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773
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Retrieving Package Metadata from Bioconductor API: Versions and Dependencies
metaMSdata
updated 18 months ago by
shepherl
4.3k • written 18 months ago by
Sadman
• 0
4
votes
12
replies
6.4k
views
How to get DMR for Infinium methylation EPIC v2
ChAMP
DMRcate
minfi
updated 18 months ago by
Tim Peters
▴ 230 • written 2.2 years ago by
rae.alshammari
▴ 20
0
votes
3
replies
1.0k
views
Trouble with creating Series RNA-seq normalized counts matrix
GEO
rnaseqGene
RNA
18 months ago
gallantk5
• 0
0
votes
3
replies
1.1k
views
Error when trying to do different pairwise comparisons and lfcshrink than what's listed on resultsNames()
RNASeqData
DESeq2
RNASeq
DifferentialExpression
updated 18 months ago by
ATpoint
★ 5.0k • written 18 months ago by
Mark
• 0
1
vote
1
reply
1.2k
views
Why does greyListChIP return different grey lists every time I newly run the script?
GreyListChIP
updated 18 months ago by
Matt Eldridge
▴ 10 • written 18 months ago by
Giulia
• 0
0
votes
0
replies
728
views
Using variantAnnotation to put together genotype and consequence information
variantAnn
VariantAnnotation
18 months ago
ramiro.barrantes
▴ 10
0
votes
8
replies
2.0k
views
Error running tximeta
tximeta
updated 18 months ago by
Guido Hooiveld
★ 4.1k • written 18 months ago by
daria.igudesman
• 0
0
votes
4
replies
1.6k
views
Generating surrogate variables across multiple variables of interest
sva
18 months ago
Robert
• 0
1
vote
6
replies
1.4k
views
limma and Syntactically Invalid Factor Values
limma
updated 18 months ago by
Gordon Smyth
53k • written 18 months ago by
Dario Strbenac
★ 1.6k
1
vote
1
reply
1.2k
views
DEG Analysis using Limma on DSP GeoMx Data: Handling Multiple ROIs per Core
limma
DSP
GeomxTools
18 months ago
Bioinformagician
• 0
1
vote
3
replies
986
views
Doubt about model in paired samples (intercept ?)
DESeq2
updated 18 months ago by
Michael Love
43k • written 18 months ago by
picasa1983
• 0
0
votes
10
replies
2.2k
views
Two treatments, one control
DESeq2
stageR
19 months ago • updated 18 months ago
alephreish
• 0
0
votes
2
replies
2.1k
views
How to correct for a covariate in DESeq2 that is linear with the condition of interest
DESeq2
18 months ago
Fiona
• 0
2
votes
3
replies
1.0k
views
DeSeq2 Model Problems with species, tissue, and tissue status nesting
DESeq2
R
written 18 months ago by
tbiewerh
• 0
4
votes
2
replies
1.2k
views
Parallel comparison of two DNAString objects with IUPAC ambiguities
Biostrings
written 18 months ago by
maltethodberg
▴ 180
1
vote
1
reply
2.1k
views
Differences between core_enrichment from gsePathway and viewPathway
FunctionalAnalysis
clusterProfiler
viewPathway
gsePathway
updated 18 months ago by
Guido Hooiveld
★ 4.1k • written 18 months ago by
Filipe
• 0
0
votes
1
reply
755
views
methylKit problem
methylKit
updated 18 months ago by
alex.gos90
▴ 10 • written 18 months ago by
Krisztina
• 0
1
vote
3
replies
1.0k
views
Create merged ChIP heatmap across conditions
DiffBind
profileplyr
updated 18 months ago by
Rory Stark
★ 5.2k • written 18 months ago by
jesswhitts
• 0
0
votes
0
replies
486
views
ASICS to process NMR spectra
ASICS
18 months ago
KONG ZHI XIAN
• 0
0
votes
0
replies
609
views
MAST package: Most appropriate way to perform lrTest for effect of factor with multiple levels in pairwise manner?
MAST
18 months ago
Kelly
• 0
5
votes
3
replies
1.1k
views
Limma comparing gene expression between base line and one treatment
limma
updated 18 months ago by
James W. MacDonald
68k • written 18 months ago by
AL
• 0
0
votes
1
reply
1.2k
views
How to rank DEG for GSEA using DEseq2 result ?
DESeq2
limma
GeneSetEnrichment
updated 18 months ago by
ATpoint
★ 5.0k • written 18 months ago by
picasa1983
• 0
0
votes
1
reply
608
views
Run DEXSeq successfully but got a result that padj==1 in all genes
DEXSeq
updated 18 months ago by
ATpoint
★ 5.0k • written 18 months ago by
2406691063
• 0
4
votes
9
replies
2.8k
views
Get_interactions is giving the combined score
STRINGdb
updated 18 months ago by
McKayl
• 0 • written 18 months ago by
nkavabhrath03
▴ 20
2
votes
5
replies
1.2k
views
Limma - 0 downreg and upreg values
GeoMx
limma
DifferentialExpression
updated 18 months ago by
James W. MacDonald
68k • written 18 months ago by
sop
• 0
4
votes
12
replies
2.0k
views
DGE with a Continuous Variable
DESeq2
model
updated 18 months ago by
Michael Love
43k • written 18 months ago by
picasa1983
• 0
0
votes
4
replies
926
views
Error from runShinyMethyl() - is(object, "shinyMethylSet") is not TRUE
shinyMethyl
updated 18 months ago by
James W. MacDonald
68k • written 18 months ago by
Courtney
• 0
1
vote
5
replies
3.7k
views
ComplexHeatmap - alter legend position
ComplexHeatmap
19 months ago • updated 18 months ago
Lucy
▴ 60
4
votes
14
replies
2.8k
views
LIMMA 2x2 Factorial Design with Paired Samples
factorialdesign
limma
pairedsamples
updated 18 months ago by
Gordon Smyth
53k • written 18 months ago by
Michael E
• 0
0
votes
1
reply
740
views
T cell subtype annotation
SingleCellExperiment
updated 18 months ago by
James W. MacDonald
68k • written 18 months ago by
georgii.vdovin
• 0
0
votes
1
reply
821
views
minfi - bumphunter value problem
bumphunter
minfiData
minfi
bumphun
updated 18 months ago by
James W. MacDonald
68k • written 19 months ago by
kumakeren16
• 0
6
votes
7
replies
2.4k
views
findOverlaps(), queryHits and subjectHits()
GenomicFiles
updated 18 months ago by
Hervé Pagès
16k • written 18 months ago by
user_bioinfo
• 0
0
votes
0
replies
646
views
How to use GAGE with my own metagenomic KOFams data
kegg.gsets
gageData
gage
KEGG
18 months ago
cereyredondo
• 0
0
votes
1
reply
677
views
output from RAIN doesn't look rhythmic
rain
updated 18 months ago by
ATpoint
★ 5.0k • written 18 months ago by
cereyredondo
• 0
0
votes
3
replies
2.0k
views
Query regarding phyloseq object construct with QIIME output
phyloseq
microbiome
Metagenomics
updated 18 months ago by
Карина
• 0 • written 2.7 years ago by
abhisek001
• 0
1
vote
2
replies
819
views
DESeq2: two conditions two genotypes
DESeq2
19 months ago • updated 18 months ago
Rocio
• 0
2
votes
4
replies
1.4k
views
DESeq normalized counts vs CQN and statistics
DESeq2
cqn
written 19 months ago by
emlucero
• 0
1
vote
4
replies
3.0k
views
Should I perform batch correction of normalized RNA-seq counts prior to GSVA?
GSVA
GSVAdata
RNAseq
19 months ago • updated 18 months ago
Lucy
▴ 60
0
votes
2
replies
1.7k
views
Installing Bioconductor
Bioconductor
updated 18 months ago by
Lluís Revilla Sancho
▴ 760 • written 19 months ago by
mariyahgeorge14
• 0
0
votes
1
reply
643
views
featureCounts from Rsubread
Rsubread
updated 19 months ago by
Gordon Smyth
53k • written 19 months ago by
Emiliano
• 0
0
votes
0
replies
666
views
News:
EuroBioC2024 Carpentries workshops Sep 2-3
Community
Workshop
Bioconductor
EuroBioC2024
19 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 19 months ago by
Michael Love
43k • written 19 months ago by
Ειρήνη
• 0
5
votes
9
replies
2.9k
views
Inconsistent nullp and goseq enrichment results across operating systems
goseq
written 19 months ago by
Danielle
• 0
0
votes
4
replies
1.2k
views
DE analysis in EdgeR /Can any one please help me.
RNASeqData
DEGraph
RNASeq
edgeR
DegNorm
written 19 months ago by
Shaozhen
• 0
0
votes
4
replies
1.7k
views
Generating Gene Expression Levels from TSV files on GEO
GEOquery
GEO
TSV
updated 19 months ago by
Sean Davis
21k • written 19 months ago by
gallantk5
• 0
0
votes
0
replies
894
views
Linear Mixed Model for Differential Gene Expression in Single-Cell RNAseq with Batch Effects
lmer
MAST
DifferentialExpression
19 months ago
nhaus
▴ 70
3
votes
4
replies
1.4k
views
Differences in Limma and Dreamlet random effects from confounded dataset
limma
dreamlet
19 months ago
jcollier
• 0
0
votes
1
reply
1.0k
views
ChAMP analysis Error: Meth Matrix and UnMeth Matrix seems not paried correctly AND incomplete final line
MethylationArray
methylationArrayAnalysis
ChAMP
updated 14 months ago by
nereaherrera23
• 0 • written 19 months ago by
Mathu
• 0
1
vote
0
replies
657
views
RUVg spike-in assumption global expression
RUVSeq
RUVnormalize
19 months ago
Erdi
▴ 10
0
votes
0
replies
5
views
Spam:
Ground Handling Companies in Maldives
alabaster.schemas
db0
19 months ago
vvipflight01
0
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Comment: Error message that there is no package called Biobase
by
DamionLedner99
• 0
thanks for sharing!!! https://cran.r-project.org/
Answer: Confirm that OpenStats will not be archived (pryr dependency)
by
man
• 0
The best AI-powered image editor <a href='https://nanobananaart.net>[Nano Banana][1]</a> for both image and text in 2025. [1]: http…
Comment: msmsTests, inconsistent sign between lFC.Av and LogFC
by
Ben
• 0
Continued here due to posting difficulties: Extract from the results table: ``` Inhibitor Vehicle lFC.Av LogFC ... F1 0.0 27…
Answer: DESeq2 for 16S rRNA Analysis
by
James W. MacDonald
68k
The Wald test is only meant for comparison of two groups at a time, so it depends on what you mean by 'analyze across multiple groups at a …
Comment: MetaDE.pvalue: Error in xj[i]: invalid subscript type 'list'
by
varying.mastodon.isyn
• 0
Oh, that error! I remember wrestling with that one for hours when I was first learning Python. Turns out I was trying to use a list itself …
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A: DESeq2 normalization vs VST vs rlog
Answer: How to directly decet the outlier samples (libraries) in EdgeR pipeline
Answer: Confused about the CPM and TMM normalization in edgeR
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