Showing : mast • reset
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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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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
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
0
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6
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2.0k
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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
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
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
3
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3
replies
3.2k
views
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
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
5
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3
replies
2.6k
views
single-cells RNA-seq analysis by MAST with unbalanced group size
mast single-cell rna-seq differential analysis
updated 25 days ago by ▴ 10 • written 7.3 years ago by ▴ 100
2
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3
replies
2.6k
views
Using MAST with DropSeq data
MAST mast dropseq
updated 7.2 years ago by ▴ 280 • written 7.2 years ago by ▴ 10
3
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3
replies
1.2k
views
Robust way of dealing with low number of samples for Differential Gene Expression
limma edgeR DESeq2 MAST
written 6 months ago by • 0
0
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3
replies
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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3
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1.9k
views
MAST invalid Hypothesis, class objectORconnection error
R MAST scRNASeq
4.7 years ago TriS ▴ 200
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
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
0
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2
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1.6k
views
Warning in bayes fit in MAST GSEA
MAST GSEA bayesglm.fit
6.6 years ago santos22903 • 0
3
votes
2
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2.8k
views
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
2
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2
replies
2.6k
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Input for MAST
MAST
2.2 years ago • updated 2.1 years ago zuljiamel1991 ▴ 10
1
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2
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924
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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
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 7.1 years ago by ▴ 20
0
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1
reply
1.6k
views
Removal of batch effects before non-linear clustering for scRNAseq
scrnaseq MAST
8.0 years ago Andrew_McDavid ▴ 280
2
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1
reply
5.0k
views
Intepretation of Z scores for gene set enrichment analysis in MAST
MAST scRNA GSEA
updated 7.7 years ago by ▴ 280 • written 7.8 years ago by • 0
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
votes
1
reply
1.3k
views
How to load data csv in MAST
mast
7.0 years ago francesco.brundu@gmail.com ▴ 40
0
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1
reply
1.4k
views
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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1
reply
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
0
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1
reply
1.9k
views
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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1
reply
1.6k
views
How to do pairwise multiple comparisons in MAST
MAST
updated 9 months ago by • 0 • written 4.2 years ago by • 0
0
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1
reply
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
0
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1
reply
807
views
Mismatch between MAST DE results and expression dot plot
MAST mastR
15 months ago Simon • 0
0
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1
reply
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
0
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1
reply
632
views
Which input data is acceptable for MAST?
SCTransform MAST
updated 6 months ago by ▴ 280 • written 6 months ago by • 0
0
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1
reply
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
0
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0
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842
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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
0
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0
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381
views
MAST package: Most appropriate way to perform lrTest for effect of factor with multiple levels in pairwise manner?
MAST
9 months ago Kelly • 0
0
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0
replies
683
views
MAST for single cell ATAC data
MAST
2.2 years ago zuljiamel1991 ▴ 10
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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0
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940
views
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
1
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0
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875
views
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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0
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1.1k
views
Issues geting meaninfull results for single cell DGE using MAST
MAST SingleCell
3.3 years ago zroger499 • 0
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
0
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0
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402
views
Z-score Interpretation across components
MAST
7 months ago GJ • 0
0
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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
0
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0
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1.1k
views
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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0
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599
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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
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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0
replies
814
views
How to extract P-Values and LogFC from lrTest in MAST?
pvalue logFC lrtest MAST
2.0 years ago Tadeoye ▴ 20
0
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0
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180
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Confidence interval contains 0 but p<0.05
MAST
4 months ago Adelyn • 0
49 results • Page 1 of 1
Recent ...
Replies
Comment: GSEA preranked analysis downstream of DEseq2 by Ajay • 0
`logFC * -log10(pval)` seems to be the pi-score proposed in this [paper][1] [1]: https://pmc.ncbi.nlm.nih.gov/articles/PMC3957066/
Comment: error in ChAMP loading file by janwilseo • 0
Any update on this post? I also had an issue with this. [erosion control](https://charlestonhydroseeding.com/)
Answer: CluserProfiler message "No gene can be mapped" by James W. MacDonald 68k
Two things. First, the order of your term2gene is backwards (should be term and then gene, like the name), and by default `enricher` adjust…
Comment: Controlling for batch and estrus cycle using DESeq2 in RNA-seq analysis by donnycrimson • 0
One potential workaround might be to adjust for these factors using a combination of design matrices perhaps including batch as a covariate…
Comment: DESeq2 Design controlling for gender by donnycrimson • 0
On a lighter note, while you are tackling such complex data, you might enjoy a quick break playing the [Slope Game](https://slopegame.lol)…
Votes
DiffBind; Error: No sites have activity greater than filter value
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
A: Unbalanced experiment with multiple samples from each patient.
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