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MAST
•
reset
0
votes
0
replies
132
views
Confidence interval contains 0 but p<0.05
MAST
10 weeks ago
Adelyn
• 0
3
votes
3
replies
1.0k
views
Robust way of dealing with low number of samples for Differential Gene Expression
limma
edgeR
DESeq2
MAST
written 3 months ago by
Satoshi
• 0
0
votes
1
reply
416
views
Which input data is acceptable for MAST?
SCTransform
MAST
updated 4 months ago by
Andrew_McDavid
▴ 270 • written 4 months ago by
james.watson1
• 0
0
votes
0
replies
360
views
Z-score Interpretation across components
MAST
5 months ago
GJ
• 0
0
votes
0
replies
325
views
MAST package: Most appropriate way to perform lrTest for effect of factor with multiple levels in pairwise manner?
MAST
7 months ago
Kelly
• 0
0
votes
0
replies
527
views
Linear Mixed Model for Differential Gene Expression in Single-Cell RNAseq with Batch Effects
lmer
MAST
DifferentialExpression
7 months ago
nhaus
▴ 70
1
vote
2
replies
749
views
Extracting genomic sequences using agat and bedtools yields different results
MAST
updated 11 months ago by
ATpoint
★ 4.7k • written 11 months ago by
maximilian.beikirch
• 0
0
votes
0
replies
722
views
Error: grouping factors must have > 1 sampled level
Mast
mastR
MAST
updated 11 months ago by
James W. MacDonald
68k • written 11 months ago by
Andrew
• 0
0
votes
0
replies
379
views
Comparing the effects of a condition over time in two seperate tissues
MAST
12 months ago
Dillon
• 0
0
votes
1
reply
712
views
Mismatch between MAST DE results and expression dot plot
MAST
mastR
13 months ago
Simon
• 0
0
votes
0
replies
760
views
How to extract P-Values and LogFC from lrTest in MAST?
pvalue
logFC
lrtest
MAST
22 months ago
Tadeoye
▴ 20
1
vote
7
replies
2.0k
views
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
0
votes
0
replies
627
views
MAST for single cell ATAC data
MAST
23 months ago
zuljiamel1991
▴ 10
2
votes
2
replies
2.3k
views
Input for MAST
MAST
2.0 years ago • updated 23 months ago
zuljiamel1991
▴ 10
0
votes
0
replies
1.4k
views
How to interpret MAST coefficients
DifferentialExpression
MAST
2.3 years ago
Ismail
• 0
0
votes
0
replies
698
views
How does MAST caculate log fc
MAST
2.5 years ago
Chenghao
• 0
0
votes
0
replies
898
views
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
0
votes
0
replies
1.0k
views
Performing DGE analysis with MAST on a variable with more than 2 levels
MAST
DEG
SingleCell
2.8 years ago
zroger499
• 0
0
votes
1
reply
1.3k
views
Low logFCs using MAST for scRNA-seq
MAST
updated 5 months ago by
nhaus
▴ 70 • written 2.9 years ago by
learner_MD
• 0
0
votes
0
replies
1.0k
views
Issues geting meaninfull results for single cell DGE using MAST
MAST
SingleCell
3.1 years ago
zroger499
• 0
1
vote
0
replies
845
views
When I run `zlm` with several clusters, how to compare 1 cluster versus all the others?
MAST
3.5 years ago
Dan
• 0
0
votes
1
reply
1.2k
views
Differentially expressed genes across three different conditions
MAST
SingleCell
diffGeneAnalysis
updated 3.6 years ago by
James W. MacDonald
68k • written 3.6 years ago by
sofia.puvogel
• 0
0
votes
1
reply
1.2k
views
MAST zlm shows warning: Coefficients ... are never estimible and will be dropped.
MAST
updated 3.7 years ago by
shamsudheen
• 0 • written 4.0 years ago by
Helene
• 0
0
votes
1
reply
1.5k
views
How to do pairwise multiple comparisons in MAST
MAST
updated 7 months ago by
Kelly
• 0 • written 4.0 years ago by
sysumed3615
• 0
0
votes
2
replies
1.5k
views
MAST compare two conditions with several donors
MAST
updated 4.0 years ago by
Emanuele
• 0 • written 4.3 years ago by
sofia.puvogel
• 0
0
votes
3
replies
1.8k
views
MAST invalid Hypothesis, class objectORconnection error
R
MAST
scRNASeq
4.5 years ago
TriS
▴ 200
1
vote
3
replies
1.7k
views
comparing 2 models with confounders with MAST (scRNA-seq DEA)
scRNA-seq
MAST
confounders
updated 5.1 years ago by
Andrew_McDavid
▴ 270 • written 5.1 years ago by
ramonmassoni
▴ 10
0
votes
1
reply
1.7k
views
About getting DE genes using MAST
MAST
updated 5.1 years ago by
Andrew_McDavid
▴ 270 • written 5.1 years ago by
ahmed.abbas
• 0
0
votes
0
replies
1.1k
views
DEG among experimental and control group in MAST
MAST
DEG
batch effects
5.4 years ago
chendianyu
• 0
0
votes
1
reply
2.2k
views
Minimum number of cells required for the MAST
MAST
scRNAseq
differential expression
5.5 years ago
Andrew_McDavid
▴ 270
2
votes
3
replies
1.5k
views
Logistic regression in MAST - question
mast
updated 5.9 years ago by
Andrew_McDavid
▴ 270 • written 5.9 years ago by
Nik Tuzov
▴ 90
2
votes
7
replies
2.1k
views
Estimation of non-trivial contrasts in MAST
mast
updated 5.9 years ago by
Andrew_McDavid
▴ 270 • written 6.0 years ago by
Nik Tuzov
▴ 90
0
votes
1
reply
1.4k
views
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
rproendo
▴ 30 • written 6.0 years ago by
mcalgaro93
• 0
0
votes
2
replies
1.5k
views
Warning in bayes fit in MAST GSEA
MAST
GSEA
bayesglm.fit
6.4 years ago
santos22903
• 0
0
votes
6
replies
1.8k
views
Error in zlm function model matrix
MAST
6.8 years ago
jka8119
▴ 10
2
votes
4
replies
2.3k
views
Interpretation of cngeneson when doing differential expression analysis in MAST
mast
differential gene expression
updated 6.8 years ago by
Andrew_McDavid
▴ 270 • written 6.8 years ago by
francesco.brundu@gmail.com
▴ 40
2
votes
1
reply
3.0k
views
MAST: testing differential expression with a nested factorial design
MAST
single-cell
rna-seq
updated 6.8 years ago by
Andrew_McDavid
▴ 270 • written 6.9 years ago by
khandarius
▴ 20
2
votes
1
reply
1.3k
views
How to load data csv in MAST
mast
6.8 years ago
francesco.brundu@gmail.com
▴ 40
0
votes
4
replies
1.6k
views
MAST: What does the function gseaAfterBoot do exactly?
MAST
6.9 years ago
dfm2129
• 0
0
votes
8
replies
2.3k
views
MAST - not getting Hurdle p values
MAST
updated 7.0 years ago by
Andrew_McDavid
▴ 270 • written 7.0 years ago by
jka8119
▴ 10
2
votes
3
replies
2.4k
views
Using MAST with DropSeq data
MAST
mast
dropseq
updated 7.0 years ago by
Andrew_McDavid
▴ 270 • written 7.0 years ago by
jeremycfd
▴ 10
4
votes
3
replies
2.4k
views
single-cells RNA-seq analysis by MAST with unbalanced group size
mast
single-cell
rna-seq
differential analysis
updated 7.1 years ago by
Andrew_McDavid
▴ 270 • written 7.1 years ago by
shao
▴ 100
0
votes
2
replies
1.6k
views
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
votes
3
replies
3.1k
views
How do you test a contrast in MAST?
MAST
single-cell
differential gene expression
updated 7.4 years ago by
Andrew_McDavid
▴ 270 • written 7.4 years ago by
Shian Su
▴ 40
4
votes
1
reply
2.2k
views
NAs in continuous coefficient and fold change in `zlm`
scrnaseq
MAST
differential gene expression
7.5 years ago
Andrew_McDavid
▴ 270
2
votes
1
reply
4.9k
views
Intepretation of Z scores for gene set enrichment analysis in MAST
MAST
scRNA
GSEA
updated 7.6 years ago by
Andrew_McDavid
▴ 270 • written 7.6 years ago by
siajunren
• 0
0
votes
3
replies
1.8k
views
Modeling Dose-response data in MAST
MAST
sc-rnaseq
scrnaseq
updated 7.6 years ago by
Andrew_McDavid
▴ 270 • written 7.6 years ago by
eleanorahowe
• 0
0
votes
1
reply
1.5k
views
Removal of batch effects before non-linear clustering for scRNAseq
scrnaseq
MAST
7.8 years ago
Andrew_McDavid
▴ 270
3
votes
2
replies
2.7k
views
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: SingleR with multiple single cell references
by
Aaron Lun
★ 28k
> Is it necessary to piece together the individual steps manually (e.g. aggregateReference, trainSingleR, classifySingleR, combineRecompute…
Answer: Automatically install dependencies
by
ATpoint
★ 4.7k
The BiocManager, which is sort of an extended wrapper around `install.packages`, installs all R dependencies. If you see errors then this i…
Answer: To count or not to count multi-overlapping reads?
by
Gordon Smyth
52k
> How does it handle reads that map to a gene that is located in a region that also has another gene but on the alternate strand? Overlapp…
Comment: Weird p-values using DESeq2?
by
ATpoint
★ 4.7k
This does not look like normalized counts but raw counts. Consider using `counts(dds, normalized = TRUE)` or the output of `normTransform()…
Answer: Weird p-values using DESeq2?
by
Wolfgang Huber
★ 13k
Dear Ingrid, thank you for asking. Can you provide the input count matrix (you can "pseudonymize" the biological conditions and the gene n…
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A: Fraction count for multi mapping reads; how to generate input file for Deseq2 fo
Comment: Weird p-values using DESeq2?
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Answer: Store Matrix in DataFrame Cell
Answer: enrichGOgradient color change
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