Showing : mast • reset
1
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2
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285
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Extracting genomic sequences using agat and bedtools yields different results
MAST
updated 6 weeks ago by ★ 4.1k • written 6 weeks ago by • 0
0
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0
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204
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Error: grouping factors must have > 1 sampled level
Mast mastR MAST
updated 8 weeks ago by 65k • written 8 weeks ago by • 0
0
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0
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168
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Comparing the effects of a condition over time in two seperate tissues
MAST
10 weeks ago Dillon • 0
0
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1
reply
294
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Mismatch between MAST DE results and expression dot plot
MAST mastR
3 months ago Simon • 0
0
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0
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434
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How to extract P-Values and LogFC from lrTest in MAST?
pvalue logFC lrtest MAST
12 months ago Tadeoye ▴ 20
1
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7
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1.3k
views
Likelihood ratio test (lrTest) in MAST comparing full to reduced model; and another question on controlling for CDR
MAST
14 months ago • updated 13 months ago Ken C • 0
0
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0
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407
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MAST for single cell ATAC data
MAST
14 months ago zuljiamel1991 ▴ 10
1
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2
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1.2k
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Input for MAST
MAST
14 months ago zuljiamel1991 ▴ 10
0
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0
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938
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How to interpret MAST coefficients
DifferentialExpression MAST
18 months ago Ismail • 0
0
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0
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477
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How does MAST caculate log fc
MAST
20 months ago Chenghao • 0
0
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0
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680
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Differential expression with single cell data: any good two component (hurdle) models recently?
SingleCellWorkflow DifferentialExpression SingleCell SingleCellMultiModal MAST
22 months ago Nik Tuzov ▴ 80
0
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0
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706
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Performing DGE analysis with MAST on a variable with more than 2 levels
MAST DEG SingleCell
24 months ago zroger499 • 0
0
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0
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880
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Low logFCs using MAST for scRNA-seq
MAST
2.1 years ago learner_MD • 0
0
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0
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734
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Issues geting meaninfull results for single cell DGE using MAST
MAST SingleCell
2.3 years ago zroger499 • 0
1
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0
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641
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When I run `zlm` with several clusters, how to compare 1 cluster versus all the others?
MAST
2.7 years ago Dan • 0
0
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1
reply
933
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Differentially expressed genes across three different conditions
MAST SingleCell diffGeneAnalysis
updated 2.8 years ago by 65k • written 2.8 years ago by • 0
0
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1
reply
865
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MAST zlm shows warning: Coefficients ... are never estimible and will be dropped.
MAST
updated 2.9 years ago by • 0 • written 3.2 years ago by • 0
0
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0
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1.0k
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How to do pairwise multiple comparisons in MAST
MAST
3.2 years ago sysumed3615 • 0
0
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2
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1.1k
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MAST compare two conditions with several donors
MAST
updated 3.2 years ago by • 0 • written 3.5 years ago by • 0
0
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3
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1.5k
views
MAST invalid Hypothesis, class objectORconnection error
R MAST scRNASeq
3.7 years ago TriS ▴ 200
1
vote
3
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1.2k
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comparing 2 models with confounders with MAST (scRNA-seq DEA)
scRNA-seq MAST confounders
updated 4.3 years ago by ▴ 270 • written 4.3 years ago by ▴ 10
0
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1
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1.3k
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About getting DE genes using MAST
MAST
updated 4.4 years ago by ▴ 270 • written 4.4 years ago by • 0
0
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0
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879
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DEG among experimental and control group in MAST
MAST DEG batch effects
4.6 years ago chendianyu • 0
0
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1
reply
1.6k
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Minimum number of cells required for the MAST
MAST scRNAseq differential expression
4.7 years ago Andrew_McDavid ▴ 270
2
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3
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1.2k
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Logistic regression in MAST - question
mast
updated 5.2 years ago by ▴ 270 • written 5.2 years ago by ▴ 80
2
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7
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1.7k
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Estimation of non-trivial contrasts in MAST
mast
updated 5.2 years ago by ▴ 270 • written 5.2 years ago by ▴ 80
0
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1
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1.1k
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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 6 weeks ago by ▴ 20 • written 5.2 years ago by • 0
0
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2
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1.2k
views
Warning in bayes fit in MAST GSEA
MAST GSEA bayesglm.fit
5.7 years ago santos22903 • 0
0
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6
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1.4k
views
Error in zlm function model matrix
MAST
6.0 years ago jka8119 ▴ 10
2
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4
replies
1.8k
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Interpretation of cngeneson when doing differential expression analysis in MAST
mast differential gene expression
updated 6.0 years ago by ▴ 270 • written 6.0 years ago by ▴ 40
2
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1
reply
2.3k
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MAST: testing differential expression with a nested factorial design
MAST single-cell rna-seq
updated 6.0 years ago by ▴ 270 • written 6.1 years ago by ▴ 20
2
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1
reply
1.1k
views
How to load data csv in MAST
mast
6.0 years ago francesco.brundu@gmail.com ▴ 40
0
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4
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1.3k
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MAST: What does the function gseaAfterBoot do exactly?
MAST
6.1 years ago dfm2129 • 0
0
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8
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1.8k
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MAST - not getting Hurdle p values
MAST
updated 6.2 years ago by ▴ 270 • written 6.2 years ago by ▴ 10
2
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3
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2.1k
views
Using MAST with DropSeq data
MAST mast dropseq
updated 6.2 years ago by ▴ 270 • written 6.2 years ago by ▴ 10
4
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3
replies
2.0k
views
single-cells RNA-seq analysis by MAST with unbalanced group size
mast single-cell rna-seq differential analysis
updated 6.3 years ago by ▴ 270 • written 6.3 years ago by ▴ 100
0
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2
replies
1.3k
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What is the most useful distance measure to use for cell clustering based on MAST deviance residuals?
MAST
6.6 years ago alexanderaivazidis • 0
3
votes
3
replies
2.4k
views
How do you test a contrast in MAST?
MAST single-cell differential gene expression
updated 6.6 years ago by ▴ 270 • written 6.6 years ago by ▴ 40
4
votes
1
reply
1.8k
views
NAs in continuous coefficient and fold change in `zlm`
scrnaseq MAST differential gene expression
6.7 years ago Andrew_McDavid ▴ 270
2
votes
1
reply
4.2k
views
Intepretation of Z scores for gene set enrichment analysis in MAST
MAST scRNA GSEA
updated 6.8 years ago by ▴ 270 • written 6.8 years ago by • 0
0
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3
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1.4k
views
Modeling Dose-response data in MAST
MAST sc-rnaseq scrnaseq
updated 6.8 years ago by ▴ 270 • written 6.8 years ago by • 0
0
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1
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1.3k
views
Removal of batch effects before non-linear clustering for scRNAseq
scrnaseq MAST
7.0 years ago Andrew_McDavid ▴ 270
3
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2
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2.2k
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MAST reported warning "Coefficients ... are never estimible and will be dropped."
mast sc-rnaseq
7.1 years ago shao ▴ 100
43 results • Page 1 of 1
Recent ...
Replies
Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2 by Kim • 0
Thank you Tim, this is a great help in getting me started!
Comment: Too many significant genes when integrating gtex and tcga by Michael Love 41k
Yes, this was one of the aspects we highlighted in the 2014 paper, and it's also in the workflow. Check these places first. Also take a st…
Votes
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
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