Showing : Mast • reset
3
votes
3
replies
798
views
Robust way of dealing with low number of samples for Differential Gene Expression
limma edgeR DESeq2 MAST
written 19 days ago by • 0
0
votes
1
reply
231
views
Which input data is acceptable for MAST?
SCTransform MAST
updated 6 weeks ago by ▴ 270 • written 6 weeks ago by • 0
0
votes
0
replies
312
views
Z-score Interpretation across components
MAST
10 weeks ago Greg • 0
0
votes
0
replies
255
views
MAST package: Most appropriate way to perform lrTest for effect of factor with multiple levels in pairwise manner?
MAST
3 months ago Kelly • 0
0
votes
0
replies
375
views
Linear Mixed Model for Differential Gene Expression in Single-Cell RNAseq with Batch Effects
lmer MAST DifferentialExpression
4 months ago nhaus ▴ 70
1
vote
2
replies
607
views
Extracting genomic sequences using agat and bedtools yields different results
MAST
updated 8 months ago by ★ 4.5k • written 8 months ago by • 0
0
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0
replies
570
views
Error: grouping factors must have > 1 sampled level
Mast mastR MAST
updated 8 months ago by 67k • written 8 months ago by • 0
0
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0
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330
views
Comparing the effects of a condition over time in two seperate tissues
MAST
8 months ago Dillon • 0
0
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1
reply
588
views
Mismatch between MAST DE results and expression dot plot
MAST mastR
10 months ago Simon • 0
0
votes
0
replies
665
views
How to extract P-Values and LogFC from lrTest in MAST?
pvalue logFC lrtest MAST
19 months ago Tadeoye ▴ 20
1
vote
7
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1.8k
views
Likelihood ratio test (lrTest) in MAST comparing full to reduced model; and another question on controlling for CDR
MAST
20 months ago • updated 19 months ago Ken C • 0
0
votes
0
replies
565
views
MAST for single cell ATAC data
MAST
20 months ago zuljiamel1991 ▴ 10
2
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2
replies
1.9k
views
Input for MAST
MAST
21 months ago • updated 20 months ago zuljiamel1991 ▴ 10
0
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0
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1.3k
views
How to interpret MAST coefficients
DifferentialExpression MAST
2.1 years ago Ismail • 0
0
votes
0
replies
628
views
How does MAST caculate log fc
MAST
2.2 years ago Chenghao • 0
0
votes
0
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855
views
Differential expression with single cell data: any good two component (hurdle) models recently?
SingleCellWorkflow DifferentialExpression SingleCell SingleCellMultiModal MAST
2.4 years ago Nik Tuzov ▴ 90
0
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0
replies
926
views
Performing DGE analysis with MAST on a variable with more than 2 levels
MAST DEG SingleCell
2.5 years ago zroger499 • 0
0
votes
1
reply
1.2k
views
Low logFCs using MAST for scRNA-seq
MAST
updated 11 weeks ago by ▴ 70 • written 2.6 years ago by • 0
0
votes
0
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960
views
Issues geting meaninfull results for single cell DGE using MAST
MAST SingleCell
2.8 years ago zroger499 • 0
1
vote
0
replies
786
views
When I run `zlm` with several clusters, how to compare 1 cluster versus all the others?
MAST
3.3 years ago Dan • 0
0
votes
1
reply
1.1k
views
Differentially expressed genes across three different conditions
MAST SingleCell diffGeneAnalysis
updated 3.4 years ago by 67k • written 3.4 years ago by • 0
0
votes
1
reply
1.1k
views
MAST zlm shows warning: Coefficients ... are never estimible and will be dropped.
MAST
updated 3.5 years ago by • 0 • written 3.7 years ago by • 0
0
votes
1
reply
1.4k
views
How to do pairwise multiple comparisons in MAST
MAST
updated 3 months ago by • 0 • written 3.7 years ago by • 0
0
votes
2
replies
1.3k
views
MAST compare two conditions with several donors
MAST
updated 3.8 years ago by • 0 • written 4.0 years ago by • 0
0
votes
3
replies
1.7k
views
MAST invalid Hypothesis, class objectORconnection error
R MAST scRNASeq
4.3 years ago • updated 4.2 years ago TriS ▴ 200
1
vote
3
replies
1.6k
views
comparing 2 models with confounders with MAST (scRNA-seq DEA)
scRNA-seq MAST confounders
updated 4.9 years ago by ▴ 270 • written 4.9 years ago by ▴ 10
0
votes
1
reply
1.6k
views
About getting DE genes using MAST
MAST
updated 4.9 years ago by ▴ 270 • written 4.9 years ago by • 0
0
votes
0
replies
1.0k
views
DEG among experimental and control group in MAST
MAST DEG batch effects
5.1 years ago chendianyu • 0
0
votes
1
reply
2.0k
views
Minimum number of cells required for the MAST
MAST scRNAseq differential expression
5.2 years ago Andrew_McDavid ▴ 270
2
votes
3
replies
1.4k
views
Logistic regression in MAST - question
mast
updated 5.7 years ago by ▴ 270 • written 5.7 years ago by ▴ 90
2
votes
7
replies
2.0k
views
Estimation of non-trivial contrasts in MAST
mast
updated 5.7 years ago by ▴ 270 • written 5.7 years ago by ▴ 90
0
votes
1
reply
1.3k
views
How can I compute AIC for MAST hurdle model fitted in the whole dataset?
MAST AIC calcuation Parameters single cell hurdle model
updated 8 months ago by ▴ 30 • written 5.8 years ago by • 0
0
votes
2
replies
1.4k
views
Warning in bayes fit in MAST GSEA
MAST GSEA bayesglm.fit
6.2 years ago santos22903 • 0
0
votes
6
replies
1.7k
views
Error in zlm function model matrix
MAST
6.5 years ago jka8119 ▴ 10
2
votes
4
replies
2.2k
views
Interpretation of cngeneson when doing differential expression analysis in MAST
mast differential gene expression
updated 6.6 years ago by ▴ 270 • written 6.6 years ago by ▴ 40
2
votes
1
reply
2.8k
views
MAST: testing differential expression with a nested factorial design
MAST single-cell rna-seq
updated 6.6 years ago by ▴ 270 • written 6.6 years ago by ▴ 20
2
votes
1
reply
1.2k
views
How to load data csv in MAST
mast
6.6 years ago francesco.brundu@gmail.com ▴ 40
0
votes
4
replies
1.5k
views
MAST: What does the function gseaAfterBoot do exactly?
MAST
6.6 years ago dfm2129 • 0
0
votes
8
replies
2.2k
views
MAST - not getting Hurdle p values
MAST
updated 6.7 years ago by ▴ 270 • written 6.7 years ago by ▴ 10
2
votes
3
replies
2.3k
views
Using MAST with DropSeq data
MAST mast dropseq
updated 6.8 years ago by ▴ 270 • written 6.8 years ago by ▴ 10
4
votes
3
replies
2.3k
views
single-cells RNA-seq analysis by MAST with unbalanced group size
mast single-cell rna-seq differential analysis
updated 6.9 years ago by ▴ 270 • written 6.9 years ago by ▴ 100
0
votes
2
replies
1.6k
views
What is the most useful distance measure to use for cell clustering based on MAST deviance residuals?
MAST
7.1 years ago alexanderaivazidis • 0
3
votes
3
replies
2.9k
views
How do you test a contrast in MAST?
MAST single-cell differential gene expression
updated 7.2 years ago by ▴ 270 • written 7.2 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
7.3 years ago Andrew_McDavid ▴ 270
2
votes
1
reply
4.7k
views
Intepretation of Z scores for gene set enrichment analysis in MAST
MAST scRNA GSEA
updated 7.3 years ago by ▴ 270 • written 7.3 years ago by • 0
0
votes
3
replies
1.7k
views
Modeling Dose-response data in MAST
MAST sc-rnaseq scrnaseq
updated 7.3 years ago by ▴ 270 • written 7.3 years ago by • 0
0
votes
1
reply
1.5k
views
Removal of batch effects before non-linear clustering for scRNAseq
scrnaseq MAST
7.6 years ago Andrew_McDavid ▴ 270
3
votes
2
replies
2.6k
views
MAST reported warning "Coefficients ... are never estimible and will be dropped."
mast sc-rnaseq
7.6 years ago shao ▴ 100
48 results • Page 1 of 1
Recent ...
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Comment: Appropriate ways to filter counts data for voom/limma by dorothylminter • 0
The proper way to filter count data for voom/limma emphasizes the importance of choosing the right filtering technique to enhance detection…
Comment: How to extract phastcons score for all protein coding genes and lncRNAs using Ge by Robert Castelo ★ 3.4k
Hi, this is a long comment thread on 4-year old post, please open a new post with you question. To increase the odds of getting useful answ…
Comment: DESeq2 rerun returns different results by ATpoint ★ 4.5k
DESeq2 is deterministic if you use same input, code and software versions. Make sure to version-control your environment by at least tracki…
Answer: [How to construct a model.matrix ] by Gordon Smyth 51k
> Initially, I simply used > `lm(Epigenetic_age ~ Age_group + Age + Sex + PC1 + PC2 + PC3 + PC4 + PC5 + B + CD4T + CD8T + Mono + NK + Neutr…
Comment: How to extract phastcons score for all protein coding genes and lncRNAs using Ge by rania.alanany • 0
Hi Robert, Thank you for the explanation, But I am still little bit confused, Is the annotation package (TxDb.Hsapiens.UCSC.hg38.knownGene)…
Votes
A: Some questions for remove batch effect by using mnnCorrect
A: Recommendations for combining multiple 10x runs into one SingleCellExperiment
Answer: [How to construct a model.matrix ]
Answer: Handling biological replicates in DESeq2
Comment: biomaRt rnorvegicus_gene_ensembl not available anymore
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