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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
6.5 years ago
alexanderaivazidis
• 0
4
votes
1
reply
1.7k
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 6.0 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
7.0 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 6.7 years ago by
Andrew_McDavid
▴ 270 • written 6.7 years ago by
eleanorahowe
• 0
1
vote
7
replies
1.2k
views
Likelihood ratio test (lrTest) in MAST comparing full to reduced model; and another question on controlling for CDR
MAST
13 months ago • updated 12 months ago
Ken C
• 0
2
votes
7
replies
1.6k
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
916
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 6.7 years ago by
Andrew_McDavid
▴ 270 • written 6.7 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 3.4 years ago by
sofia.puvogel
• 0
1
vote
2
replies
240
views
Extracting genomic sequences using agat and bedtools yields different results
MAST
updated 29 days ago by
ATpoint
★ 4.0k • written 4 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
5.9 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
1.0k
views
How can I compute AIC for MAST hurdle model fitted in the whole dataset?
MAST
AIC calcuation
Parameters
single cell
hurdle model
updated 4 weeks ago by
rproendo
▴ 20 • written 5.2 years ago by
mcalgaro93
• 0
0
votes
0
replies
868
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
836
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
262
views
Mismatch between MAST DE results and expression dot plot
MAST
mastR
3 months ago
Simon
• 0
0
votes
0
replies
913
views
How to interpret MAST coefficients
DifferentialExpression
MAST
18 months ago
Ismail
• 0
0
votes
0
replies
718
views
Issues geting meaninfull results for single cell DGE using MAST
MAST
SingleCell
2.2 years ago
zroger499
• 0
0
votes
0
replies
862
views
Low logFCs using MAST for scRNA-seq
MAST
2.1 years ago
learner_MD
• 0
0
votes
0
replies
409
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
169
views
Error: grouping factors must have > 1 sampled level
Mast
mastR
MAST
updated 6 weeks ago by
James W. MacDonald
65k • written 6 weeks ago by
Andrew
• 0
0
votes
0
replies
390
views
MAST for single cell ATAC data
MAST
13 months ago
zuljiamel1991
▴ 10
0
votes
0
replies
153
views
Comparing the effects of a condition over time in two seperate tissues
MAST
8 weeks ago
Dillon
• 0
0
votes
0
replies
657
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
623
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
461
views
How does MAST caculate log fc
MAST
20 months ago
Chenghao
• 0
0
votes
0
replies
691
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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Answer: OrgDb for maize
by
Guido Hooiveld
★ 3.9k
I notice the data you are working with is based on `ensembl` ids. This is important, because the `OrgDb` are annotation databases that are …
Comment: Theoretical WGCNA Question
by
Garrett
• 0
Thanks Peter!
Comment: FGSEA pre-ranked input in increasing order or decreasing
by
sropri
• 0
Thank you!
Comment: FGSEA pre-ranked input in increasing order or decreasing
by
alserg
▴ 240
They are reorder in the decreasing order.
Comment: significant difference of p-values with dream() after updating VariancePartition
by
Le
• 0
Thanks for your reply @gabrielhoffman ! I've been trying to isolate the changes, and v1.32.5 had the same results as v1.33.1 while v1.30.0…
Votes
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
Comment: DEXSeq DEXSeqDataSet count matrix duplication
Comment: Error in champ.load(): The following specified files do not exist
Answer: Error in read.metharray(basenames = files, extended = extended, verbose = verbos
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