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MAST
•
reset
0
votes
4
replies
1.3k
views
MAST: What does the function gseaAfterBoot do exactly?
MAST
6.1 years ago
dfm2129
• 0
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
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
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
Andrew_McDavid
▴ 270 • written 6.6 years ago by
Shian Su
▴ 40
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
Andrew_McDavid
▴ 270 • written 6.3 years ago by
shao
▴ 100
2
votes
3
replies
2.0k
views
Using MAST with DropSeq data
MAST
mast
dropseq
updated 6.2 years ago by
Andrew_McDavid
▴ 270 • written 6.2 years ago by
jeremycfd
▴ 10
1
vote
2
replies
1.2k
views
Input for MAST
MAST
14 months ago • updated 13 months ago
zuljiamel1991
▴ 10
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
Andrew_McDavid
▴ 270 • written 6.1 years ago by
khandarius
▴ 20
2
votes
1
reply
1.1k
views
How to load data csv in MAST
mast
6.0 years ago
francesco.brundu@gmail.com
▴ 40
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
Andrew_McDavid
▴ 270 • written 6.0 years ago by
francesco.brundu@gmail.com
▴ 40
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
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
3
replies
1.4k
views
Modeling Dose-response data in MAST
MAST
sc-rnaseq
scrnaseq
updated 6.8 years ago by
Andrew_McDavid
▴ 270 • written 6.8 years ago by
eleanorahowe
• 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
2
votes
7
replies
1.7k
views
Estimation of non-trivial contrasts in MAST
mast
updated 5.1 years ago by
Andrew_McDavid
▴ 270 • written 5.1 years ago by
Nik Tuzov
▴ 80
0
votes
1
reply
929
views
Differentially expressed genes across three different conditions
MAST
SingleCell
diffGeneAnalysis
updated 2.8 years ago by
James W. MacDonald
65k • written 2.8 years ago by
sofia.puvogel
• 0
2
votes
3
replies
1.2k
views
Logistic regression in MAST - question
mast
updated 5.1 years ago by
Andrew_McDavid
▴ 270 • written 5.1 years ago by
Nik Tuzov
▴ 80
0
votes
8
replies
1.7k
views
MAST - not getting Hurdle p values
MAST
updated 6.2 years ago by
Andrew_McDavid
▴ 270 • written 6.2 years ago by
jka8119
▴ 10
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
2
votes
1
reply
4.2k
views
Intepretation of Z scores for gene set enrichment analysis in MAST
MAST
scRNA
GSEA
updated 6.8 years ago by
Andrew_McDavid
▴ 270 • written 6.8 years ago by
siajunren
• 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
Andrew_McDavid
▴ 270 • written 4.3 years ago by
ramonmassoni
▴ 10
0
votes
1
reply
1.2k
views
About getting DE genes using MAST
MAST
updated 4.3 years ago by
Andrew_McDavid
▴ 270 • written 4.3 years ago by
ahmed.abbas
• 0
0
votes
2
replies
1.1k
views
MAST compare two conditions with several donors
MAST
updated 3.2 years ago by
Emanuele
• 0 • written 3.5 years ago by
sofia.puvogel
• 0
1
vote
2
replies
265
views
Extracting genomic sequences using agat and bedtools yields different results
MAST
updated 5 weeks ago by
ATpoint
★ 4.0k • written 5 weeks ago by
maximilian.beikirch
• 0
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
2
replies
1.2k
views
Warning in bayes fit in MAST GSEA
MAST
GSEA
bayesglm.fit
5.6 years ago
santos22903
• 0
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
rproendo
▴ 20 • written 5.2 years ago by
mcalgaro93
• 0
0
votes
0
replies
873
views
DEG among experimental and control group in MAST
MAST
DEG
batch effects
4.6 years ago
chendianyu
• 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
849
views
MAST zlm shows warning: Coefficients ... are never estimible and will be dropped.
MAST
updated 2.9 years ago by
shamsudheen
• 0 • written 3.2 years ago by
Helene
• 0
0
votes
1
reply
279
views
Mismatch between MAST DE results and expression dot plot
MAST
mastR
3 months ago
Simon
• 0
0
votes
0
replies
923
views
How to interpret MAST coefficients
DifferentialExpression
MAST
18 months ago
Ismail
• 0
0
votes
0
replies
730
views
Issues geting meaninfull results for single cell DGE using MAST
MAST
SingleCell
2.3 years ago
zroger499
• 0
0
votes
0
replies
870
views
Low logFCs using MAST for scRNA-seq
MAST
2.1 years ago
learner_MD
• 0
0
votes
0
replies
417
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
188
views
Error: grouping factors must have > 1 sampled level
Mast
mastR
MAST
updated 7 weeks ago by
James W. MacDonald
65k • written 7 weeks ago by
Andrew
• 0
0
votes
0
replies
396
views
MAST for single cell ATAC data
MAST
14 months ago
zuljiamel1991
▴ 10
0
votes
0
replies
162
views
Comparing the effects of a condition over time in two seperate tissues
MAST
9 weeks ago
Dillon
• 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
635
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
700
views
Performing DGE analysis with MAST on a variable with more than 2 levels
MAST
DEG
SingleCell
23 months ago
zroger499
• 0
43 results • Page
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Recent ...
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Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
pl23
• 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions
by
Michael Love
41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
by
ussarizona
▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative?
by
Michael Love
41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Answer: ATACseq merge peaks
by
ATpoint
★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Votes
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
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