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SingleR Label.Ont
SingleR
written 16 months ago by
saeed.khalili
• 0
34
votes
11
replies
42k
views
Differential expression of FPKM from RNA-seq data using limma and voom()
limma
written 11.2 years ago by
Jon Bråte
▴ 260
17
votes
11
replies
37k
views
DESeq2 and shrinkage of log2 fold changes
deseq2
updated 7 months ago by
Michael Love
43k • written 9.0 years ago by
ribioinfo
▴ 100
14
votes
22
replies
31k
views
DESEq2 Paired samples Before and after treatment
deseq2
paired samples
updated 11 months ago by
Michael Love
43k • written 8.6 years ago by
adesrichard
▴ 30
3
votes
6
replies
28k
views
Deseq: What does "BaseMean" mean?
deseq2
written 6.4 years ago by
183227851
• 0
5
votes
2
replies
26k
views
DESeq2: thousands of NA for pvalues?
deseq2
rna-seq
DEGs
cooks cutoff
written 6.0 years ago by
aishu.jp
▴ 30
10
votes
20
replies
22k
views
Batch Effect in DESeq2, how to control, how to remove it, how to address biological question
deseq2
batch effect
batch
updated 3 months ago by
James W. MacDonald
67k • written 5.7 years ago by
Mozart
▴ 30
5
votes
8
replies
21k
views
Confused about the CPM and TMM normalization in edgeR
RNASeq
R
edgeR
updated 5 months ago by
Ahdee
▴ 50 • written 2.6 years ago by
Mohamed
▴ 30
34
votes
29
replies
15k
views
[DESeq2] time series strain-specific differences over time
deseq2
timecourse
updated 4 months ago by
Michael Love
43k • written 9.9 years ago by
john
▴ 130
3
votes
3
replies
15k
views
How to fix 'long vectors not supported yet' error in R
r
updated 9 months ago by
Amruta
• 0 • written 5.9 years ago by
r.tor
• 0
0
votes
9
replies
15k
views
How to generate a volcano plot when p-values from DESeq2 are zero?
deseq2
pvalue
visualization
enhancedvolcano
rnaseq
written 6.0 years ago by
ricardo3889
• 0
12
votes
10
replies
13k
views
biomaRt not working - lazy table error
error
lazy
R
biomaRt
table
updated 10 months ago by
juo5
• 0 • written 15 months ago by
Abhishek
▴ 20
3
votes
3
replies
13k
views
How to find rsID with biomaRt in R
biomaRt
updated 11 months ago by
James W. MacDonald
67k • written 3.9 years ago by
Federica
▴ 10
1
vote
3
replies
13k
views
Sorting columns in pheatmap
pheatmap
updated 6 months ago by
HAK
• 0 • written 3.8 years ago by
Linda
• 0
4
votes
5
replies
11k
views
[sva] Error in density.default(x, adjust = adj) : 'x' contains missing values
sva
updated 5 months ago by
ndphuc1605
• 0 • written 7.3 years ago by
anton.kratz
▴ 60
17
votes
8
replies
11k
views
remove microarray batch effects using Limma
Microarray
updated 7 months ago by
Gordon Smyth
52k • written 14.3 years ago by
Xie, Zhi NIH/NHLBI [E]
▴ 120
0
votes
5
replies
10k
views
tximport all(file.exists(files)) is not TRUE
bioconductor
tximport
rnaseq
R
updated 10 months ago by
Eva
• 0 • written 8.3 years ago by
ctl
• 0
12
votes
13
replies
10k
views
GSEA many significant gene sets despite no differentially expressed genes
GSEA
GeneSetEnrichment
DifferentialExpression
updated 11 months ago by
ATpoint
★ 4.6k • written 2.9 years ago by
nhaus
▴ 70
17
votes
4
replies
9.9k
views
Tutorial:
Updated Support Site Editor
support.bioconductor.org
editor
markdown
updates
Tutorial
updated 10 months ago by
Mj.A.
• 0 • written 6.0 years ago by
shepherl
4.1k
5
votes
8
replies
9.8k
views
Limma design with continuous and categorical covariates
limma
batch effect
covariates
microarray
updated 9 months ago by
hortense96
• 0 • written 8.5 years ago by
dmcleanuk
▴ 30
3
votes
4
replies
9.4k
views
Gene-gene correlation analysis with RNA-seq
edgeR
updated 11 months ago by
JG13
• 0 • written 11.6 years ago by
Makis Motakis
▴ 30
7
votes
5
replies
9.3k
views
biomaRt server error, and mirrors do not help
ensembl
biomaRt
R
updated 9 weeks ago by
Ke
• 0 • written 2.7 years ago by
kieran.short
▴ 40
1
vote
7
replies
8.8k
views
scater runUMAP fails with error "function 'as_cholmod_sparse' not provided by package 'Matrix'"
runUMAP
scater
Matrix
updated 11 months ago by
Hervé Pagès
16k • written 14 months ago by
inzirio
▴ 10
6
votes
6
replies
8.7k
views
minfi support of illumina Infinium methylationEPIC v2.0
methylationEPICv2.0
minfi
updated 3 months ago by
wl_xxz
• 0 • written 22 months ago by
luca.s
▴ 50
9
votes
12
replies
8.7k
views
Multi factor design edgeR/Deseq2
deseq2
edgeR
rna-seq
updated 9 months ago by
Elizabeth
• 0 • written 9.6 years ago by
gthm
▴ 30
9
votes
38
replies
8.5k
views
manipulate bedpe format files
GRanges
bedpe
structural variants
rtracklayer
written 9.0 years ago by
tangming2005
▴ 200
12
votes
5
replies
8.3k
views
Theoretical WGCNA Question
WGCNA
Theory
Scale-Free Topology
updated 9 months ago by
Garrett
• 0 • written 9.8 years ago by
brohawndg
▴ 150
4
votes
16
replies
8.3k
views
Normalised counts from RUVg in RUVSeq
RUVg
ruvseq
rnaseq
updated 10 months ago by
Shaimaa Gamal
• 0 • written 9.7 years ago by
Pauly Lin
▴ 160
1
vote
3
replies
8.2k
views
problem in installing Bio conductor package
bioconductorpackages
Install
updated 11 months ago by
Guru
• 0 • written 4.2 years ago by
k200987
• 0
9
votes
14
replies
8.0k
views
Where can I find EnsDb.Hsapiens.v105?
Ensembl
Rstudio
ensembldb
AnnotationHub
ensdb
updated 6 months ago by
shepherl
4.1k • written 3.0 years ago by
jon.klonowski
▴ 40
16
votes
12
replies
7.9k
views
Diffbind: edgeR or DESeq2 ?
diffbind
medip-seq
edger
deseq2
updated 4 months ago by
khanwaled68
• 0 • written 8.9 years ago by
florian.noack
▴ 60
10
votes
41
replies
7.6k
views
Ensembl plants at annotationHub?
ensembl
ensembldb
plant
arabidopsis thaliana
annotationhub
updated 8 months ago by
Daniele
• 0 • written 6.2 years ago by
Guido Hooiveld
★ 4.1k
0
votes
4
replies
7.4k
views
Any tools to convert .gff to .gtf format
AnnotationData
CrispRdesignR
BSgenome
updated 29 days ago by
ControlF5
• 0 • written 2.4 years ago by
Manoj Kumar R
• 0
0
votes
12
replies
7.3k
views
ChAMP input: Beta Matrix?
champ
dmr analysis
updated 7 months ago by
tahirah.yasmin2014
• 0 • written 8.9 years ago by
Shicheng Guo
• 0
6
votes
12
replies
7.2k
views
BiocFileCache/ExperimentHub/AnnotationHub temporary ERROR
BiocFileCache
AnnotationHub
ExperimentHub
15 months ago • updated 9 months ago
shepherl
4.1k
17
votes
9
replies
7.2k
views
How to use removeBatchEffect for removing effect of multiple confounding variables
limma
removebatcheffect
deseq2
updated 4 months ago by
James W. MacDonald
67k • written 8.7 years ago by
ompandey
▴ 10
7
votes
28
replies
7.2k
views
Rsubread::featureCounts extremely slow on some annotations
rsubread
featurecounts
updated 11 months ago by
Gordon Smyth
52k • written 9.9 years ago by
Ryan C. Thompson
★ 7.9k
7
votes
4
replies
7.0k
views
WGCNA sample size minimum: why?
wgcna
updated 6 months ago by
Edoardo
• 0 • written 5.5 years ago by
charles.foster
▴ 160
8
votes
5
replies
6.9k
views
Understanding interaction term in DESeq2
deseq2
design formula
log fold change
updated 5 months ago by
Michael Love
43k • written 4.5 years ago by
jason.taotaotan
▴ 40
6
votes
3
replies
6.5k
views
DESeq2 with proteomics data
deseq2
updated 4 months ago by
Michael Love
43k • written 6.5 years ago by
shyu
▴ 10
1
vote
7
replies
6.5k
views
DESeq2 with unbalanced experimental design
deseq2
updated 3 months ago by
Satoshi
• 0 • written 9.9 years ago by
celine
• 0
8
votes
6
replies
6.5k
views
Using the plotting functions of clusterProfiler / enrichplot with enrichment results from other programs
clusterProfiler
enrichplot
updated 8 months ago by
jovel_juan
▴ 30 • written 5.7 years ago by
charles.foster
▴ 160
1
vote
9
replies
6.4k
views
Installing Bioconductor packages in Docker
Bioconductor
DOCKER
RShiny
updated 4 months ago by
devarti.mahakalkar
• 0 • written 4.0 years ago by
adklts
• 0
3
votes
11
replies
6.3k
views
GO enrichment analysis on Solanum lycopersicum proteomics dataset (UniProt IDs)
clusterProfiler
AnnotationHub
GO
uniprot
updated 11 months ago by
Guido Hooiveld
★ 4.1k • written 4.0 years ago by
Alberto
• 0
2
votes
13
replies
5.3k
views
Tximport with RSEM error
RSEM
updated 10 weeks ago by
Michael Love
43k • written 7.3 years ago by
hs.lansdell
▴ 20
6
votes
11
replies
5.3k
views
How to properly average normalized counts of biological replicates
DESeq2
Normalization
RNASeqR
updated 10 months ago by
Priya
• 0 • written 3.9 years ago by
Marina
▴ 40
2
votes
2
replies
5.1k
views
Unable to install the package "tissuesGeneExpression"
bioconductor
updated 6 months ago by
Muhammad Abdullah
• 0 • written 7.5 years ago by
mdroog
▴ 10
2
votes
9
replies
4.9k
views
enrichGOgradient color change
clusterProfiler
updated 24 days ago by
lewis.roper
• 0 • written 14 months ago by
inna.gur
• 0
12
votes
5
replies
4.8k
views
Rsamtools is not available for (for R version 4.0.2)
Rsamtools
updated 6 months ago by
Paul
• 0 • written 4.6 years ago by
yusuke_suita
▴ 40
3
votes
5
replies
4.8k
views
plotMDS in edgeR
edger
rnaseq
written 9.3 years ago by
gthm
▴ 30
1,430 results • Page
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Answer: Postdoc/RA position: Software Engineer For R and High-Performance Computing
by
delhirussianescortscom
• 0
Our escorts are well-groomed and well-trained to give you ultimate seduction and deep pleasure. If you're looking for hot Delhi air hostess…
Answer: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio
by
Robert Castelo
★ 3.4k
Following the discussion of this post, the package [gDNAx](https://bioconductor.org/packages/gDNAx) has been fixed in devel and release 1.4…
Answer: Selection of correct coefficients or contrasts in DESeq2
by
James W. MacDonald
67k
Using R's model formulation for three-way interactions is probably not the way to go here. Or at least I wouldn't do it that way. An easier…
Comment: How to generate circular cnetplot and color nodes and edges in the same plot ?
by
Blandine
• 0
Thank you so much ! It's working !
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K?
by
James W. MacDonald
67k
Yes. If you have the Illumina IDs, then all the annotation data that `cpg.annotate` uses will be based on hg19. It doesn't matter if TCGA l…
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A: DESeq2 interaction term
Comment: Recount3 data correspond to TCGA data
Answer: DESeq2- merging technical vs biological replicates
Answer: SingleCellExperiment convenience function for metadata+expression?
How to correct for tumor purity using DESeq2 to analyze TCGA tumor sample expression.
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