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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
2.0k
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
2.1k
views
Using MAST with DropSeq data
MAST
mast
dropseq
updated 6.2 years ago by
Andrew_McDavid
▴ 270 • written 6.3 years ago by
jeremycfd
▴ 10
1
vote
2
replies
1.2k
views
Input for MAST
MAST
14 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 6.1 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
6.1 years ago
francesco.brundu@gmail.com
▴ 40
2
votes
4
replies
1.9k
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
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
14 months ago • updated 13 months ago
Ken C
• 0
2
votes
7
replies
1.7k
views
Estimation of non-trivial contrasts in MAST
mast
updated 5.2 years ago by
Andrew_McDavid
▴ 270 • written 5.2 years ago by
Nik Tuzov
▴ 80
0
votes
1
reply
937
views
Differentially expressed genes across three different conditions
MAST
SingleCell
diffGeneAnalysis
updated 2.9 years ago by
James W. MacDonald
65k • written 2.9 years ago by
sofia.puvogel
• 0
2
votes
3
replies
1.2k
views
Logistic regression in MAST - question
mast
updated 5.2 years ago by
Andrew_McDavid
▴ 270 • written 5.2 years ago by
Nik Tuzov
▴ 80
0
votes
8
replies
1.8k
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
4.7 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
1.3k
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
1.3k
views
About getting DE genes using MAST
MAST
updated 4.4 years ago by
Andrew_McDavid
▴ 270 • written 4.4 years ago by
ahmed.abbas
• 0
0
votes
2
replies
1.1k
views
MAST compare two conditions with several donors
MAST
updated 3.3 years ago by
Emanuele
• 0 • written 3.5 years ago by
sofia.puvogel
• 0
1
vote
2
replies
291
views
Extracting genomic sequences using agat and bedtools yields different results
MAST
updated 6 weeks ago by
ATpoint
★ 4.1k • written 6 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
5.7 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 7 weeks ago by
rproendo
▴ 20 • written 5.2 years ago by
mcalgaro93
• 0
0
votes
0
replies
879
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
870
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
300
views
Mismatch between MAST DE results and expression dot plot
MAST
mastR
3 months ago
Simon
• 0
0
votes
0
replies
941
views
How to interpret MAST coefficients
DifferentialExpression
MAST
19 months ago
Ismail
• 0
0
votes
0
replies
738
views
Issues geting meaninfull results for single cell DGE using MAST
MAST
SingleCell
2.3 years ago
zroger499
• 0
0
votes
0
replies
886
views
Low logFCs using MAST for scRNA-seq
MAST
2.1 years ago
learner_MD
• 0
0
votes
0
replies
436
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
211
views
Error: grouping factors must have > 1 sampled level
Mast
mastR
MAST
updated 9 weeks ago by
James W. MacDonald
65k • written 9 weeks ago by
Andrew
• 0
0
votes
0
replies
409
views
MAST for single cell ATAC data
MAST
14 months ago
zuljiamel1991
▴ 10
0
votes
0
replies
172
views
Comparing the effects of a condition over time in two seperate tissues
MAST
10 weeks ago
Dillon
• 0
0
votes
0
replies
683
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
644
views
When I run `zlm` with several clusters, how to compare 1 cluster versus all the others?
MAST
2.8 years ago
Dan
• 0
0
votes
0
replies
477
views
How does MAST caculate log fc
MAST
20 months ago
Chenghao
• 0
0
votes
0
replies
709
views
Performing DGE analysis with MAST on a variable with more than 2 levels
MAST
DEG
SingleCell
24 months ago
zroger499
• 0
43 results • Page
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Recent ...
Replies
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
by
Hervé Pagès
16k
Indeed. Calculations involving floating point arithmetic are architecture-dependent, and testing the results should be done with `all.equal…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Poonam
• 0
I will follow what you suggested. I didn't use max gap anywhere. I was following statistic I and regarding the size of features, my small…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Michael Love
41k
Oh I see, for the second question, I don't have a great answer. I typically think of one set as the anchor, whose ascertainment is driving …
Comment: Help with running egsea()
by
James W. MacDonald
65k
Oh, right. Ideally you would use NCBI (aka Entrez gene) IDs because they are way more likely to be unique. Gene symbols are broken down int…
Comment: Help with running egsea()
by
Chris
• 0
Thanks James! I update the question. The last question mean when we use `buildIdx()`, could we use gene symbol instead of entrezID. However…
Votes
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Help with running egsea()
Answer: Trim/Filter out-of-bounds GRanges
Comment: Help with running egsea()
Answer: How to save the DEXSeq results
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