Showing : mast • reset
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305
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Confidence interval contains 0 but p<0.05
MAST
13 months ago Adelyn • 0
3
votes
3
replies
1.6k
views
Robust way of dealing with low number of samples for Differential Gene Expression
limma edgeR DESeq2 MAST
written 14 months ago by • 0
0
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1
reply
1.0k
views
Which input data is acceptable for MAST?
SCTransform MAST
updated 15 months ago by ▴ 280 • written 15 months ago by • 0
0
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0
replies
510
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Z-score Interpretation across components
MAST
16 months ago GJ • 0
0
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0
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583
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MAST package: Most appropriate way to perform lrTest for effect of factor with multiple levels in pairwise manner?
MAST
18 months ago Kelly • 0
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0
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853
views
Linear Mixed Model for Differential Gene Expression in Single-Cell RNAseq with Batch Effects
lmer MAST DifferentialExpression
18 months ago nhaus ▴ 70
1
vote
2
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1.4k
views
Extracting genomic sequences using agat and bedtools yields different results
MAST
updated 22 months ago by ★ 5.0k • written 22 months ago by • 0
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0
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1.1k
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Error: grouping factors must have > 1 sampled level
Mast mastR MAST
updated 22 months ago by 68k • written 22 months ago by • 0
0
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0
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580
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Comparing the effects of a condition over time in two seperate tissues
MAST
23 months ago Dillon • 0
0
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1
reply
1.1k
views
Mismatch between MAST DE results and expression dot plot
MAST mastR
2.0 years ago Simon • 0
0
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0
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1.0k
views
How to extract P-Values and LogFC from lrTest in MAST?
pvalue logFC lrtest MAST
2.7 years ago Tadeoye ▴ 20
1
vote
7
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2.8k
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Likelihood ratio test (lrTest) in MAST comparing full to reduced model; and another question on controlling for CDR
MAST
2.9 years ago • updated 2.8 years ago Ken C • 0
0
votes
0
replies
856
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MAST for single cell ATAC data
MAST
2.9 years ago zuljiamel1991 ▴ 10
2
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2
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3.0k
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Input for MAST
MAST
2.9 years ago zuljiamel1991 ▴ 10
0
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1
reply
2.5k
views
How to interpret MAST coefficients
DifferentialExpression MAST
updated 7 months ago by ▴ 10 • written 3.3 years ago by • 0
0
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1
reply
1.4k
views
How does MAST caculate log fc
MAST
3.4 years ago • updated 7 months ago Chenghao ▴ 10
0
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0
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1.2k
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Differential expression with single cell data: any good two component (hurdle) models recently?
SingleCellWorkflow DifferentialExpression SingleCell SingleCellMultiModal MAST
3.6 years ago Nik Tuzov ▴ 90
0
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0
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1.3k
views
Performing DGE analysis with MAST on a variable with more than 2 levels
MAST DEG SingleCell
3.7 years ago zroger499 • 0
0
votes
1
reply
1.6k
views
Low logFCs using MAST for scRNA-seq
MAST
updated 16 months ago by ▴ 70 • written 3.8 years ago by • 0
0
votes
0
replies
1.3k
views
Issues geting meaninfull results for single cell DGE using MAST
MAST SingleCell
4.0 years ago zroger499 • 0
1
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0
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1.0k
views
When I run `zlm` with several clusters, how to compare 1 cluster versus all the others?
MAST
4.5 years ago Dan • 0
0
votes
1
reply
1.5k
views
Differentially expressed genes across three different conditions
MAST SingleCell diffGeneAnalysis
updated 4.6 years ago by 68k • written 4.6 years ago by • 0
0
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1
reply
1.4k
views
MAST zlm shows warning: Coefficients ... are never estimible and will be dropped.
MAST
updated 4.6 years ago by • 0 • written 4.9 years ago by • 0
0
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1
reply
1.9k
views
How to do pairwise multiple comparisons in MAST
MAST
updated 18 months ago by • 0 • written 4.9 years ago by • 0
0
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2
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1.9k
views
MAST compare two conditions with several donors
MAST
updated 5.0 years ago by • 0 • written 5.2 years ago by • 0
0
votes
3
replies
2.1k
views
MAST invalid Hypothesis, class objectORconnection error
R MAST scRNASeq
5.4 years ago TriS ▴ 200
1
vote
3
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2.1k
views
comparing 2 models with confounders with MAST (scRNA-seq DEA)
scRNA-seq MAST confounders
updated 6.0 years ago by ▴ 280 • written 6.0 years ago by ▴ 10
0
votes
1
reply
2.1k
views
About getting DE genes using MAST
MAST
updated 6.1 years ago by ▴ 280 • written 6.1 years ago by • 0
0
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0
replies
1.3k
views
DEG among experimental and control group in MAST
MAST DEG batch effects
6.3 years ago chendianyu • 0
0
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1
reply
2.7k
views
Minimum number of cells required for the MAST
MAST scRNAseq differential expression
6.4 years ago Andrew_McDavid ▴ 280
2
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3
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1.9k
views
Logistic regression in MAST - question
mast
updated 6.9 years ago by ▴ 280 • written 6.9 years ago by ▴ 90
2
votes
7
replies
2.6k
views
Estimation of non-trivial contrasts in MAST
mast
updated 6.9 years ago by ▴ 280 • written 6.9 years ago by ▴ 90
0
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1
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1.7k
views
How can I compute AIC for MAST hurdle model fitted in the whole dataset?
MAST AIC calcuation Parameters single cell hurdle model
updated 22 months ago by ▴ 30 • written 6.9 years ago by • 0
0
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2
replies
1.8k
views
Warning in bayes fit in MAST GSEA
MAST GSEA bayesglm.fit
7.4 years ago santos22903 • 0
0
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6
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2.3k
views
Error in zlm function model matrix
MAST
7.7 years ago jka8119 ▴ 10
2
votes
4
replies
2.7k
views
Interpretation of cngeneson when doing differential expression analysis in MAST
mast differential gene expression
updated 7.7 years ago by ▴ 280 • written 7.7 years ago by ▴ 40
2
votes
1
reply
1.5k
views
How to load data csv in MAST
mast
7.8 years ago francesco.brundu@gmail.com ▴ 40
2
votes
1
reply
3.7k
views
MAST: testing differential expression with a nested factorial design
MAST single-cell rna-seq
updated 7.8 years ago by ▴ 280 • written 7.8 years ago by ▴ 20
0
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4
replies
1.9k
views
MAST: What does the function gseaAfterBoot do exactly?
MAST
7.8 years ago dfm2129 • 0
0
votes
8
replies
2.7k
views
MAST - not getting Hurdle p values
MAST
updated 7.9 years ago by ▴ 280 • written 7.9 years ago by ▴ 10
2
votes
3
replies
2.9k
views
Using MAST with DropSeq data
MAST mast dropseq
updated 7.9 years ago by ▴ 280 • written 7.9 years ago by ▴ 10
5
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3
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3.0k
views
single-cells RNA-seq analysis by MAST with unbalanced group size
mast single-cell rna-seq differential analysis
updated 9 months ago by ▴ 10 • written 8.0 years ago by ▴ 100
0
votes
2
replies
2.0k
views
What is the most useful distance measure to use for cell clustering based on MAST deviance residuals?
MAST
8.3 years ago alexanderaivazidis • 0
3
votes
3
replies
3.6k
views
How do you test a contrast in MAST?
MAST single-cell differential gene expression
updated 8.3 years ago by ▴ 280 • written 8.3 years ago by ▴ 40
4
votes
1
reply
2.6k
views
NAs in continuous coefficient and fold change in `zlm`
scrnaseq MAST differential gene expression
8.4 years ago Andrew_McDavid ▴ 280
2
votes
1
reply
5.4k
views
Intepretation of Z scores for gene set enrichment analysis in MAST
MAST scRNA GSEA
updated 8.5 years ago by ▴ 280 • written 8.5 years ago by • 0
0
votes
3
replies
2.1k
views
Modeling Dose-response data in MAST
MAST sc-rnaseq scrnaseq
updated 8.5 years ago by ▴ 280 • written 8.5 years ago by • 0
0
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1
reply
1.8k
views
Removal of batch effects before non-linear clustering for scRNAseq
scrnaseq MAST
8.7 years ago Andrew_McDavid ▴ 280
3
votes
2
replies
3.1k
views
MAST reported warning "Coefficients ... are never estimible and will be dropped."
mast sc-rnaseq
8.8 years ago shao ▴ 100
49 results • Page 1 of 1
Recent ...
Replies
Answer: When to use edgeR or limma by Gordon Smyth 53k
The short answer is that we generally prefer edgeR for applications with lots of small counts and limma for complex designs with random eff…
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
I updated the above answer today.
Answer: When to use edgeR or limma by James W. MacDonald 68k
I would use edgeR's quasi-likelihood model for any analysis with a smaller number of observations (like 3 vs 3 or similar), but if you have…
Answer: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
The short answer is that limpa reads standard feature-level intensities from Spectronaut or other quantifications tools. limpa is designed …
Comment: Question about the filterByExpr function inputs in edgeR by mohammedtoufiq91 ▴ 10
@gordonsmyth Noted, thank you very much.
Votes
A: deseq2 - paired samples in 2 sequencing types with very different library sizes
Comment: Question about the filterByExpr function inputs in edgeR
Answer: Question about the filterByExpr function inputs in edgeR
Answer: Question about the filterByExpr function inputs in edgeR
A: DESeq2: What is the unit of DESeq2 normalized read count (VST)? Is it tag per mi
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