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nanostringdiff
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1.4k
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fgsea/clusterProfiler Packages for nCounter data enrichment analysis
NanoStringDiff
clusterProfiler
fgsea
17 months ago
pg45863
▴ 10
0
votes
2
replies
1.2k
views
Nanostring data differential expression analysis: limma or DESeq2?
DESeq2
NanoStringDiff
limma
18 months ago
pg45863
▴ 10
0
votes
1
reply
827
views
Micro Array GEO data analysis
GEOquery
MicroarrayData
Normalization
Microarray
NanoStringDiff
updated 21 months ago by
James W. MacDonald
67k • written 21 months ago by
Aleksandra
• 0
0
votes
2
replies
659
views
NanoStringDiff contrast vectors
NanoStringDiff
updated 23 months ago by
James W. MacDonald
67k • written 23 months ago by
Paraskevi
• 0
0
votes
0
replies
704
views
NanoStringDiff
DifferentialExpression
NanoStringDiff
2.9 years ago
sanrie10
• 0
5
votes
7
replies
1.8k
views
Nanostringdiff - defining contrast values for blocking variables in glm
limma
edgeR
DESeq2
NanoStringDiff
updated 3.2 years ago by
James W. MacDonald
67k • written 3.2 years ago by
reberya
• 0
3
votes
2
replies
1.2k
views
R NanoStringDiff: DE analysis, from 2 group comparison method how "logFC" generated?
Nan
NanoStringDiff
3.4 years ago
choijamts
• 0
3
votes
6
replies
2.2k
views
Why NanoStringDiff package so slow?
NanoStringDiff
NanoString
nCounter
DE analysis
updated 12 months ago by
georgersmith
• 0 • written 5.3 years ago by
lim6432
▴ 50
0
votes
0
replies
801
views
NanoStringDiff - housekeeping genes variation
NanoStringDiff
3.7 years ago
YM
• 0
1
vote
1
reply
1.1k
views
NanoStringDiff Not Recognized as Numeric
Bioconductor
Transcriptomics
NanoStringDiff
updated 4.1 years ago by
Laurent Gatto
1.6k • written 4.1 years ago by
Pedro
▴ 10
1
vote
7
replies
1.3k
views
NanoStringDiff glm.LRT not finishing after 20 hours
NanoStringDiff
4.8 years ago
stephen.pollo
• 0
0
votes
2
replies
1.0k
views
NanoStringDiff correction for variation between patient
NanoStringDiff
GLM
Gene expression
updated 5.2 years ago by
James W. MacDonald
67k • written 5.2 years ago by
Guillaume Robert
• 0
3
votes
3
replies
1.6k
views
NanoStringDiff counts not numeric
NanoStringDiff
updated 9 months ago by
pjanas
• 0 • written 5.5 years ago by
noelleenright
▴ 10
1
vote
6
replies
2.2k
views
How to access normalized data in the NanoStringDiff package?
nanostringdiff
nanostring
NanoStringDiff
updated 6.4 years ago by
James W. MacDonald
67k • written 6.4 years ago by
casey.rimland
▴ 170
0
votes
0
replies
1.5k
views
design matrix and contrast for paired experiment using NanoStringDiff for nCounter data
nanostring
NanoStringDiff
design and contrast matrix
differential gene expression
ncounter
7.3 years ago
c.kohler
• 0
15 results • Page
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Replies
Comment: How to extract phastcons score for all protein coding genes and lncRNAs using Ge
by
Robert Castelo
★ 3.4k
Hi, this is a long comment thread on 4-year old post, please open a new post with you question. To increase the odds of getting useful answ…
Answer: DESeq2 rerun returns different results
by
ATpoint
★ 4.5k
DESeq2 is deterministic if you use same input, code and software versions. Make sure to version-control your environment by at least tracki…
Answer: [How to construct a model.matrix ]
by
Gordon Smyth
51k
> Initially, I simply used > `lm(Epigenetic_age ~ Age_group + Age + Sex + PC1 + PC2 + PC3 + PC4 + PC5 + B + CD4T + CD8T + Mono + NK + Neutr…
Comment: How to extract phastcons score for all protein coding genes and lncRNAs using Ge
by
rania.alanany
• 0
Hi Robert, Thank you for the explanation, But I am still little bit confused, Is the annotation package (TxDb.Hsapiens.UCSC.hg38.knownGene)…
Comment: Merge Replicates vs Mixed Model
by
abadgerw
• 0
@gabrielhoffman any insight?
Votes
Comment: ColData and ERROR: rows did not converge in beta, labelled in mcols(object)$beta
A: Some questions for remove batch effect by using mnnCorrect
A: Recommendations for combining multiple 10x runs into one SingleCellExperiment
Answer: [How to construct a model.matrix ]
Answer: Handling biological replicates in DESeq2
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Robert Castelo
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Michael Stadler
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ATpoint
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James W. MacDonald
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