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How to adjust for Cell Type Differences between groups in Pseudo-Bulk Differential Gene Expression analysis in scRNA-seq?
SingleCellData
DESeq2
pseudobulk
sing
3 minutes ago • updated just now
Sara
• 0
0
votes
0
replies
52
views
Error in convertMSImagingArrays2Experiment / estimateDomain in Cardinal
Mass
Cardinal
4 days ago
Mark Dunning
★ 1.1k
0
votes
1
reply
268
views
Does anyone have the command to download all of the core_nt using blast_db_get()
rBLAST
BiocFileCache
updated 4 days ago by
shepherl
4.1k • written 4 days ago by
Matthew Thornton
▴ 380
0
votes
0
replies
52
views
Error in retrieving clinical data
TCGAbiolinks
5 days ago
silickas
• 0
1
vote
0
replies
1.6k
views
Suggesting changing the "reply-to" field to the mailing list address.
updated 6 days ago by
shepherl
4.1k • written 15.6 years ago by
Peng Yu
▴ 950
0
votes
0
replies
52
views
Help with mouse cell type annotation
annotation
SingleR
mouse
SingleCellData
scRNAseq
10 days ago
Muhammad
• 0
0
votes
0
replies
45
views
Unable to restore chromosome sequence lengths or other metadata in BSgenome.Mfascicularis.NCBI.6.0
BSgenome.Mfascicularis.NCBI.6.0
10 days ago
Genevieve
• 0
0
votes
0
replies
35
views
Generating Biphasic Curves in Offline GR Metrics Package
GRmetrics
11 days ago
Jasmitha
• 0
3
votes
5
replies
1.0k
views
Overcoming confounding in batch effect correction
sva
BiologicalQuestion
12 days ago • updated 11 days ago
bbao
▴ 10
0
votes
5
replies
577
views
For some reason I can't update BiocManager to 3.20
Bioconductor
updated 7 days ago by
shepherl
4.1k • written 13 days ago by
azm.ana2
• 0
0
votes
0
replies
56
views
Help with MetagenomeSeq, understanding the 75th quantile
metagenomeSeq
cumulativesumscaling
updated 14 days ago by
James W. MacDonald
68k • written 17 days ago by
boone5jones
• 0
0
votes
0
replies
168
views
Methylation data - different probes are classified differently based on transcript? (Illumina methylation arrays, using minfi)
minf
minfiDataEPIC
MethylationArrayData
MethylationArray
EPICv2manifest
17 days ago
charlie.wright
• 0
0
votes
4
replies
416
views
Web accessibility of Bioconductor.org
website
Website
updated 13 days ago by
Sean Davis
21k • written 19 days ago by
lizhare
• 0
0
votes
0
replies
86
views
Batch Correction while implementing QSEA package
qsea
MEDIPS
MEDIPSData
DNAMethylation
25 days ago
User3088
• 0
0
votes
1
reply
118
views
building samplesheet and plot profile
DiffBind
26 days ago • updated 24 days ago
yf
• 0
0
votes
0
replies
51
views
DBT JRF & PhD Scholar
BiologicalQuestion
OmicsMLRepoR
27 days ago
Manisha
• 0
0
votes
0
replies
84
views
My DEXSeqDataSetFromSE is returning an Error, but all of my checks to seem to indicate that this error is not present
DifferentialSplicing
RNASeqData
DEXSeq
27 days ago
cftattersfield
• 0
0
votes
2
replies
509
views
How to visualize these pathways using pathview
Salmo_salar
RNASeq
KEGG
pathview
28 days ago • updated 11 days ago
ingrid.h
• 0
0
votes
0
replies
65
views
Problem with PCAtool as dependencie
COTAN
PCAtools
5 weeks ago
Silvia
• 0
0
votes
0
replies
69
views
cnvEQTL : Error in cpm.default(y, lib.size = lib.size) : NA counts not allowed
CNVRanger
5 weeks ago
xiaofeiwang18266
▴ 50
0
votes
0
replies
120
views
gsameth GSA: probe annotation to multiple genes
missMethyl
gsameth
6 weeks ago
nurkenber
• 0
0
votes
0
replies
155
views
Testing Differential Expression with Interaction Effect Between Categorical and Continuous Variable with Repeated (Paired) Measures using variancePar…
limma
variancePartition
6 weeks ago
GJ
• 0
0
votes
1
reply
215
views
org.Hs.eg.db issue
org.Hs.eg.db
updated 6 weeks ago by
shepherl
4.1k • written 6 weeks ago by
k.panov
• 0
0
votes
2
replies
422
views
Paired analysis in proteomics data for DE while interested in only a particular subset of the data
limma
modelmatrix
pairedanalysis
Proteomics
written 6 weeks ago by
svlachavas
▴ 840
0
votes
0
replies
99
views
Issue when attempting to use output from DECIPHER IDtaxa (pr2 V5) with dada2/phyloseq
DECIPHER
taxonomyassignment
phyloseq
dada2
Pr2V5
6 weeks ago
Maggie
• 0
0
votes
0
replies
92
views
Trouble with double delimiters in .fcs file (flowCore package)
flowCore
FlowCytometry
FlowCytometryData
7 weeks ago
vpochic
• 0
0
votes
1
reply
379
views
ChAMP.DMR error - Error in makeGenomicRatioSetFromMatrix
ChAMP
updated 8 weeks ago by
O'Brien
• 0 • written 9 weeks ago by
André
• 0
0
votes
1
reply
195
views
Errors running learn.bn function from Pigengene in windows environment
Pigengene
written 10 weeks ago by
Thomas
• 0
0
votes
0
replies
10
views
Spam:
Best Hotels In Maui
prebs
10 weeks ago
2zrcj3448p
0
0
votes
7
replies
911
views
DESeq2: Gene is DEG in one experiment but not in the other depite similar baseMean, L2FC, ...
DESeq2
updated 10 weeks ago by
txema.heredia
• 0 • written 11 weeks ago by
fjrsa
• 0
0
votes
0
replies
137
views
Confidence interval contains 0 but p<0.05
MAST
11 weeks ago
Adelyn
• 0
0
votes
0
replies
152
views
Pathway abundance data from Curatedmetagenomics
curatedMetagenomicData
ExperimentHubData
11 weeks ago
Edward
• 0
1
vote
4
replies
463
views
pathview - multiple states
pathview
Pathways
KEGG
11 weeks ago
Philippine
• 0
0
votes
5
replies
454
views
fail to use addPerROIQC in Rmd
stand
standR
updated 12 weeks ago by
liu.n
• 0 • written 12 weeks ago by
joseph.joonsang
• 0
4
votes
8
replies
1.1k
views
how to apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K?
DMRcate
minfi
12 weeks ago • updated 7 days ago
xiaofeiwang198266
• 0
0
votes
1
reply
239
views
rrvgo::calculateSimMatrix() error
rrvgo
updated 12 weeks ago by
Phila
• 0 • written 12 weeks ago by
Michelle
• 0
0
votes
0
replies
172
views
Lipidomics Barplot: raw values or non-log, lipidr-normalized values?
Normalization
Lipidomics
lipidr
3 months ago
David R
▴ 90
0
votes
1
reply
255
views
WGCNA with TPM tables
RNASeq
WGCNA
ComparativeGenomics
updated 3 months ago by
ATpoint
★ 4.7k • written 3 months ago by
siobhan.dietz
• 0
0
votes
1
reply
203
views
eRNAs count
RNASeq
DESeq2
updated 3 months ago by
ATpoint
★ 4.7k • written 3 months ago by
Irene
• 0
0
votes
0
replies
192
views
WGCNA module preservation using only adjacency matrix
WGCNA
3 months ago
yang1641
• 0
0
votes
0
replies
113
views
ChemmineOB avaiable for macOS Binary (arm64)?
ChemmineOB
3 months ago
Simone
• 0
0
votes
2
replies
463
views
installation error for BiocNeighbors package
BiocNeighbors
3 months ago
育
• 0
0
votes
0
replies
249
views
Errors trying to load EPIC v2 data in ChAMP
ChAMP
ChAMPdata
3 months ago
elgomez
• 0
1
vote
3
replies
517
views
makeContrastsDream for Interaction
limma
DifferentialExpression
variancePartition
dream
3 months ago • updated 12 weeks ago
abadgerw
• 0
0
votes
5
replies
756
views
Merge Replicates vs Mixed Model
limma
DifferentialExpression
variancePartition
dream
3 months ago • updated 12 weeks ago
abadgerw
• 0
0
votes
0
replies
186
views
ChIP peaks comparison
ChIPSeqData
genomes
ChIPSeq
3 months ago
user_bioinfo
• 0
0
votes
0
replies
267
views
Diffbind: Cut&Run: E-coli spike-in
Normalization
DiffBind
3 months ago
kim
• 0
0
votes
0
replies
192
views
Help using reduceSimMatrix with a custom annotation
AnnotationHub
GOSemSim
rrvgo
3 months ago
daccar98
• 0
0
votes
0
replies
186
views
Combining two closely related bacterial annotated genomes to analyze as one pooled group
genomes
RNASeq
3 months ago
brayas13
• 0
0
votes
0
replies
167
views
export processed data from flowploidy
flowPloidy
3 months ago
Zdenek Skala
• 0
1,000 results • Page
1 of 20
Recent ...
Replies
Comment: Plot title for PCA in DESeq2
by
AL
• 0
Thank you!
Answer: Interpreting DESEQ2 interaction term and inclusion of covariate
by
swbarnes2
★ 1.4k
"ecotypehigh.rearing_high" will basically do a 4 group comparison, and tell you if any genes that change going from high to low change diff…
Comment: error in ChAMP loading file
by
Ashley
• 0
This error in ChAMP loading file and the solutions provided here are good and there are people who need these solutions. To get the [Rockin…
Answer: cameraPR() non directional test
by
Hugo Varet
▴ 80
Dear Gordon, thank you for your answer, that's exactly what I wanted to know. Happy to see you'll make it available in the next version o…
Answer: DEseq2 design for additive treatment
by
ATpoint
★ 4.7k
See https://support.bioconductor.org/p/69104/#69197, https://support.bioconductor.org/p/129755/ for testing against an average. Many other …
Votes
Interpreting DESEQ2 interaction term and inclusion of covariate
A: Seurat/DESeq2 - single cell RNA-seq differential expression
Answer: Plot title for PCA in DESeq2
A: DESeq2: detect significantly increasing across an ordinal variable
Answer: DEseq2 design for additive treatment
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