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8
replies
3.0k
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Two controls in RNAseq formula for DESeq2
deseq2
formula
controls
design
updated 6.5 years ago by
Michael Love
43k • written 6.5 years ago by
taveluz
• 0
0
votes
2
replies
4.4k
views
DESeq2: How to correct for multiple comparisons
deseq2
updated 6.5 years ago by
Michael Love
43k • written 6.5 years ago by
NG
• 0
0
votes
6
replies
2.5k
views
analysis of multiple batches and multiple treatment conditions in scRNA-seq
limma
deseq2
edger
scRNAseq
combat
updated 6.5 years ago by
Andrew_McDavid
▴ 280 • written 6.5 years ago by
Bogdan
▴ 670
2
votes
2
replies
1.3k
views
vcountPDict fails on PDict
Biostrings
updated 6.5 years ago by
Hervé Pagès
16k • written 6.5 years ago by
Aditya
▴ 160
0
votes
0
replies
601
views
Research Associate in statistical modelling
Icens truncation
6.5 years ago
fabiana.gordon
• 0
1
vote
6
replies
2.1k
views
Can't install TopmedPipeline Package
TopmedPipeline
updated 6.5 years ago by
shepherl
4.3k • written 6.5 years ago by
winstondunnmd
▴ 10
1
vote
4
replies
1.1k
views
Is the colnames of model.matrix on the page 34 in edgeR User's Guide?
edger
updated 6.5 years ago by
Gordon Smyth
53k • written 6.5 years ago by
2002ymx02
• 0
0
votes
0
replies
1.1k
views
pathview : kegg gene ID in the visualisation ?
pathview
6.5 years ago
cedric.vmdl
• 0
1
vote
3
replies
2.0k
views
seqVCF2GDS Error Converting VCF to GDS file
software error
SeqArray
seqVCF2GDS
updated 6.5 years ago by
zhengx
▴ 30 • written 6.5 years ago by
winstondunnmd
▴ 10
2
votes
2
replies
1.6k
views
How to create two columns for model matrix used in limma?
limma
edger
updated 6.5 years ago by
Gordon Smyth
53k • written 6.5 years ago by
Ahdee
▴ 60
8
votes
5
replies
5.6k
views
the normalization methods of MRN and TMM methods supplied by DESeq2 and edgeR
normalization
DESeq2
edgeR
updated 6.5 years ago by
Gordon Smyth
53k • written 6.5 years ago by
15958021290
▴ 10
4
votes
8
replies
26k
views
Variance stabilising transformation for machine learning
deseq2
vst
rna-seq
machine-learning
updated 6.5 years ago by
Michael Love
43k • written 6.5 years ago by
Manik Garg
▴ 20
0
votes
1
reply
796
views
DESeq2 question about design formula with nested variables
deseq2
updated 6.5 years ago by
Michael Love
43k • written 6.5 years ago by
Bash
• 0
0
votes
8
replies
1.4k
views
Suggestions for avoiding False Positives while identifying differentially expressed genes with more than 3 samples per group
deseq2
updated 6.5 years ago by
Michael Love
43k • written 6.5 years ago by
HD
• 0
0
votes
4
replies
1.6k
views
tximport query for un-normalized and TPM data
tximport
updated 6.5 years ago by
Michael Love
43k • written 6.5 years ago by
HKS
• 0
0
votes
8
replies
3.0k
views
tximport not working on tsv files
tximport
6.5 years ago
HKS
• 0
0
votes
2
replies
2.0k
views
a newbie question on ConsensusClusterPlus
consensusclusterplus
heatmap
6.5 years ago
niki.nowhere
• 0
2
votes
3
replies
1.9k
views
DEP package: error in plot_heatmap
DEP
updated 6.5 years ago by
arne.smits
▴ 70 • written 6.5 years ago by
Rob
• 0
0
votes
0
replies
1.1k
views
SPME-GC-MS: metaMS missing peaks. Improve performance vs AMDIS.
metams
6.5 years ago
ryan.high
• 0
0
votes
2
replies
4.2k
views
R Version 3.6.1
software error
Tutorial
updated 6.5 years ago by
Laurent Gatto
1.6k • written 6.5 years ago by
naeemurself
• 0
7
votes
4
replies
3.3k
views
RNA-seq normalization without filtering
deseq2
edger
normalization
RNAseq
updated 6.5 years ago by
Steve Lianoglou
★ 13k • written 6.5 years ago by
Lin
▴ 50
0
votes
3
replies
1.5k
views
Diffbind batch effect blocking error
Diffbind
ATAC
batch correction
blocking factor
updated 6.5 years ago by
Rory Stark
★ 5.2k • written 6.5 years ago by
rm1238
• 0
1
vote
5
replies
4.8k
views
how to get normalized count data from edgeR using TMM methods
edger
normalization
6.5 years ago
15958021290
▴ 10
1
vote
5
replies
2.3k
views
custom gatingMethod not functioning / registering as expected (openCyto) (minDensity)
openCyto
registerPlugin
gatingMethod
minDensity
6.5 years ago
k.teijgeler
• 0
1
vote
1
reply
1.4k
views
pRoloc - phenoDisco - issue with example
pRoloc
phenoDisco
fcol
updated 6.5 years ago by
Laurent Gatto
1.6k • written 6.5 years ago by
johnscrn
• 0
0
votes
4
replies
1.5k
views
design matrix for 4 groups in edgeR
edger
updated 6.5 years ago by
Gordon Smyth
53k • written 6.5 years ago by
sandraggava
• 0
0
votes
0
replies
1.0k
views
News:
Course in Berlin- Genomics with R and Bioconductor - September 16-20
deseq2
edger
limma
News
6.5 years ago
info
▴ 10
1
vote
2
replies
877
views
abnormal deseq2 normalization
deseq2
updated 6.5 years ago by
Michael Love
43k • written 6.5 years ago by
Charls
• 0
1
vote
3
replies
1.6k
views
k argument in buildSNNGraph
scran
updated 6.5 years ago by
Aaron Lun
★ 29k • written 6.5 years ago by
Angelos Armen
• 0
0
votes
1
reply
1.1k
views
Eliminate redundancy in biomaRt (2.38.0) query
biomaRt
Ensembl
updated 6.5 years ago by
Mike Smith
★ 6.6k • written 6.5 years ago by
olibee1315
• 0
5
votes
3
replies
1.7k
views
DESeq2 with multiple treatments but no replicates
deseq2
rna-seq
updated 6.5 years ago by
Michael Love
43k • written 6.5 years ago by
jpc41
▴ 20
1
vote
1
reply
2.4k
views
DESeq2 test LRT or WALD
deseq2
LRT
WALD
updated 6.5 years ago by
Michael Love
43k • written 6.5 years ago by
annesoalvarez
• 0
0
votes
2
replies
2.0k
views
lfcShrink in DESeq2
deseq2
apeglm
updated 6.5 years ago by
Michael Love
43k • written 6.5 years ago by
Meghdad
• 0
1
vote
1
reply
1.9k
views
Using RUVs with known batches
ruvseq
deseq2
updated 6.5 years ago by
Michael Love
43k • written 6.5 years ago by
Frederik Ziebell
▴ 30
0
votes
0
replies
815
views
Adding standard error bars to points on an Anaquin correlation plot
sequin correlations
error bars
plotLinear
Anaquin
6.5 years ago
William.Glynn
• 0
5
votes
1
reply
5.7k
views
Error with DropletUtils::EmptyDrops()
DropletUtils
EmptyDrops
simpleSingleCell
updated 3.5 years ago by
Stefano Mangiola
▴ 40 • written 6.5 years ago by
shbrief
▴ 20
0
votes
4
replies
5.2k
views
edgeR DGEList and design matrix
edger
DGE
updated 6.5 years ago by
Yunshun Chen
▴ 900 • written 6.5 years ago by
ctstackh
• 0
4
votes
4
replies
6.3k
views
TMM Normalization: DESeqDataSet: some values in assay are negative
deseq2
deseq
normalization
updated 6.5 years ago by
wunderl
▴ 40 • written 6.5 years ago by
neekonsu
• 0
2
votes
4
replies
1.1k
views
understanding DEseq2 interactions before/after releveling the baseline
deseq2
updated 6.5 years ago by
Michael Love
43k • written 6.5 years ago by
assaf www
▴ 140
1
vote
0
replies
1.3k
views
Cell cycle analysis subG1
flowploidy
apoptosis
cell cycle
flowCore
6.5 years ago
nina.hahn
• 0
1
vote
1
reply
1.3k
views
Request for offset slot in DESeqDataSet objects
deseq2
EDASeq
updated 6.5 years ago by
Michael Love
43k • written 6.5 years ago by
jeroen.gilis
▴ 100
0
votes
1
reply
1.7k
views
Help with installation of readat package
readat
error
updated 6.5 years ago by
shepherl
4.3k • written 6.5 years ago by
tbryson1
• 0
0
votes
0
replies
954
views
what is the role of 'itemLabels' in 'bhc' function
bhc
6.5 years ago
sk.rhyeu
• 0
1
vote
7
replies
2.7k
views
Error while running normOffsets in diffhic
diffhic
csaw
updated 6.5 years ago by
Aaron Lun
★ 29k • written 6.5 years ago by
shopnil99
• 0
0
votes
2
replies
1.5k
views
factorFootprints, bindingSites and Profile.segmentation
ATACSeqQC
factorFootprints
updated 6.5 years ago by
Julie Zhu
★ 4.3k • written 6.5 years ago by
Nick Gomez
• 0
1
vote
2
replies
1.0k
views
appropriate design formula
deseq2
updated 6.5 years ago by
Michael Love
43k • written 6.5 years ago by
mr6518849
▴ 10
1
vote
6
replies
3.7k
views
How to subset a BSgenome
BSgenome
BSgenome.Mmusculus.UCSC.mm10
updated 6.5 years ago by
shepherl
4.3k • written 6.5 years ago by
Aditya
▴ 160
0
votes
3
replies
1.2k
views
Most (90%) DE genes of a contrast were upregulated: implication on the assumptions of TMM-normalisation?
limma
edger
normalization
updated 6.5 years ago by
Gordon Smyth
53k • written 6.5 years ago by
mikhael.manurung
▴ 280
0
votes
1
reply
1.2k
views
unequal sample sizes in groups for testCovariate argument in dmrseq
dmrseq
6.5 years ago
Stephanie Hicks
▴ 80
0
votes
10
replies
3.4k
views
tximport Error in attr(x, "names") <- as.character(value) : 'names' attribute [2] must be the same length as the vector [1]
software error
RNAseq
tximport
R
updated 6.5 years ago by
Michael Love
43k • written 6.5 years ago by
ScafioRuo
• 0
46,742 results • Page
201 of 935
Recent ...
Replies
Comment: The Call for Abstracts for BioC2026 is open!
by
antoniodaniels990
• 0
All submitters must register for an account on the OpenReview submission system at least two weeks prior to the abstract deadline. To avoid…
Comment: using limma trend workflow in CAMERA
by
Gordon Smyth
53k
No, `trend.var=TRUE` and `trend=TRUE` are not needed in any voom pipeline, because the trend is already incorporated into the voom weights.
Comment: Questions about bacon QC and correction on EWAS results
by
Tikaaa2sahaaaq2c
• 0
In the world of mobile games, the 88ef game download has gained traction for its performance driven design [free download][1], similar to …
Comment: using limma trend workflow in CAMERA
by
A.Barden
▴ 20
Do you need to set trend.var=TRUE when using camera in the limma-voom pipeline with RNA-Seq data (as apposed to limma-trend pipeline)?
Comment: Upcoming Ensembl API and data access changes - new blog post available
by
Tikaaa2sahaaaq2c
• 0
Just as the Ensembl team transitions to a new platform for streamlined data access, diners can benefit from a digital newks menu prices con…
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Answer: What happens to genes with low dispersion during dispersion shrinkage in DESeq2
Comment: Are transformed values from rlog /vst log2 normalized counts?
Answer: Are transformed values from rlog /vst log2 normalized counts?
A: DESeq2 normalization vs VST vs rlog
Answer: How to directly decet the outlier samples (libraries) in EdgeR pipeline
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