Showing : MAST • reset
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112
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Confidence interval contains 0 but p<0.05
MAST
5 weeks ago Adelyn • 0
3
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3
replies
938
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Robust way of dealing with low number of samples for Differential Gene Expression
limma edgeR DESeq2 MAST
written 11 weeks ago by • 0
0
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1
reply
331
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Which input data is acceptable for MAST?
SCTransform MAST
updated 3 months ago by ▴ 270 • written 3 months ago by • 0
0
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0
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346
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Z-score Interpretation across components
MAST
4 months ago GJ • 0
0
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0
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298
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MAST package: Most appropriate way to perform lrTest for effect of factor with multiple levels in pairwise manner?
MAST
6 months ago Kelly • 0
0
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0
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454
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Linear Mixed Model for Differential Gene Expression in Single-Cell RNAseq with Batch Effects
lmer MAST DifferentialExpression
6 months ago nhaus ▴ 70
1
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2
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686
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Extracting genomic sequences using agat and bedtools yields different results
MAST
updated 10 months ago by ★ 4.6k • written 10 months ago by • 0
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0
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663
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Error: grouping factors must have > 1 sampled level
Mast mastR MAST
updated 10 months ago by 67k • written 10 months ago by • 0
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0
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362
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Comparing the effects of a condition over time in two seperate tissues
MAST
10 months ago Dillon • 0
0
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1
reply
667
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Mismatch between MAST DE results and expression dot plot
MAST mastR
12 months ago Simon • 0
0
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0
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725
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How to extract P-Values and LogFC from lrTest in MAST?
pvalue logFC lrtest MAST
21 months ago Tadeoye ▴ 20
1
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7
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1.9k
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Likelihood ratio test (lrTest) in MAST comparing full to reduced model; and another question on controlling for CDR
MAST
22 months ago Ken C • 0
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0
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606
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MAST for single cell ATAC data
MAST
22 months ago zuljiamel1991 ▴ 10
2
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2
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2.1k
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Input for MAST
MAST
23 months ago • updated 22 months ago zuljiamel1991 ▴ 10
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0
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1.4k
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How to interpret MAST coefficients
DifferentialExpression MAST
2.3 years ago Ismail • 0
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0
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662
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How does MAST caculate log fc
MAST
2.4 years ago Chenghao • 0
0
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0
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879
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Differential expression with single cell data: any good two component (hurdle) models recently?
SingleCellWorkflow DifferentialExpression SingleCell SingleCellMultiModal MAST
2.6 years ago Nik Tuzov ▴ 90
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0
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991
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Performing DGE analysis with MAST on a variable with more than 2 levels
MAST DEG SingleCell
2.7 years ago zroger499 • 0
0
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1
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1.2k
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Low logFCs using MAST for scRNA-seq
MAST
updated 4 months ago by ▴ 70 • written 2.8 years ago by • 0
0
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0
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996
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Issues geting meaninfull results for single cell DGE using MAST
MAST SingleCell
3.0 years ago zroger499 • 0
1
vote
0
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820
views
When I run `zlm` with several clusters, how to compare 1 cluster versus all the others?
MAST
3.4 years ago Dan • 0
0
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1
reply
1.2k
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Differentially expressed genes across three different conditions
MAST SingleCell diffGeneAnalysis
updated 3.5 years ago by 67k • written 3.5 years ago by • 0
0
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1
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1.1k
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MAST zlm shows warning: Coefficients ... are never estimible and will be dropped.
MAST
updated 3.6 years ago by • 0 • written 3.9 years ago by • 0
0
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1
reply
1.4k
views
How to do pairwise multiple comparisons in MAST
MAST
updated 5 months ago by • 0 • written 3.9 years ago by • 0
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2
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1.4k
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MAST compare two conditions with several donors
MAST
updated 4.0 years ago by • 0 • written 4.2 years ago by • 0
0
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3
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1.8k
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MAST invalid Hypothesis, class objectORconnection error
R MAST scRNASeq
4.4 years ago TriS ▴ 200
1
vote
3
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1.6k
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comparing 2 models with confounders with MAST (scRNA-seq DEA)
scRNA-seq MAST confounders
updated 5.0 years ago by ▴ 270 • written 5.0 years ago by ▴ 10
0
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1
reply
1.7k
views
About getting DE genes using MAST
MAST
updated 5.1 years ago by ▴ 270 • written 5.1 years ago by • 0
0
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0
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1.1k
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DEG among experimental and control group in MAST
MAST DEG batch effects
5.3 years ago chendianyu • 0
0
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1
reply
2.1k
views
Minimum number of cells required for the MAST
MAST scRNAseq differential expression
5.4 years ago Andrew_McDavid ▴ 270
2
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3
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1.5k
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Logistic regression in MAST - question
mast
updated 5.9 years ago by ▴ 270 • written 5.9 years ago by ▴ 90
2
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7
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2.0k
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Estimation of non-trivial contrasts in MAST
mast
updated 5.9 years ago by ▴ 270 • written 5.9 years ago by ▴ 90
0
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1
reply
1.3k
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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 10 months ago by ▴ 30 • written 5.9 years ago by • 0
0
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2
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1.5k
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Warning in bayes fit in MAST GSEA
MAST GSEA bayesglm.fit
6.4 years ago santos22903 • 0
0
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6
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1.8k
views
Error in zlm function model matrix
MAST
6.7 years ago jka8119 ▴ 10
2
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4
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2.2k
views
Interpretation of cngeneson when doing differential expression analysis in MAST
mast differential gene expression
updated 6.7 years ago by ▴ 270 • written 6.7 years ago by ▴ 40
2
votes
1
reply
2.9k
views
MAST: testing differential expression with a nested factorial design
MAST single-cell rna-seq
updated 6.7 years ago by ▴ 270 • written 6.8 years ago by ▴ 20
2
votes
1
reply
1.3k
views
How to load data csv in MAST
mast
6.7 years ago francesco.brundu@gmail.com ▴ 40
0
votes
4
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1.6k
views
MAST: What does the function gseaAfterBoot do exactly?
MAST
6.8 years ago dfm2129 • 0
0
votes
8
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2.2k
views
MAST - not getting Hurdle p values
MAST
updated 6.9 years ago by ▴ 270 • written 6.9 years ago by ▴ 10
2
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3
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2.4k
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Using MAST with DropSeq data
MAST mast dropseq
updated 6.9 years ago by ▴ 270 • written 6.9 years ago by ▴ 10
4
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3
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2.4k
views
single-cells RNA-seq analysis by MAST with unbalanced group size
mast single-cell rna-seq differential analysis
updated 7.0 years ago by ▴ 270 • written 7.0 years ago by ▴ 100
0
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2
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1.6k
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What is the most useful distance measure to use for cell clustering based on MAST deviance residuals?
MAST
7.3 years ago alexanderaivazidis • 0
3
votes
3
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3.0k
views
How do you test a contrast in MAST?
MAST single-cell differential gene expression
updated 7.3 years ago by ▴ 270 • written 7.3 years ago by ▴ 40
4
votes
1
reply
2.1k
views
NAs in continuous coefficient and fold change in `zlm`
scrnaseq MAST differential gene expression
7.4 years ago Andrew_McDavid ▴ 270
2
votes
1
reply
4.8k
views
Intepretation of Z scores for gene set enrichment analysis in MAST
MAST scRNA GSEA
updated 7.5 years ago by ▴ 270 • written 7.5 years ago by • 0
0
votes
3
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1.8k
views
Modeling Dose-response data in MAST
MAST sc-rnaseq scrnaseq
updated 7.5 years ago by ▴ 270 • written 7.5 years ago by • 0
0
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1
reply
1.5k
views
Removal of batch effects before non-linear clustering for scRNAseq
scrnaseq MAST
7.7 years ago Andrew_McDavid ▴ 270
3
votes
2
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2.7k
views
MAST reported warning "Coefficients ... are never estimible and will be dropped."
mast sc-rnaseq
7.8 years ago shao ▴ 100
49 results • Page 1 of 1
Recent ...
Replies
Answer: DESeq2 Heatmap by James W. MacDonald 67k
Two things. First, `scale` is already vectorized, so you don't have to use `apply`. You can instead just do `t(scale(t(mat)))` . Second, th…
Answer: Improve performance of qusage aggregateGeneSet by James W. MacDonald 67k
This support site is meant mostly to help people with questions about using Bioconductor packages rather than posting code improvements. I …
Answer: promoters_txdb <- promoters(txdb, upstream = 2000) is not 2000 by James W. MacDonald 67k
If you use `promoters` and do not provide an argument for something that has a default, you will get the default argument. Your last call t…
Comment: org.Hs.eg.db issue by k.panov • 0
installed R on another PC, works perfectly. ergo, problem outside of R probably..... :-(
Comment: MBDseq analysis using qsea package by Lukas ▴ 20
Hi, I checked in with Matthias and here is his response: You need to indicate "samples": "The indices of the samples for which individu…
Votes
Comment: DESeq2 for single cell pseudobulk processing
C: Limma: how to get same output as topTable but for all the genes ?
A: Processing agilent data by limma
A: Linear regression in DESeq2
Answer: Is there any chance to solve "the model matrix is not full rank" in DESeq2?
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