Showing : MAST • reset
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Confidence interval contains 0 but p<0.05
MAST
12 months ago Adelyn • 0
3
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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
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1
reply
920
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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
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0
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493
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Z-score Interpretation across components
MAST
15 months ago GJ • 0
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0
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539
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MAST package: Most appropriate way to perform lrTest for effect of factor with multiple levels in pairwise manner?
MAST
17 months ago Kelly • 0
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0
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811
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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
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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 21 months ago by ★ 5.0k • written 21 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
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0
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548
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Comparing the effects of a condition over time in two seperate tissues
MAST
22 months ago Dillon • 0
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1
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1.0k
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Mismatch between MAST DE results and expression dot plot
MAST mastR
23 months ago Simon • 0
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0
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1.0k
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How to extract P-Values and LogFC from lrTest in MAST?
pvalue logFC lrtest MAST
2.7 years ago Tadeoye ▴ 20
1
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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
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0
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831
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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
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1
reply
2.4k
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How to interpret MAST coefficients
DifferentialExpression MAST
updated 6 months ago by ▴ 10 • written 3.2 years ago by • 0
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1
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1.4k
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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
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0
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1.3k
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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
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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
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0
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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
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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
4.4 years ago Dan • 0
0
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1
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1.5k
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Differentially expressed genes across three different conditions
MAST SingleCell diffGeneAnalysis
updated 4.5 years ago by 68k • written 4.5 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
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1
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1.8k
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How to do pairwise multiple comparisons in MAST
MAST
updated 17 months ago by • 0 • written 4.8 years ago by • 0
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2
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1.8k
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MAST compare two conditions with several donors
MAST
updated 4.9 years ago by • 0 • written 5.1 years ago by • 0
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3
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2.0k
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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
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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
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2.1k
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About getting DE genes using MAST
MAST
updated 6.0 years ago by ▴ 280 • written 6.0 years ago by • 0
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0
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1.3k
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DEG among experimental and control group in MAST
MAST DEG batch effects
6.2 years ago chendianyu • 0
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1
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2.6k
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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
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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
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2.5k
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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
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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 6.9 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
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Error in zlm function model matrix
MAST
7.6 years ago jka8119 ▴ 10
2
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4
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2.6k
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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
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1
reply
3.6k
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MAST: testing differential expression with a nested factorial design
MAST single-cell rna-seq
updated 7.7 years ago by ▴ 280 • written 7.7 years ago by ▴ 20
2
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1
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1.5k
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How to load data csv in MAST
mast
7.7 years ago francesco.brundu@gmail.com ▴ 40
0
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4
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1.9k
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MAST: What does the function gseaAfterBoot do exactly?
MAST
7.7 years ago dfm2129 • 0
0
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8
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2.7k
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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
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2.9k
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Using MAST with DropSeq data
MAST mast dropseq
updated 7.9 years ago by ▴ 280 • written 7.9 years ago by ▴ 10
5
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3
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3.0k
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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
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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
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3
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3.5k
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How do you test a contrast in MAST?
MAST single-cell differential gene expression
updated 8.3 years ago by ▴ 280 • written 8.3 years ago by ▴ 40
4
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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
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1
reply
5.4k
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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
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3
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2.1k
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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
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1.8k
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Removal of batch effects before non-linear clustering for scRNAseq
scrnaseq MAST
8.6 years ago Andrew_McDavid ▴ 280
3
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2
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3.1k
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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: Bioinformatician at the Lausanne University Hospital by eja.ger.m • 0
For individuals looking to improve communication and collaboration in demanding medical or research environments like the Genetic Medicine …
Answer: NUPOP usage by shepherl 4.2k
You should read the documentation in the package especially the package vignette https://bioconductor.org/packages/release/bioc/html/NuPoP.…
Comment: How can I correctly use phyloseq with Docker? by fnfgame • 0
In a rocker image, this error usually means the Bioconductor install happened as root but the runtime library paths used by the shiny user …
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.
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
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