Showing : MAST • reset
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132
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Confidence interval contains 0 but p<0.05
MAST
11 weeks ago Adelyn • 0
3
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3
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1.0k
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Robust way of dealing with low number of samples for Differential Gene Expression
limma edgeR DESeq2 MAST
written 3 months ago by • 0
0
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1
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432
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Which input data is acceptable for MAST?
SCTransform MAST
updated 4 months ago by ▴ 270 • written 4 months ago by • 0
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360
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Z-score Interpretation across components
MAST
5 months ago GJ • 0
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0
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326
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MAST package: Most appropriate way to perform lrTest for effect of factor with multiple levels in pairwise manner?
MAST
7 months ago Kelly • 0
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0
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530
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Linear Mixed Model for Differential Gene Expression in Single-Cell RNAseq with Batch Effects
lmer MAST DifferentialExpression
7 months ago nhaus ▴ 70
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2
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759
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Extracting genomic sequences using agat and bedtools yields different results
MAST
updated 11 months ago by ★ 4.7k • written 11 months ago by • 0
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732
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Error: grouping factors must have > 1 sampled level
Mast mastR MAST
updated 11 months ago by 68k • written 11 months ago by • 0
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379
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Comparing the effects of a condition over time in two seperate tissues
MAST
12 months ago Dillon • 0
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1
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716
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Mismatch between MAST DE results and expression dot plot
MAST mastR
13 months ago Simon • 0
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0
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766
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How to extract P-Values and LogFC from lrTest in MAST?
pvalue logFC lrtest MAST
22 months ago Tadeoye ▴ 20
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7
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2.0k
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Likelihood ratio test (lrTest) in MAST comparing full to reduced model; and another question on controlling for CDR
MAST
23 months ago Ken C • 0
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629
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MAST for single cell ATAC data
MAST
24 months ago zuljiamel1991 ▴ 10
2
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2
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2.3k
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Input for MAST
MAST
2.0 years ago • updated 23 months ago zuljiamel1991 ▴ 10
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0
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1.4k
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How to interpret MAST coefficients
DifferentialExpression MAST
2.4 years ago Ismail • 0
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0
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703
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How does MAST caculate log fc
MAST
2.5 years ago Chenghao • 0
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0
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898
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Differential expression with single cell data: any good two component (hurdle) models recently?
SingleCellWorkflow DifferentialExpression SingleCell SingleCellMultiModal MAST
2.7 years ago Nik Tuzov ▴ 90
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0
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1.0k
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Performing DGE analysis with MAST on a variable with more than 2 levels
MAST DEG SingleCell
2.8 years ago zroger499 • 0
0
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1
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1.3k
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Low logFCs using MAST for scRNA-seq
MAST
updated 5 months ago by ▴ 70 • written 2.9 years ago by • 0
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0
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1.0k
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Issues geting meaninfull results for single cell DGE using MAST
MAST SingleCell
3.1 years ago zroger499 • 0
1
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0
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847
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When I run `zlm` with several clusters, how to compare 1 cluster versus all the others?
MAST
3.5 years ago Dan • 0
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1
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1.2k
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Differentially expressed genes across three different conditions
MAST SingleCell diffGeneAnalysis
updated 3.6 years ago by 68k • written 3.6 years ago by • 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 4.0 years ago by • 0
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1
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1.5k
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How to do pairwise multiple comparisons in MAST
MAST
updated 7 months ago by • 0 • written 4.0 years ago by • 0
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2
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1.5k
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MAST compare two conditions with several donors
MAST
updated 4.0 years ago by • 0 • written 4.3 years ago by • 0
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3
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1.8k
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MAST invalid Hypothesis, class objectORconnection error
R MAST scRNASeq
4.5 years ago TriS ▴ 200
1
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3
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1.7k
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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
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1.8k
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About getting DE genes using MAST
MAST
updated 5.2 years ago by ▴ 270 • written 5.2 years ago by • 0
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0
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1.1k
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DEG among experimental and control group in MAST
MAST DEG batch effects
5.4 years ago chendianyu • 0
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1
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2.2k
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Minimum number of cells required for the MAST
MAST scRNAseq differential expression
5.5 years ago Andrew_McDavid ▴ 270
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3
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1.5k
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Logistic regression in MAST - question
mast
updated 6.0 years ago by ▴ 270 • written 6.0 years ago by ▴ 90
2
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7
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2.1k
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Estimation of non-trivial contrasts in MAST
mast
updated 6.0 years ago by ▴ 270 • written 6.0 years ago by ▴ 90
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1
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1.4k
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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 11 months ago by ▴ 30 • written 6.0 years ago by • 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
6.5 years ago santos22903 • 0
0
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6
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1.8k
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Error in zlm function model matrix
MAST
6.8 years ago jka8119 ▴ 10
2
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4
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2.3k
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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
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1
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3.0k
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MAST: testing differential expression with a nested factorial design
MAST single-cell rna-seq
updated 6.8 years ago by ▴ 270 • written 6.9 years ago by ▴ 20
2
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1
reply
1.3k
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How to load data csv in MAST
mast
6.8 years ago francesco.brundu@gmail.com ▴ 40
0
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4
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1.6k
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MAST: What does the function gseaAfterBoot do exactly?
MAST
6.9 years ago dfm2129 • 0
0
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8
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2.3k
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MAST - not getting Hurdle p values
MAST
updated 7.0 years ago by ▴ 270 • written 7.0 years ago by ▴ 10
2
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3
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2.4k
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Using MAST with DropSeq data
MAST mast dropseq
updated 7.0 years ago by ▴ 270 • written 7.0 years ago by ▴ 10
4
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3
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2.5k
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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
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2
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1.7k
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What is the most useful distance measure to use for cell clustering based on MAST deviance residuals?
MAST
7.4 years ago alexanderaivazidis • 0
3
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3
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3.1k
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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
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1
reply
2.2k
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NAs in continuous coefficient and fold change in `zlm`
scrnaseq MAST differential gene expression
7.5 years ago Andrew_McDavid ▴ 270
2
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1
reply
4.9k
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Intepretation of Z scores for gene set enrichment analysis in MAST
MAST scRNA GSEA
updated 7.6 years ago by ▴ 270 • written 7.6 years ago by • 0
0
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3
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1.8k
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Modeling Dose-response data in MAST
MAST sc-rnaseq scrnaseq
updated 7.6 years ago by ▴ 270 • written 7.6 years ago by • 0
0
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1
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1.6k
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Removal of batch effects before non-linear clustering for scRNAseq
scrnaseq MAST
7.8 years ago Andrew_McDavid ▴ 270
3
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2
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2.7k
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MAST reported warning "Coefficients ... are never estimible and will be dropped."
mast sc-rnaseq
7.9 years ago shao ▴ 100
49 results • Page 1 of 1
Recent ...
Replies
Answer: EuroBioC2023 abstract submission is open! by cirwin009 • 0
Submit here https://openreview.net/group?id=bioconductor.org/EuroBioC/2023/ [Block Blast][1] This article offers a thorough and in-depth…
Comment: How to formulate 2 factor nested design in DESeq2 by Mariane • 0
Hi JK Kim, I'm having a problem similar to the one you reported. Could you please tell me how you solved this problem? Thanks
Comment: batch effect removal for agilent microarray data by gaye.yilmaz • 0
Thank you
Answer: Pathview visualisation not including positive log2 fold changes by James W. MacDonald 68k
Without providing a self-contained example, nobody can tell you if/where you went wrong. Since you get a KEGG pathway with some of the gene…
Comment: Differential variance analysis - can i use deseq2 by Marwan • 0
Thanks Michael for your answer, i didnt mean to use Deseq2 directly for the variance testing, but more like asking if using the (VST) data…
Votes
Answer: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
Suggesting changing the "reply-to" field to the mailing list address.
Answer: UniProt.ws query for single UniRef90 ID takes several minutes
A: How to extract DESeq2 results for an interaction design
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K?
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