Showing : MAST • reset
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180
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Confidence interval contains 0 but p<0.05
MAST
4 months ago Adelyn • 0
3
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3
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1.2k
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Robust way of dealing with low number of samples for Differential Gene Expression
limma edgeR DESeq2 MAST
written 5 months ago by • 0
0
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1
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629
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Which input data is acceptable for MAST?
SCTransform MAST
updated 6 months ago by ▴ 280 • written 6 months ago by • 0
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0
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402
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Z-score Interpretation across components
MAST
7 months ago GJ • 0
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0
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381
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MAST package: Most appropriate way to perform lrTest for effect of factor with multiple levels in pairwise manner?
MAST
9 months ago Kelly • 0
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0
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598
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Linear Mixed Model for Differential Gene Expression in Single-Cell RNAseq with Batch Effects
lmer MAST DifferentialExpression
9 months ago nhaus ▴ 70
1
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2
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916
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Extracting genomic sequences using agat and bedtools yields different results
MAST
updated 13 months ago by ★ 4.8k • written 13 months ago by • 0
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0
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840
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Error: grouping factors must have > 1 sampled level
Mast mastR MAST
updated 13 months ago by 68k • written 13 months ago by • 0
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0
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415
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Comparing the effects of a condition over time in two seperate tissues
MAST
14 months ago Dillon • 0
0
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1
reply
805
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Mismatch between MAST DE results and expression dot plot
MAST mastR
15 months ago Simon • 0
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0
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812
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How to extract P-Values and LogFC from lrTest in MAST?
pvalue logFC lrtest MAST
2.0 years ago Tadeoye ▴ 20
1
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7
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2.2k
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Likelihood ratio test (lrTest) in MAST comparing full to reduced model; and another question on controlling for CDR
MAST
2.1 years ago Ken C • 0
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0
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683
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MAST for single cell ATAC data
MAST
2.2 years ago zuljiamel1991 ▴ 10
2
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2
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2.6k
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Input for MAST
MAST
2.2 years ago • updated 2.1 years ago zuljiamel1991 ▴ 10
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0
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1.6k
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How to interpret MAST coefficients
DifferentialExpression MAST
2.5 years ago Ismail • 0
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0
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757
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How does MAST caculate log fc
MAST
2.7 years ago Chenghao • 0
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0
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940
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Differential expression with single cell data: any good two component (hurdle) models recently?
SingleCellWorkflow DifferentialExpression SingleCell SingleCellMultiModal MAST
2.8 years ago Nik Tuzov ▴ 90
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0
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1.1k
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Performing DGE analysis with MAST on a variable with more than 2 levels
MAST DEG SingleCell
3.0 years ago zroger499 • 0
0
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1
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1.4k
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Low logFCs using MAST for scRNA-seq
MAST
updated 8 months ago by ▴ 70 • written 3.1 years ago by • 0
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0
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1.1k
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Issues geting meaninfull results for single cell DGE using MAST
MAST SingleCell
3.3 years ago zroger499 • 0
1
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0
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874
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When I run `zlm` with several clusters, how to compare 1 cluster versus all the others?
MAST
3.7 years ago Dan • 0
0
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1
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1.3k
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Differentially expressed genes across three different conditions
MAST SingleCell diffGeneAnalysis
updated 3.8 years ago by 68k • written 3.8 years ago by • 0
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1
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1.2k
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MAST zlm shows warning: Coefficients ... are never estimible and will be dropped.
MAST
updated 3.9 years ago by • 0 • written 4.2 years ago by • 0
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1
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1.6k
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How to do pairwise multiple comparisons in MAST
MAST
updated 9 months ago by • 0 • written 4.2 years ago by • 0
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2
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1.6k
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MAST compare two conditions with several donors
MAST
updated 4.2 years ago by • 0 • written 4.5 years ago by • 0
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3
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1.9k
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MAST invalid Hypothesis, class objectORconnection error
R MAST scRNASeq
4.7 years ago TriS ▴ 200
1
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3
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1.8k
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comparing 2 models with confounders with MAST (scRNA-seq DEA)
scRNA-seq MAST confounders
updated 5.3 years ago by ▴ 280 • written 5.3 years ago by ▴ 10
0
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1
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1.9k
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About getting DE genes using MAST
MAST
updated 5.3 years ago by ▴ 280 • written 5.3 years ago by • 0
0
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0
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1.2k
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DEG among experimental and control group in MAST
MAST DEG batch effects
5.6 years ago chendianyu • 0
0
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1
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2.4k
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Minimum number of cells required for the MAST
MAST scRNAseq differential expression
5.6 years ago Andrew_McDavid ▴ 280
2
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3
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1.6k
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Logistic regression in MAST - question
mast
updated 6.1 years ago by ▴ 280 • written 6.1 years ago by ▴ 90
2
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7
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2.2k
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Estimation of non-trivial contrasts in MAST
mast
updated 6.1 years ago by ▴ 280 • written 6.1 years ago by ▴ 90
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1
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1.4k
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How can I compute AIC for MAST hurdle model fitted in the whole dataset?
MAST AIC calcuation Parameters single cell hurdle model
updated 13 months ago by ▴ 30 • written 6.2 years ago by • 0
0
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2
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1.6k
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Warning in bayes fit in MAST GSEA
MAST GSEA bayesglm.fit
6.6 years ago santos22903 • 0
0
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6
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1.9k
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Error in zlm function model matrix
MAST
7.0 years ago jka8119 ▴ 10
2
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4
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2.4k
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Interpretation of cngeneson when doing differential expression analysis in MAST
mast differential gene expression
updated 7.0 years ago by ▴ 280 • written 7.0 years ago by ▴ 40
2
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1
reply
3.2k
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MAST: testing differential expression with a nested factorial design
MAST single-cell rna-seq
updated 7.0 years ago by ▴ 280 • written 7.0 years ago by ▴ 20
2
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1
reply
1.3k
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How to load data csv in MAST
mast
7.0 years ago francesco.brundu@gmail.com ▴ 40
0
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4
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1.7k
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MAST: What does the function gseaAfterBoot do exactly?
MAST
7.1 years ago dfm2129 • 0
0
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8
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2.4k
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MAST - not getting Hurdle p values
MAST
updated 7.2 years ago by ▴ 280 • written 7.2 years ago by ▴ 10
2
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3
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2.6k
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Using MAST with DropSeq data
MAST mast dropseq
updated 7.2 years ago by ▴ 280 • written 7.2 years ago by ▴ 10
5
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3
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2.6k
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single-cells RNA-seq analysis by MAST with unbalanced group size
mast single-cell rna-seq differential analysis
updated 23 days ago by ▴ 10 • written 7.3 years ago by ▴ 100
0
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2
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1.7k
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What is the most useful distance measure to use for cell clustering based on MAST deviance residuals?
MAST
7.6 years ago alexanderaivazidis • 0
3
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3
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3.2k
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How do you test a contrast in MAST?
MAST single-cell differential gene expression
updated 7.6 years ago by ▴ 280 • written 7.6 years ago by ▴ 40
4
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1
reply
2.2k
views
NAs in continuous coefficient and fold change in `zlm`
scrnaseq MAST differential gene expression
7.7 years ago Andrew_McDavid ▴ 280
2
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1
reply
5.0k
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Intepretation of Z scores for gene set enrichment analysis in MAST
MAST scRNA GSEA
updated 7.7 years ago by ▴ 280 • written 7.7 years ago by • 0
0
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3
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1.9k
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Modeling Dose-response data in MAST
MAST sc-rnaseq scrnaseq
updated 7.8 years ago by ▴ 280 • written 7.8 years ago by • 0
0
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1
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1.6k
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Removal of batch effects before non-linear clustering for scRNAseq
scrnaseq MAST
8.0 years ago Andrew_McDavid ▴ 280
3
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2
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2.8k
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MAST reported warning "Coefficients ... are never estimible and will be dropped."
mast sc-rnaseq
8.1 years ago • updated 8.0 years ago shao ▴ 100
49 results • Page 1 of 1
Recent ...
Replies
Comment: Differing results with DESeq2 by JKim • 0
My two cents. I think it would be more straightforward if you use cellmeans model. Have a look at [A guide to creating design matrices for …
Answer: CluserProfiler message "No gene can be mapped" by James W. MacDonald 68k
Your gene IDs are things like this: `Mpyr-NLJ1B.v3.hap1.scaffold1.g290550`, and the genes in your term2gene table are things like this: `Mp…
Answer: RNA-seq input to GRaNIE by James W. MacDonald 68k
This is [covered in the vignette.][1] [1]: https://bioconductor.org/packages/release/bioc/vignettes/GRaNIE/inst/doc/GRaNIE_packageDe…
Answer: Help using reduceSimMatrix with a custom annotation by sergisayolspuig ▴ 80
Hi there, `reduceSimMatrix()` expects a "GOALL" keytype in the OrgDb object when called with `children=TRUE` (which is the default for thi…
Answer: Analyzing TnSeq data with DESeq2 by cold.wolverine.arku • 0
That's a great use case of DESeq2! Even though it's not specifically tailored for TnSeq data, your approach to normalize and run explorator…
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A: Unbalanced experiment with multiple samples from each patient.
A: Understanding contrasts limma
Answer: ROAST for small sets
Answer: ROAST for small sets
A: conceptual question about FDR, FDR adjusted p-value and q-value
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