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2
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3
replies
1.0k
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Comparing one group against multiple groups in DESeq2
DESeq2
written 23 months ago by
tamivico
• 0
0
votes
2
replies
1.1k
views
Validity of SingleR with very small bulk RNAseq reference
SingleR
updated 9 months ago by
Rohit
• 0 • written 17 months ago by
nhaus
▴ 70
2
votes
3
replies
3.1k
views
Plot PCA with ellipses using ggplot
DESeq2
ggplot
PCA
written 17 months ago by
robledoj13
• 0
1
vote
0
replies
923
views
News:
Bioconductor Package Download Rate Limitation (HTTP 429)
downloads
http429
http
Bioconductor
17 months ago
shepherl
4.2k
0
votes
3
replies
1.9k
views
How to plot gene names in Gviz plotTracks and get the ideogram track to work (US-based)?
gviz
Saccharomyces_cerevisiae
Gviz
ideogram
updated 17 months ago by
Maryna
• 0 • written 2.3 years ago by
Michael
• 0
0
votes
0
replies
620
views
Sigmatrix should not contain missing values error in deconvolution using granule
granulator
17 months ago
louis.der.hammer
• 0
0
votes
9
replies
2.3k
views
'path' must be string
HELP
path
updated 17 months ago by
James W. MacDonald
68k • written 17 months ago by
cpierce2
• 0
0
votes
4
replies
1.4k
views
Recount3: PCR duplicates
pcrduplicates
recount3
multimappingreads
updated 17 months ago by
ATpoint
★ 5.0k • written 2.6 years ago by
seline.natalie
• 0
3
votes
6
replies
1.4k
views
A question occur when using DESeq2 on a complex design
DESeq2
rnaseqGene
RNASeq
written 17 months ago by
MedocRafael
• 0
4
votes
3
replies
1.6k
views
DESeq fitNbinomGLMs Warning Issue: In fitNbinomGLMs(objectNZ[fitidx, , drop = FALSE], alpha_hat = alpha_hat[fitidx], : 4189rows had non-positive e…
DESeq2
RNAseq
written 17 months ago by
mila
▴ 10
0
votes
0
replies
687
views
Error in serialization
scDblFinder
BiocParallel
17 months ago
Lluís Revilla Sancho
▴ 760
0
votes
1
reply
762
views
Retrieving Package Metadata from Bioconductor API: Versions and Dependencies
metaMSdata
updated 17 months ago by
shepherl
4.2k • written 17 months ago by
Sadman
• 0
4
votes
12
replies
6.0k
views
How to get DMR for Infinium methylation EPIC v2
ChAMP
DMRcate
minfi
updated 17 months ago by
Tim Peters
▴ 230 • written 2.1 years ago by
rae.alshammari
▴ 20
0
votes
3
replies
979
views
Trouble with creating Series RNA-seq normalized counts matrix
GEO
rnaseqGene
RNA
17 months ago
gallantk5
• 0
0
votes
3
replies
1.0k
views
Error when trying to do different pairwise comparisons and lfcshrink than what's listed on resultsNames()
RNASeqData
DESeq2
RNASeq
DifferentialExpression
updated 17 months ago by
ATpoint
★ 5.0k • written 17 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 17 months ago by
Matt Eldridge
▴ 10 • written 17 months ago by
Giulia
• 0
0
votes
0
replies
685
views
Using variantAnnotation to put together genotype and consequence information
variantAnn
VariantAnnotation
17 months ago
ramiro.barrantes
▴ 10
0
votes
8
replies
1.9k
views
Error running tximeta
tximeta
updated 17 months ago by
Guido Hooiveld
★ 4.1k • written 17 months ago by
daria.igudesman
• 0
0
votes
4
replies
1.5k
views
Generating surrogate variables across multiple variables of interest
sva
17 months ago
Robert
• 0
1
vote
6
replies
1.3k
views
limma and Syntactically Invalid Factor Values
limma
updated 17 months ago by
Gordon Smyth
53k • written 17 months ago by
Dario Strbenac
★ 1.6k
1
vote
1
reply
1.1k
views
DEG Analysis using Limma on DSP GeoMx Data: Handling Multiple ROIs per Core
limma
DSP
GeomxTools
17 months ago
Bioinformagician
• 0
1
vote
3
replies
965
views
Doubt about model in paired samples (intercept ?)
DESeq2
updated 17 months ago by
Michael Love
43k • written 17 months ago by
picasa1983
• 0
0
votes
10
replies
2.2k
views
Two treatments, one control
DESeq2
stageR
18 months ago • updated 17 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
17 months ago
Fiona
• 0
2
votes
3
replies
999
views
DeSeq2 Model Problems with species, tissue, and tissue status nesting
DESeq2
R
written 17 months ago by
tbiewerh
• 0
4
votes
2
replies
1.1k
views
Parallel comparison of two DNAString objects with IUPAC ambiguities
Biostrings
written 17 months ago by
maltethodberg
▴ 180
1
vote
1
reply
1.6k
views
Differences between core_enrichment from gsePathway and viewPathway
FunctionalAnalysis
clusterProfiler
viewPathway
gsePathway
updated 17 months ago by
Guido Hooiveld
★ 4.1k • written 17 months ago by
Filipe
• 0
0
votes
1
reply
706
views
methylKit problem
methylKit
updated 17 months ago by
alex.gos90
▴ 10 • written 17 months ago by
Krisztina
• 0
1
vote
3
replies
954
views
Create merged ChIP heatmap across conditions
DiffBind
profileplyr
updated 17 months ago by
Rory Stark
★ 5.2k • written 17 months ago by
jesswhitts
• 0
0
votes
0
replies
472
views
ASICS to process NMR spectra
ASICS
17 months ago
KONG ZHI XIAN
• 0
0
votes
0
replies
563
views
MAST package: Most appropriate way to perform lrTest for effect of factor with multiple levels in pairwise manner?
MAST
17 months ago
Kelly
• 0
5
votes
3
replies
1.1k
views
Limma comparing gene expression between base line and one treatment
limma
updated 17 months ago by
James W. MacDonald
68k • written 17 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 17 months ago by
ATpoint
★ 5.0k • written 17 months ago by
picasa1983
• 0
0
votes
1
reply
572
views
Run DEXSeq successfully but got a result that padj==1 in all genes
DEXSeq
updated 17 months ago by
ATpoint
★ 5.0k • written 17 months ago by
2406691063
• 0
4
votes
9
replies
2.3k
views
Get_interactions is giving the combined score
STRINGdb
updated 17 months ago by
McKayl
• 0 • written 17 months ago by
nkavabhrath03
▴ 20
2
votes
5
replies
1.2k
views
Limma - 0 downreg and upreg values
GeoMx
limma
DifferentialExpression
updated 17 months ago by
James W. MacDonald
68k • written 17 months ago by
sop
• 0
4
votes
12
replies
1.9k
views
DGE with a Continuous Variable
DESeq2
model
updated 17 months ago by
Michael Love
43k • written 17 months ago by
picasa1983
• 0
0
votes
4
replies
902
views
Error from runShinyMethyl() - is(object, "shinyMethylSet") is not TRUE
shinyMethyl
updated 17 months ago by
James W. MacDonald
68k • written 17 months ago by
Courtney
• 0
1
vote
5
replies
3.3k
views
ComplexHeatmap - alter legend position
ComplexHeatmap
18 months ago • updated 17 months ago
Lucy
▴ 60
4
votes
14
replies
2.7k
views
LIMMA 2x2 Factorial Design with Paired Samples
factorialdesign
limma
pairedsamples
updated 17 months ago by
Gordon Smyth
53k • written 17 months ago by
Michael E
• 0
0
votes
1
reply
709
views
T cell subtype annotation
SingleCellExperiment
updated 17 months ago by
James W. MacDonald
68k • written 17 months ago by
georgii.vdovin
• 0
0
votes
1
reply
786
views
minfi - bumphunter value problem
bumphunter
minfiData
minfi
bumphun
updated 17 months ago by
James W. MacDonald
68k • written 18 months ago by
kumakeren16
• 0
6
votes
7
replies
2.2k
views
findOverlaps(), queryHits and subjectHits()
GenomicFiles
updated 17 months ago by
Hervé Pagès
16k • written 17 months ago by
user_bioinfo
• 0
0
votes
0
replies
620
views
How to use GAGE with my own metagenomic KOFams data
kegg.gsets
gageData
gage
KEGG
17 months ago
cereyredondo
• 0
0
votes
1
reply
632
views
output from RAIN doesn't look rhythmic
rain
updated 17 months ago by
ATpoint
★ 5.0k • written 17 months ago by
cereyredondo
• 0
0
votes
3
replies
1.9k
views
Query regarding phyloseq object construct with QIIME output
phyloseq
microbiome
Metagenomics
updated 17 months ago by
Карина
• 0 • written 2.6 years ago by
abhisek001
• 0
1
vote
2
replies
784
views
DESeq2: two conditions two genotypes
DESeq2
18 months ago • updated 17 months ago
Rocio
• 0
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
2.7k
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
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