRNAseq
18 months ago
Damini
• 0
0
votes
1
reply
732
views
single excel file containing methylation beta values does not get loaded in ChAMP
ChAMP
updated 18 months ago by
Basti
▴ 780 • written 18 months ago by
tahirah.yasmin2014
• 0
1
vote
2
replies
816
views
How to get the DMR?
ENmix
18 months ago
Alex
• 0
0
votes
0
replies
415
views
Remove Control Probes from Affymetrix Human Gene 1.0 ST Array probeset version
AffymetrixDataTestFiles
AffymetrixChip
18 months ago
drexjaramel
• 0
0
votes
3
replies
1.0k
views
How to search Pubmed Central or other fulltext literature base using regex?
metaMSdata
Bioconductor
18 months ago
Abiologist
• 0
0
votes
1
reply
3.9k
views
converting Seurat V5 with BPcells matrix to SingleCellExperiment
SeuratV5
SingleCellExperiment
BPCells
SingleCellExper
updated 18 months ago by
yxsee
• 0 • written 18 months ago by
Le
• 0
0
votes
0
replies
518
views
Understanding Differentially Abundant Neighbourhood Identification
miloR
18 months ago
Dario Strbenac
★ 1.6k
2
votes
2
replies
5.6k
views
Unable to install the package "tissuesGeneExpression"
bioconductor
updated 18 months ago by
Muhammad Abdullah
• 0 • written 8.5 years ago by
mdroog
▴ 10
1
vote
13
replies
2.6k
views
Ranking the GSEA Results
fgsea
log2FC
18 months ago
V_Vibes
• 0
1
vote
8
replies
2.0k
views
Advice on appropriateness of an offset in glmGamPoi/edgeR
DESeq2
glmGamPoi
offset
edgeR
scRNAseq
updated 18 months ago by
Gordon Smyth
53k • written 18 months ago by
Alec
• 0
0
votes
2
replies
1.3k
views
Species level information couldn't find with DADA2 bioconductor package
Metagenomics
dada2
MicrobiomeData
18 months ago • updated 16 months ago
abhisek001
• 0
3
votes
1
reply
2.2k
views
Difference between enrichGO results and Enrichr website results
Pathways
GO.db
clusterProfiler
updated 18 months ago by
Guido Hooiveld
★ 4.1k • written 18 months ago by
adrip
▴ 10
0
votes
1
reply
588
views
Risa package missing from Bioconductor 3.19
3.19
Risa
updated 18 months ago by
James W. MacDonald
68k • written 18 months ago by
rkjulian
• 0
1
vote
2
replies
1.2k
views
Struggling to convert a large list of non-model genes into human orthologs, any suggestions?
annotation
18 months ago
ronin
• 0
0
votes
0
replies
744
views
Cell type deconvolution of RNAseq data- Create signature matrix of cells
deconvolution
rnaseqGene
RNAseq
18 months ago
JG13
• 0
0
votes
1
reply
785
views
BiomaRt listAttributes - which are external ?
Bioconductor
getBM
updated 18 months ago by
James W. MacDonald
68k • written 18 months ago by
Abiologist
• 0
0
votes
0
replies
841
views
Blacklist regions on DBA object (diffbind)
DiffBind
chipseq
18 months ago
gamma.jian
▴ 10
1
vote
2
replies
3.4k
views
Why does DESeq2 give negative log2 fold change in treatment vs control for some genes when normalized counts are higher in treatment.
DESeq2
18 months ago
sropri
• 0
46,709 results • Page
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Comment: Guitar R package requires update due to dependency GenomicFeatures
by
ferran.llobet.cabau
▴ 10
Thank you @seandavi for your feedback. I followed your recommendations and generated a [pull request][1] including the fix for this issue…
Comment: Ensembl plants at annotationHub?
by
Guido Hooiveld
★ 4.1k
Hope you don't mind I am not Johannes... ;-) Note that you nowadays can generate these yourselves using the `docker` image Johannes made av…
Comment: How does contrasts.fit do in limma to extract comparisons with a model having in
by
jtsy6383
• 0
Thanks for the reminder about DiffVar (for that project I ended up using GAMLSS in the end and haven't touched DiffVar since) and the alter…
Comment: Ensembl plants at annotationHub?
by
jwp48
• 0
Dear Johannes, Would it be possible to generate a EnsDb for the newest Medicago V5 genome release? Medicago truncatula A17 r5.0 This woul…
Answer: please provide a BibTeX citation for "Advanced Single-Cell Analysis with Biocond
by
Ludwig Geistlinger
▴ 80
When referring to the OSCA book including individual sub-books please cite the OSCA paper: Amezquita, R.A., Lun, A.T.L., Becht, E. et a…
Votes
Comment: Guitar R package requires update due to dependency GenomicFeatures
A: how to control age and gender effect in expression data using DESeq2
A: how to control age and gender effect in expression data using DESeq2
how to control age and gender effect in expression data using DESeq2
Answer: please provide a BibTeX citation for "Advanced Single-Cell Analysis with Biocond
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