Showing : Mast • reset
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124
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Confidence interval contains 0 but p<0.05
MAST
7 weeks ago Adelyn • 0
3
votes
3
replies
961
views
Robust way of dealing with low number of samples for Differential Gene Expression
limma edgeR DESeq2 MAST
written 3 months ago by • 0
0
votes
1
reply
368
views
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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354
views
Z-score Interpretation across components
MAST
5 months ago GJ • 0
0
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0
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313
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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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482
views
Linear Mixed Model for Differential Gene Expression in Single-Cell RNAseq with Batch Effects
lmer MAST DifferentialExpression
6 months ago nhaus ▴ 70
1
vote
2
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709
views
Extracting genomic sequences using agat and bedtools yields different results
MAST
updated 10 months ago by ★ 4.6k • written 10 months ago by • 0
0
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0
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689
views
Error: grouping factors must have > 1 sampled level
Mast mastR MAST
updated 11 months ago by 67k • written 11 months ago by • 0
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0
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371
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Comparing the effects of a condition over time in two seperate tissues
MAST
11 months ago Dillon • 0
0
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1
reply
687
views
Mismatch between MAST DE results and expression dot plot
MAST mastR
12 months ago Simon • 0
0
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0
replies
737
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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
vote
7
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1.9k
views
Likelihood ratio test (lrTest) in MAST comparing full to reduced model; and another question on controlling for CDR
MAST
23 months ago • updated 22 months ago Ken C • 0
0
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0
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615
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MAST for single cell ATAC data
MAST
23 months ago zuljiamel1991 ▴ 10
2
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2
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2.2k
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Input for MAST
MAST
23 months ago zuljiamel1991 ▴ 10
0
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0
replies
1.4k
views
How to interpret MAST coefficients
DifferentialExpression MAST
2.3 years ago Ismail • 0
0
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0
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676
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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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890
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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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1.0k
views
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
reply
1.3k
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Low logFCs using MAST for scRNA-seq
MAST
updated 5 months ago by ▴ 70 • written 2.8 years ago by • 0
0
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0
replies
1.0k
views
Issues geting meaninfull results for single cell DGE using MAST
MAST SingleCell
3.0 years ago zroger499 • 0
1
vote
0
replies
836
views
When I run `zlm` with several clusters, how to compare 1 cluster versus all the others?
MAST
3.5 years ago Dan • 0
0
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1
reply
1.2k
views
Differentially expressed genes across three different conditions
MAST SingleCell diffGeneAnalysis
updated 3.6 years ago by 67k • written 3.6 years ago by • 0
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 3.7 years ago by • 0 • written 3.9 years ago by • 0
0
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1
reply
1.5k
views
How to do pairwise multiple comparisons in MAST
MAST
updated 6 months ago by • 0 • written 4.0 years ago by • 0
0
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2
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1.4k
views
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
views
MAST invalid Hypothesis, class objectORconnection error
R MAST scRNASeq
4.5 years ago TriS ▴ 200
1
vote
3
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1.6k
views
comparing 2 models with confounders with MAST (scRNA-seq DEA)
scRNA-seq MAST confounders
updated 5.1 years ago by ▴ 270 • written 5.1 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
replies
1.1k
views
DEG among experimental and control group in MAST
MAST DEG batch effects
5.4 years ago chendianyu • 0
0
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1
reply
2.2k
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
views
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
replies
2.1k
views
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
views
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 6.0 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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2.3k
views
Interpretation of cngeneson when doing differential expression analysis in MAST
mast differential gene expression
updated 6.8 years ago by ▴ 270 • written 6.8 years ago by ▴ 40
2
votes
1
reply
3.0k
views
MAST: testing differential expression with a nested factorial design
MAST single-cell rna-seq
updated 6.8 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
6.8 years ago francesco.brundu@gmail.com ▴ 40
0
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4
replies
1.6k
views
MAST: What does the function gseaAfterBoot do exactly?
MAST
6.9 years ago dfm2129 • 0
0
votes
8
replies
2.3k
views
MAST - not getting Hurdle p values
MAST
updated 6.9 years ago by ▴ 270 • written 6.9 years ago by ▴ 10
2
votes
3
replies
2.4k
views
Using MAST with DropSeq data
MAST mast dropseq
updated 7.0 years ago by ▴ 270 • written 7.0 years ago by ▴ 10
4
votes
3
replies
2.4k
views
single-cells RNA-seq analysis by MAST with unbalanced group size
mast single-cell rna-seq differential analysis
updated 7.1 years ago by ▴ 270 • written 7.1 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
7.3 years ago alexanderaivazidis • 0
3
votes
3
replies
3.0k
views
How do you test a contrast in MAST?
MAST single-cell differential gene expression
updated 7.4 years ago by ▴ 270 • written 7.4 years ago by ▴ 40
4
votes
1
reply
2.2k
views
NAs in continuous coefficient and fold change in `zlm`
scrnaseq MAST differential gene expression
7.5 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
replies
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
votes
1
reply
1.5k
views
Removal of batch effects before non-linear clustering for scRNAseq
scrnaseq MAST
7.8 years ago Andrew_McDavid ▴ 270
3
votes
2
replies
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 ...
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Answer: I am having issues with bowtie2_build by James W. MacDonald 67k
Is proof.fa an actual FASTA file? Have you tried using the demo data that comes with the package? See the [vignette under Build Bowtie Inde…
Answer: DEG analysis across multiple timepoints, treatments and tissues by Michael Love 43k
Yes, if you think the entire time course can be modified by tissue effects then you would include another set of interaction terms. I re…
Comment: How to visualize these pathways using pathview by Guido Hooiveld ★ 4.1k
FYI: a similar, if not identical issue has been reported before (`pathview` has problems visualizing some pathways, but not all). You likel…
Comment: Why select top highly expressed genes based on normalized counts, but then plot by Quang NN ▴ 10
I see. Thank you ATpoint!
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by Prakash Sah • 0
Thanks James!
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Answer: Selection of correct coefficients or contrasts in DESeq2
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