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SingleCell
•
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0
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replies
23
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Differential expression with single cell data: any good two component (hurdle) models recently?
SingleCellWorkflow
DifferentialExpression
SingleCell
SingleCellMultiModal
MAST
21 hours ago • updated 17 hours ago
Nik Tuzov
▴ 70
0
votes
0
replies
75
views
Performing DGE analysis with MAST on a variable with more than 2 levels
MAST
DEG
SingleCell
6 weeks ago
zroger499
• 0
2
votes
1
reply
110
views
() followed by [] within an argument in singlecell OSCA workflow
SingleCell
R
OSCA
updated 9 weeks ago by
jeroen.gilis
▴ 70 • written 9 weeks ago by
BioInfoBeginnerrr
• 0
2
votes
1
reply
326
views
Convert AnnotatedDataFrame S4 object from GEO datasets to Seurat Object
biobase
SingleCellData
seurat
SingleCell
updated 5 months ago by
James W. MacDonald
60k • written 5 months ago by
NGS_enthusiast
• 0
0
votes
0
replies
141
views
Issues geting meaninfull results for single cell DGE using MAST
MAST
SingleCell
5 months ago
zroger499
• 0
0
votes
0
replies
274
views
Job:
Postdoc Opening in Bioinformatics or Computational Biology
SpatialData
scRNAseq
SingleCell
Omixer
5 months ago
Sebastian Lewandowski
• 0
1
vote
2
replies
359
views
velociraptor preparation
SingleCellExperiment
singlecell
velociraptor
scvelo
updated 6 months ago by
ATpoint
★ 1.3k • written 6 months ago by
Pietro
▴ 30
0
votes
0
replies
217
views
Job:
Research Scientists/Postdoctoral Candidates/Computational Biologists and Programmers excited about computational challenges in modeling CRISPR genome…
CRISPR
SingleCell
Genomics
8 months ago
lpinello
• 0
1
vote
2
replies
355
views
Using limma duplicateCorrelation to account for donor/dataset effects in scRNA-Seq pseudobulk counts from multiple sources
limma
SingleCell
8 months ago
Andrew Pattison
• 0
0
votes
0
replies
185
views
Spike-In Cells for Normalization?
SpikeIn
SingleCell
10 months ago
mb1996
• 0
0
votes
0
replies
239
views
Job:
Computational postdoctoral fellow for cancer disparities research (Boston University)
DNASeq
RNASeq
SingleCell
10 months ago
camp
• 0
0
votes
0
replies
267
views
Job:
Senior Bioinformatician - University of Alabama at Birmingham
JobPosting
Transcriptomics
SingleCell
RNA-seq
11 months ago
lianov
• 0
0
votes
1
reply
259
views
Differentially expressed genes across three different conditions
MAST
SingleCell
diffGeneAnalysis
updated 12 months ago by
James W. MacDonald
60k • written 12 months ago by
sofia.puvogel
• 0
2
votes
4
replies
2.7k
views
How to convert large gene counts data into matrix?
R
singlecell
bioinformatics
seurat
updated 16 months ago by
aedin
• 0 • written 2.9 years ago by
sambunga094
• 0
3
votes
2
replies
483
views
Merging only those samples sequenced over multiple batches - scRNA-seq
SingleCell
SingleCellExperiment
scater
16 months ago
camerond
• 0
0
votes
0
replies
411
views
Job:
Computational Biologist at Denali Therapeutics
Transcriptomics
SingleCell
JobPosting
18 months ago
Steve Lianoglou
13k
0
votes
2
replies
551
views
Removal of cell cycle effect using batchelor::regressBatches() and proper usage of corrected UMI matrix
scRNAseq
batchelor
SingleCell
SingleCellExperiment
scran
18 months ago
jirkanov
• 0
2
votes
1
reply
799
views
DESeq2 DE gene expression of scRNA-seq pseudobulk
DESeq2
SingleCell
updated 19 months ago by
Michael Love
37k • written 19 months ago by
Christian
• 0
0
votes
1
reply
312
views
improving running time of runNMF
runNMF
scater
singlecell
SingleCellExperiment
updated 19 months ago by
Aaron Lun
★ 27k • written 19 months ago by
lirongrossmann
▴ 40
0
votes
0
replies
266
views
Creating a stable batch-corrected scRNA-Seq data with multiple datasets and multiple integrations
scater
singlecell
scran
BatchEffect
19 months ago
hamza_karakurt
▴ 50
2
votes
6
replies
864
views
Discarding ambient RNA using estimateAmbience
emptyDrop
ambient
singlecell
estimateAmbience
updated 21 months ago by
Aaron Lun
★ 27k • written 21 months ago by
lirongrossmann
▴ 40
0
votes
6
replies
883
views
Discrepancy between cell type and cluster using SingleCellExperiment and SingleR
singlecell
singlecellexperiment
umap
singleR
updated 22 months ago by
Aaron Lun
★ 27k • written 22 months ago by
lirongrossmann
▴ 60
0
votes
2
replies
541
views
most correlated genes in SingleR
singlecell
singleR
updated 22 months ago by
Aaron Lun
★ 27k • written 22 months ago by
lirongrossmann
▴ 40
0
votes
1
reply
423
views
predicting cell type of clusters using singleR
singleR
singlecell
updated 22 months ago by
Aaron Lun
★ 27k • written 22 months ago by
lirongrossmann
▴ 40
0
votes
3
replies
968
views
marker genes in singleR
singleR
singlecell
singlecellexperiment
updated 22 months ago by
Aaron Lun
★ 27k • written 22 months ago by
lirongrossmann
▴ 40
0
votes
1
reply
327
views
Error in .updateHubDB(hub_bfc, .class, url, proxy, localHub) :
annotation
singlecell
rna-seq
updated 2.4 years ago by
shepherl
3.1k • written 2.4 years ago by
panxingxin16
• 0
5
votes
5
replies
637
views
Association analysis between gene expression and Phenotype
rna
singlecell
limma
updated 3.2 years ago by
Aaron Lun
★ 27k • written 3.2 years ago by
hrishi27n
▴ 20
27 results • Page
1 of 1
Recent ...
Replies
Comment: LogFC: how do you determine the cutoff for differentially expressed genes?
by
OE
• 0
Hi Aaron, I have been performing some Diffrential Methylation Analysis and found some logFC values really closer to 0 ( from - 0.07 to 0.1…
Comment: Macbook M1 install genefilter failed
by
matt.broerman
• 0
This error is similar to this one: https://stackoverflow.com/questions/66817276/how-to-install-rcpparmadillo-on-apple-silicon-m1-macs So i…
Comment: miRNA differential expression analysis - treat as transcript level?
by
BG
• 0
Hi, attached is the plot for the inferential variance (code according to the fishpond vignette). How does this look to you? The first plot …
Answer: miRNA differential expression analysis - treat as transcript level?
by
Michael Love
37k
If it's "ok" depends on the amount of inferential uncertainty. We have benchmarked typical gene-level methods and found that we don't gain …
Comment: RSEM - tximport; where is effective_length information used? Implications for sc
by
Michael Love
37k
@atpoint is correct -- it's not enough to say single-cell. In the tximport vignette we have a note about transcript length correction for 3…
Votes
Comment: RSEM - tximport; where is effective_length information used? Implications for sc
Answer: Help with limma contrast, difference of a difference?
Answer: Help with limma contrast, difference of a difference?
Answer: Help with limma contrast, difference of a difference?
Answer: Is it possible to speed up VariantAnnotation's rowRanges function when convertin
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Michael Love
37k
Popular Question
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Gordon Smyth
45k
Scholar
to
James W. MacDonald
60k
Popular Question
to
Nik Tuzov
▴ 70
Teacher
to
Kevin Blighe
3.5k
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