Showing : MAST • reset
1
vote
2
replies
261
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
184
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
159
views
Comparing the effects of a condition over time in two seperate tissues
MAST
9 weeks ago Dillon • 0
0
votes
1
reply
275
views
Mismatch between MAST DE results and expression dot plot
MAST mastR
3 months ago Simon • 0
0
votes
0
replies
415
views
How to extract P-Values and LogFC from lrTest in MAST?
pvalue logFC lrtest MAST
12 months ago Tadeoye ▴ 20
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
0
replies
394
views
MAST for single cell ATAC data
MAST
14 months ago zuljiamel1991 ▴ 10
1
vote
2
replies
1.2k
views
Input for MAST
MAST
14 months ago • updated 13 months ago zuljiamel1991 ▴ 10
0
votes
0
replies
920
views
How to interpret MAST coefficients
DifferentialExpression MAST
18 months ago Ismail • 0
0
votes
0
replies
466
views
How does MAST caculate log fc
MAST
20 months ago Chenghao • 0
0
votes
0
replies
667
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
0
votes
0
replies
697
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
869
views
Low logFCs using MAST for scRNA-seq
MAST
2.1 years ago learner_MD • 0
0
votes
0
replies
726
views
Issues geting meaninfull results for single cell DGE using MAST
MAST SingleCell
2.3 years ago zroger499 • 0
1
vote
0
replies
630
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
1
reply
925
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
1
reply
846
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
1.0k
views
How to do pairwise multiple comparisons in MAST
MAST
3.2 years ago sysumed3615 • 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
0
votes
3
replies
1.5k
views
MAST invalid Hypothesis, class objectORconnection error
R MAST scRNASeq
3.7 years ago TriS ▴ 200
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
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
0
votes
0
replies
871
views
DEG among experimental and control group in MAST
MAST DEG batch effects
4.6 years ago chendianyu • 0
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
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
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
1.1k
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
2
replies
1.2k
views
Warning in bayes fit in MAST GSEA
MAST GSEA bayesglm.fit
5.6 years ago santos22903 • 0
0
votes
6
replies
1.4k
views
Error in zlm function model matrix
MAST
6.0 years ago jka8119 ▴ 10
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
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
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 6.0 years ago by ▴ 20
0
votes
4
replies
1.3k
views
MAST: What does the function gseaAfterBoot do exactly?
MAST
6.1 years ago dfm2129 • 0
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
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
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
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
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
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 6.7 years ago by • 0
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
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
43 results • Page 1 of 1
Recent ...
Replies
Comment: How to retrieve gene ontology GO class from gene list? by bandconductor • 0
Thanks, this is potentially a much faster way than parsing BiomRt. However, it is only returning one GO term right now (biomaRt returns a f…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
Both `RUVseq` and `sva` are meant to be used to remove technical variability. The problem is the identification of variability that is tech…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0
Hello James, Thank you very much for your answer and taking the time to read my post. I understand your remark, but isn't the approach o…
Comment: PCA plot suggestions by JKim • 0
cross post: https://www.biostars.org/p/9593486/
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
You cannot correct for technical variability due to batch if samples are nested in batch. The technical and biological differences are comp…
Votes
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Awards • All
Scholar to James W. MacDonald 65k
Supporter to JKim • 0
Popular Question to Gordon Smyth 50k
Popular Question to Chris • 0
Supporter to Jonathan ▴ 10
Locations • All
Germany, 1 minute ago
United States, 7 minutes ago
France, 17 minutes ago
United Kingdom, 22 minutes ago
United States, 23 minutes ago
Traffic: 1086 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6