Showing : MAST • reset
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Extracting genomic sequences using agat and bedtools yields different results
MAST
updated 4 weeks ago by ★ 4.0k • written 4 weeks ago by • 0
0
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1
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1.0k
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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 4 weeks ago by ▴ 20 • written 5.2 years ago by • 0
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170
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Error: grouping factors must have > 1 sampled level
Mast mastR MAST
updated 6 weeks ago by 65k • written 6 weeks ago by • 0
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0
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153
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Comparing the effects of a condition over time in two seperate tissues
MAST
8 weeks ago Dillon • 0
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1
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262
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Mismatch between MAST DE results and expression dot plot
MAST mastR
3 months ago Simon • 0
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0
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410
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How to extract P-Values and LogFC from lrTest in MAST?
pvalue logFC lrtest MAST
12 months ago Tadeoye ▴ 20
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7
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1.3k
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Likelihood ratio test (lrTest) in MAST comparing full to reduced model; and another question on controlling for CDR
MAST
13 months ago Ken C • 0
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2
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1.2k
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Input for MAST
MAST
14 months ago • updated 13 months ago zuljiamel1991 ▴ 10
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391
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MAST for single cell ATAC data
MAST
13 months ago zuljiamel1991 ▴ 10
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0
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913
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How to interpret MAST coefficients
DifferentialExpression MAST
18 months ago Ismail • 0
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463
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How does MAST caculate log fc
MAST
20 months ago Chenghao • 0
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0
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661
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Differential expression with single cell data: any good two component (hurdle) models recently?
SingleCellWorkflow DifferentialExpression SingleCell SingleCellMultiModal MAST
22 months ago Nik Tuzov ▴ 80
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692
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Performing DGE analysis with MAST on a variable with more than 2 levels
MAST DEG SingleCell
23 months ago zroger499 • 0
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0
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863
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Low logFCs using MAST for scRNA-seq
MAST
2.1 years ago learner_MD • 0
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0
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720
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Issues geting meaninfull results for single cell DGE using MAST
MAST SingleCell
2.2 years ago zroger499 • 0
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623
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When I run `zlm` with several clusters, how to compare 1 cluster versus all the others?
MAST
2.7 years ago Dan • 0
0
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1
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917
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Differentially expressed genes across three different conditions
MAST SingleCell diffGeneAnalysis
updated 2.8 years ago by 65k • written 2.8 years ago by • 0
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1
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838
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MAST zlm shows warning: Coefficients ... are never estimible and will be dropped.
MAST
updated 2.9 years ago by • 0 • written 3.2 years ago by • 0
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0
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1.0k
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How to do pairwise multiple comparisons in MAST
MAST
3.2 years ago sysumed3615 • 0
0
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2
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1.1k
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MAST compare two conditions with several donors
MAST
updated 3.2 years ago by • 0 • written 3.4 years ago by • 0
0
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3
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1.5k
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MAST invalid Hypothesis, class objectORconnection error
R MAST scRNASeq
3.7 years ago TriS ▴ 200
1
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3
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1.2k
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comparing 2 models with confounders with MAST (scRNA-seq DEA)
scRNA-seq MAST confounders
updated 4.3 years ago by ▴ 270 • written 4.3 years ago by ▴ 10
0
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1
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1.2k
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About getting DE genes using MAST
MAST
updated 4.3 years ago by ▴ 270 • written 4.3 years ago by • 0
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0
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868
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DEG among experimental and control group in MAST
MAST DEG batch effects
4.6 years ago chendianyu • 0
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1
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1.6k
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Minimum number of cells required for the MAST
MAST scRNAseq differential expression
4.6 years ago Andrew_McDavid ▴ 270
2
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3
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1.2k
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Logistic regression in MAST - question
mast
updated 5.1 years ago by ▴ 270 • written 5.1 years ago by ▴ 80
2
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7
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1.6k
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Estimation of non-trivial contrasts in MAST
mast
updated 5.1 years ago by ▴ 270 • written 5.1 years ago by ▴ 80
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2
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1.2k
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Warning in bayes fit in MAST GSEA
MAST GSEA bayesglm.fit
5.6 years ago santos22903 • 0
0
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6
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1.4k
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Error in zlm function model matrix
MAST
6.0 years ago jka8119 ▴ 10
2
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4
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1.8k
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Interpretation of cngeneson when doing differential expression analysis in MAST
mast differential gene expression
updated 6.0 years ago by ▴ 270 • written 6.0 years ago by ▴ 40
2
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1
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2.3k
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MAST: testing differential expression with a nested factorial design
MAST single-cell rna-seq
updated 6.0 years ago by ▴ 270 • written 6.0 years ago by ▴ 20
2
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1
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1.1k
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How to load data csv in MAST
mast
6.0 years ago francesco.brundu@gmail.com ▴ 40
0
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4
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1.3k
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MAST: What does the function gseaAfterBoot do exactly?
MAST
6.1 years ago dfm2129 • 0
0
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8
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1.7k
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MAST - not getting Hurdle p values
MAST
updated 6.2 years ago by ▴ 270 • written 6.2 years ago by ▴ 10
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3
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2.0k
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Using MAST with DropSeq data
MAST mast dropseq
updated 6.2 years ago by ▴ 270 • written 6.2 years ago by ▴ 10
4
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3
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1.9k
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single-cells RNA-seq analysis by MAST with unbalanced group size
mast single-cell rna-seq differential analysis
updated 6.3 years ago by ▴ 270 • written 6.3 years ago by ▴ 100
0
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2
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1.3k
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What is the most useful distance measure to use for cell clustering based on MAST deviance residuals?
MAST
6.5 years ago alexanderaivazidis • 0
3
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3
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2.4k
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How do you test a contrast in MAST?
MAST single-cell differential gene expression
updated 6.6 years ago by ▴ 270 • written 6.6 years ago by ▴ 40
4
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1
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1.7k
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NAs in continuous coefficient and fold change in `zlm`
scrnaseq MAST differential gene expression
6.7 years ago Andrew_McDavid ▴ 270
2
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1
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4.2k
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Intepretation of Z scores for gene set enrichment analysis in MAST
MAST scRNA GSEA
updated 6.7 years ago by ▴ 270 • written 6.7 years ago by • 0
0
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3
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1.4k
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Modeling Dose-response data in MAST
MAST sc-rnaseq scrnaseq
updated 6.7 years ago by ▴ 270 • written 6.7 years ago by • 0
0
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1
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1.3k
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Removal of batch effects before non-linear clustering for scRNAseq
scrnaseq MAST
7.0 years ago Andrew_McDavid ▴ 270
3
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2
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2.2k
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MAST reported warning "Coefficients ... are never estimible and will be dropped."
mast sc-rnaseq
7.0 years ago shao ▴ 100
43 results • Page 1 of 1
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Comment: The difference when using Limma compare between 3 conditions vs 2 conditions by Robert Castelo ★ 3.2k
Hi, your `c2` object storing all the gene sets is probably a `list` object, where element names are the names of the pathways given by MSig…
Comment: Differential peaks that were not identified in diffbind were identified in diseq by lonn • 0
I tried the default normalization and got similar results as above. Perhaps I need to try identifying the difference peak without using dif…
Answer: Cannabis and KEGGgraph by deeenes ▴ 30
Hello, I'm a developer of the `OmnipathR` package, and I wrote [a function][1] to access certain KEGG data: library(OmnipathR) cs…
Answer: RNAseq:Technical replicates from different batches by Gordon Smyth 50k
I am not entirely clear what you mean by "technical" replicates in this case. Are they resequencing of the same RNA samples or are they fre…
Comment: DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, param by russ.bainer ▴ 10
Hi, I'm hitting this too. As far as I can tell my DataTrack is fine, but perhaps I am missing something. Notably the same code works on o…
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Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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