Showing : mast • reset
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289
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Confidence interval contains 0 but p<0.05
MAST
12 months ago Adelyn • 0
3
votes
3
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1.5k
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Robust way of dealing with low number of samples for Differential Gene Expression
limma edgeR DESeq2 MAST
written 13 months ago by • 0
0
votes
1
reply
913
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Which input data is acceptable for MAST?
SCTransform MAST
updated 14 months ago by ▴ 280 • written 14 months ago by • 0
0
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0
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491
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Z-score Interpretation across components
MAST
15 months ago GJ • 0
0
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0
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532
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MAST package: Most appropriate way to perform lrTest for effect of factor with multiple levels in pairwise manner?
MAST
16 months ago Kelly • 0
0
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0
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805
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Linear Mixed Model for Differential Gene Expression in Single-Cell RNAseq with Batch Effects
lmer MAST DifferentialExpression
17 months ago nhaus ▴ 70
1
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2
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1.3k
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Extracting genomic sequences using agat and bedtools yields different results
MAST
updated 20 months ago by ★ 5.0k • written 20 months ago by • 0
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0
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1.0k
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Error: grouping factors must have > 1 sampled level
Mast mastR MAST
updated 21 months ago by 68k • written 21 months ago by • 0
0
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0
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545
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Comparing the effects of a condition over time in two seperate tissues
MAST
21 months ago Dillon • 0
0
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1
reply
1.0k
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Mismatch between MAST DE results and expression dot plot
MAST mastR
23 months ago Simon • 0
0
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0
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996
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How to extract P-Values and LogFC from lrTest in MAST?
pvalue logFC lrtest MAST
2.6 years ago Tadeoye ▴ 20
1
vote
7
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2.7k
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Likelihood ratio test (lrTest) in MAST comparing full to reduced model; and another question on controlling for CDR
MAST
2.8 years ago • updated 2.7 years ago Ken C • 0
0
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0
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827
views
MAST for single cell ATAC data
MAST
2.8 years ago zuljiamel1991 ▴ 10
2
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2
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2.9k
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Input for MAST
MAST
2.8 years ago zuljiamel1991 ▴ 10
0
votes
1
reply
2.4k
views
How to interpret MAST coefficients
DifferentialExpression MAST
updated 6 months ago by ▴ 10 • written 3.2 years ago by • 0
0
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1
reply
1.4k
views
How does MAST caculate log fc
MAST
3.3 years ago • updated 6 months ago Chenghao ▴ 10
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0
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1.2k
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Differential expression with single cell data: any good two component (hurdle) models recently?
SingleCellWorkflow DifferentialExpression SingleCell SingleCellMultiModal MAST
3.5 years ago Nik Tuzov ▴ 90
0
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0
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1.3k
views
Performing DGE analysis with MAST on a variable with more than 2 levels
MAST DEG SingleCell
3.6 years ago zroger499 • 0
0
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1
reply
1.6k
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Low logFCs using MAST for scRNA-seq
MAST
updated 15 months ago by ▴ 70 • written 3.7 years ago by • 0
0
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0
replies
1.2k
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Issues geting meaninfull results for single cell DGE using MAST
MAST SingleCell
3.9 years ago zroger499 • 0
1
vote
0
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1.0k
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When I run `zlm` with several clusters, how to compare 1 cluster versus all the others?
MAST
4.3 years ago Dan • 0
0
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1
reply
1.5k
views
Differentially expressed genes across three different conditions
MAST SingleCell diffGeneAnalysis
updated 4.4 years ago by 68k • written 4.4 years ago by • 0
0
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1
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1.4k
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MAST zlm shows warning: Coefficients ... are never estimible and will be dropped.
MAST
updated 4.5 years ago by • 0 • written 4.8 years ago by • 0
0
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1
reply
1.8k
views
How to do pairwise multiple comparisons in MAST
MAST
updated 16 months ago by • 0 • written 4.8 years ago by • 0
0
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2
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1.8k
views
MAST compare two conditions with several donors
MAST
updated 4.9 years ago by • 0 • written 5.1 years ago by • 0
0
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3
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2.0k
views
MAST invalid Hypothesis, class objectORconnection error
R MAST scRNASeq
5.3 years ago TriS ▴ 200
1
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3
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2.0k
views
comparing 2 models with confounders with MAST (scRNA-seq DEA)
scRNA-seq MAST confounders
updated 5.9 years ago by ▴ 280 • written 5.9 years ago by ▴ 10
0
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1
reply
2.0k
views
About getting DE genes using MAST
MAST
updated 6.0 years ago by ▴ 280 • written 6.0 years ago by • 0
0
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0
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1.3k
views
DEG among experimental and control group in MAST
MAST DEG batch effects
6.2 years ago chendianyu • 0
0
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1
reply
2.6k
views
Minimum number of cells required for the MAST
MAST scRNAseq differential expression
6.3 years ago Andrew_McDavid ▴ 280
2
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3
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1.8k
views
Logistic regression in MAST - question
mast
updated 6.8 years ago by ▴ 280 • written 6.8 years ago by ▴ 90
2
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7
replies
2.5k
views
Estimation of non-trivial contrasts in MAST
mast
updated 6.8 years ago by ▴ 280 • written 6.8 years ago by ▴ 90
0
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1
reply
1.7k
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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 21 months ago by ▴ 30 • written 6.8 years ago by • 0
0
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2
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1.8k
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Warning in bayes fit in MAST GSEA
MAST GSEA bayesglm.fit
7.3 years ago santos22903 • 0
0
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6
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2.2k
views
Error in zlm function model matrix
MAST
7.6 years ago jka8119 ▴ 10
2
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4
replies
2.6k
views
Interpretation of cngeneson when doing differential expression analysis in MAST
mast differential gene expression
updated 7.6 years ago by ▴ 280 • written 7.6 years ago by ▴ 40
2
votes
1
reply
3.6k
views
MAST: testing differential expression with a nested factorial design
MAST single-cell rna-seq
updated 7.6 years ago by ▴ 280 • written 7.7 years ago by ▴ 20
2
votes
1
reply
1.5k
views
How to load data csv in MAST
mast
7.6 years ago francesco.brundu@gmail.com ▴ 40
0
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4
replies
1.9k
views
MAST: What does the function gseaAfterBoot do exactly?
MAST
7.7 years ago dfm2129 • 0
0
votes
8
replies
2.7k
views
MAST - not getting Hurdle p values
MAST
updated 7.8 years ago by ▴ 280 • written 7.8 years ago by ▴ 10
2
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3
replies
2.9k
views
Using MAST with DropSeq data
MAST mast dropseq
updated 7.8 years ago by ▴ 280 • written 7.8 years ago by ▴ 10
5
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3
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3.0k
views
single-cells RNA-seq analysis by MAST with unbalanced group size
mast single-cell rna-seq differential analysis
updated 8 months ago by ▴ 10 • written 7.9 years ago by ▴ 100
0
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2
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1.9k
views
What is the most useful distance measure to use for cell clustering based on MAST deviance residuals?
MAST
8.2 years ago alexanderaivazidis • 0
3
votes
3
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3.5k
views
How do you test a contrast in MAST?
MAST single-cell differential gene expression
updated 8.2 years ago by ▴ 280 • written 8.2 years ago by ▴ 40
4
votes
1
reply
2.5k
views
NAs in continuous coefficient and fold change in `zlm`
scrnaseq MAST differential gene expression
8.3 years ago Andrew_McDavid ▴ 280
2
votes
1
reply
5.4k
views
Intepretation of Z scores for gene set enrichment analysis in MAST
MAST scRNA GSEA
updated 8.4 years ago by ▴ 280 • written 8.4 years ago by • 0
0
votes
3
replies
2.1k
views
Modeling Dose-response data in MAST
MAST sc-rnaseq scrnaseq
updated 8.4 years ago by ▴ 280 • written 8.4 years ago by • 0
0
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1
reply
1.8k
views
Removal of batch effects before non-linear clustering for scRNAseq
scrnaseq MAST
8.6 years ago Andrew_McDavid ▴ 280
3
votes
2
replies
3.1k
views
MAST reported warning "Coefficients ... are never estimible and will be dropped."
mast sc-rnaseq
8.7 years ago shao ▴ 100
49 results • Page 1 of 1
Recent ...
Replies
Comment: DECIPHER DesignProbes unable to design FISH-probes by Erik Wright ▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Answer: PTM analysis in LIMPA by Gordon Smyth 53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR by James W. MacDonald 68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Awards • All
Popular Question to James W. MacDonald 68k
Popular Question to Gordon Smyth 53k
Commentator to sina.nassiri ▴ 130
Popular Question to Hervé Pagès 16k
Popular Question to jared.andrews07 ▴ 30
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