Showing : mast • reset
2
votes
1
reply
4.2k
views
Intepretation of Z scores for gene set enrichment analysis in MAST
MAST scRNA GSEA
updated 6.7 years ago by ▴ 270 • written 6.8 years ago by • 0
3
votes
3
replies
2.4k
views
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
2
votes
1
reply
2.3k
views
MAST: testing differential expression with a nested factorial design
MAST single-cell rna-seq
updated 6.0 years ago by ▴ 270 • written 6.1 years ago by ▴ 20
3
votes
2
replies
2.2k
views
MAST reported warning "Coefficients ... are never estimible and will be dropped."
mast sc-rnaseq
7.1 years ago • updated 7.0 years ago shao ▴ 100
2
votes
3
replies
2.0k
views
Using MAST with DropSeq data
MAST mast dropseq
updated 6.2 years ago by ▴ 270 • written 6.2 years ago by ▴ 10
4
votes
3
replies
1.9k
views
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
2
votes
4
replies
1.8k
views
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
4
votes
1
reply
1.8k
views
NAs in continuous coefficient and fold change in `zlm`
scrnaseq MAST differential gene expression
6.7 years ago Andrew_McDavid ▴ 270
0
votes
8
replies
1.7k
views
MAST - not getting Hurdle p values
MAST
updated 6.2 years ago by ▴ 270 • written 6.2 years ago by ▴ 10
2
votes
7
replies
1.7k
views
Estimation of non-trivial contrasts in MAST
mast
updated 5.1 years ago by ▴ 270 • written 5.1 years ago by ▴ 80
0
votes
1
reply
1.6k
views
Minimum number of cells required for the MAST
MAST scRNAseq differential expression
4.6 years ago Andrew_McDavid ▴ 270
0
votes
3
replies
1.5k
views
MAST invalid Hypothesis, class objectORconnection error
R MAST scRNASeq
3.7 years ago TriS ▴ 200
0
votes
6
replies
1.4k
views
Error in zlm function model matrix
MAST
6.0 years ago jka8119 ▴ 10
0
votes
3
replies
1.4k
views
Modeling Dose-response data in MAST
MAST sc-rnaseq scrnaseq
updated 6.8 years ago by ▴ 270 • written 6.8 years ago by • 0
0
votes
1
reply
1.3k
views
Removal of batch effects before non-linear clustering for scRNAseq
scrnaseq MAST
7.0 years ago Andrew_McDavid ▴ 270
0
votes
2
replies
1.3k
views
What is the most useful distance measure to use for cell clustering based on MAST deviance residuals?
MAST
6.6 years ago alexanderaivazidis • 0
0
votes
4
replies
1.3k
views
MAST: What does the function gseaAfterBoot do exactly?
MAST
6.1 years ago dfm2129 • 0
1
vote
7
replies
1.3k
views
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
0
votes
1
reply
1.2k
views
About getting DE genes using MAST
MAST
updated 4.3 years ago by ▴ 270 • written 4.3 years ago by • 0
1
vote
3
replies
1.2k
views
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
1
vote
2
replies
1.2k
views
Input for MAST
MAST
14 months ago • updated 13 months ago zuljiamel1991 ▴ 10
2
votes
3
replies
1.2k
views
Logistic regression in MAST - question
mast
updated 5.1 years ago by ▴ 270 • written 5.1 years ago by ▴ 80
0
votes
2
replies
1.2k
views
Warning in bayes fit in MAST GSEA
MAST GSEA bayesglm.fit
5.6 years ago santos22903 • 0
0
votes
2
replies
1.1k
views
MAST compare two conditions with several donors
MAST
updated 3.2 years ago by • 0 • written 3.5 years ago by • 0
2
votes
1
reply
1.1k
views
How to load data csv in MAST
mast
6.0 years ago francesco.brundu@gmail.com ▴ 40
0
votes
1
reply
1.1k
views
How can I compute AIC for MAST hurdle model fitted in the whole dataset?
MAST AIC calcuation Parameters single cell hurdle model
updated 5 weeks ago by ▴ 20 • written 5.2 years ago by • 0
0
votes
0
replies
1.0k
views
How to do pairwise multiple comparisons in MAST
MAST
3.2 years ago sysumed3615 • 0
0
votes
1
reply
927
views
Differentially expressed genes across three different conditions
MAST SingleCell diffGeneAnalysis
updated 2.8 years ago by 65k • written 2.8 years ago by • 0
0
votes
0
replies
923
views
How to interpret MAST coefficients
DifferentialExpression MAST
18 months ago Ismail • 0
0
votes
0
replies
872
views
DEG among experimental and control group in MAST
MAST DEG batch effects
4.6 years ago chendianyu • 0
0
votes
0
replies
870
views
Low logFCs using MAST for scRNA-seq
MAST
2.1 years ago learner_MD • 0
0
votes
1
reply
849
views
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
0
votes
0
replies
729
views
Issues geting meaninfull results for single cell DGE using MAST
MAST SingleCell
2.3 years ago zroger499 • 0
0
votes
0
replies
700
views
Performing DGE analysis with MAST on a variable with more than 2 levels
MAST DEG SingleCell
23 months ago zroger499 • 0
0
votes
0
replies
669
views
Differential expression with single cell data: any good two component (hurdle) models recently?
SingleCellWorkflow DifferentialExpression SingleCell SingleCellMultiModal MAST
22 months ago Nik Tuzov ▴ 80
1
vote
0
replies
634
views
When I run `zlm` with several clusters, how to compare 1 cluster versus all the others?
MAST
2.7 years ago Dan • 0
0
votes
0
replies
468
views
How does MAST caculate log fc
MAST
20 months ago Chenghao • 0
0
votes
0
replies
416
views
How to extract P-Values and LogFC from lrTest in MAST?
pvalue logFC lrtest MAST
12 months ago Tadeoye ▴ 20
0
votes
0
replies
396
views
MAST for single cell ATAC data
MAST
14 months ago zuljiamel1991 ▴ 10
0
votes
1
reply
278
views
Mismatch between MAST DE results and expression dot plot
MAST mastR
3 months ago Simon • 0
1
vote
2
replies
263
views
Extracting genomic sequences using agat and bedtools yields different results
MAST
updated 5 weeks ago by ★ 4.0k • written 5 weeks ago by • 0
0
votes
0
replies
186
views
Error: grouping factors must have > 1 sampled level
Mast mastR MAST
updated 7 weeks ago by 65k • written 7 weeks ago by • 0
0
votes
0
replies
160
views
Comparing the effects of a condition over time in two seperate tissues
MAST
9 weeks ago Dillon • 0
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Comment: Deseq2. decontXcounts not integers. Useful alternative? by ATpoint ★ 4.0k
I do not know this decontamination tool you use but generally: If these counts are basically "corrected" raw counts in the sense that they'…
Answer: Improving the design matrices vignette in RNAseq123 by Gordon Smyth 50k
Thanks to Shian Su, we have confirmed that the problem in the design matrices vignette html is caused by a bug in knitr 1.44 (to do with sp…
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by winwater0928 • 0
Thank you for your comment! I'll review my code from top to bottom.
Comment: Math expression in shapeCustom legend in EnhancedVolcano by James W. MacDonald 65k
So basically you are using HTML markup to set your subscripts and whatnot, and then `element_markdown` does the rest.
Comment: Math expression in shapeCustom legend in EnhancedVolcano by James W. MacDonald 65k
Oh snap. Foiled again. Here it is with spaces & ge ; and & lt ;
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Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
Answer: Cross-species analysis - how to compute the mid parent value?
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
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