Log In
Sign Up
about
faq
Ask a question
Latest
News
Jobs
Tutorials
Tags
Users
New Post
Latest
News
Jobs
Tutorials
Tags
Users
Log In
Sign Up
About
Limit
all time
today
this week
this month
this year
Unanswered
All posts
Sort
Update
Answers
Bookmarks
Creation
Replies
Rank
Views
Votes
Showing :
SingleCell
•
reset
0
votes
2
replies
583
views
Why my log2fcs are too high?
DESeq2
SingleCell
log2FC
11 months ago
paria.alipour
• 0
0
votes
1
reply
1.7k
views
Error in .updateHubDB(hub_bfc, .class, url, proxy, localHub) :
annotation
singlecell
rna-seq
updated 4.1 years ago by
shepherl
3.8k • written 4.1 years ago by
panxingxin16
• 0
0
votes
3
replies
1.9k
views
marker genes in singleR
singleR
singlecell
singlecellexperiment
updated 3.6 years ago by
Aaron Lun
★ 28k • written 3.6 years ago by
lirongrossmann
▴ 40
0
votes
1
reply
1.3k
views
predicting cell type of clusters using singleR
singleR
singlecell
updated 3.6 years ago by
Aaron Lun
★ 28k • written 3.6 years ago by
lirongrossmann
▴ 40
0
votes
2
replies
1.4k
views
most correlated genes in SingleR
singlecell
singleR
updated 3.6 years ago by
Aaron Lun
★ 28k • written 3.6 years ago by
lirongrossmann
▴ 40
0
votes
6
replies
2.5k
views
Discrepancy between cell type and cluster using SingleCellExperiment and SingleR
singlecell
singlecellexperiment
umap
singleR
updated 3.6 years ago by
Aaron Lun
★ 28k • written 3.6 years ago by
lirongrossmann
▴ 80
2
votes
6
replies
2.0k
views
Discarding ambient RNA using estimateAmbience
emptyDrop
ambient
singlecell
estimateAmbience
updated 3.5 years ago by
Aaron Lun
★ 28k • written 3.5 years ago by
lirongrossmann
▴ 40
0
votes
1
reply
803
views
improving running time of runNMF
runNMF
scater
singlecell
SingleCellExperiment
updated 3.4 years ago by
Aaron Lun
★ 28k • written 3.4 years ago by
lirongrossmann
▴ 40
2
votes
1
reply
1.8k
views
DESeq2 DE gene expression of scRNA-seq pseudobulk
DESeq2
SingleCell
updated 3.3 years ago by
Michael Love
41k • written 3.3 years ago by
Christian
• 0
0
votes
2
replies
1.4k
views
Removal of cell cycle effect using batchelor::regressBatches() and proper usage of corrected UMI matrix
scRNAseq
batchelor
SingleCell
SingleCellExperiment
scran
3.3 years ago
jirkanov
• 0
0
votes
1
reply
705
views
Set up "mock" cell type as the reference?
DESeq2
SingleCell
updated 18 months ago by
Michael Love
41k • written 18 months ago by
Yiqi
▴ 10
3
votes
2
replies
2.1k
views
Merging only those samples sequenced over multiple batches - scRNA-seq
SingleCell
SingleCellExperiment
scater
3.2 years ago • updated 3.1 years ago
camerond
• 0
0
votes
3
replies
803
views
Tissue Level Differential Expression Analysis
DESeq2
DifferentialExpression
differentialex
Pseudobulk
SingleCell
updated 15 months ago by
Michael Love
41k • written 15 months ago by
skanda.hebbale
• 0
0
votes
2
replies
887
views
how to plot a fitting line on the testPseudotime
Pseudotime
testPseudotime
TSCAN
SingleCell
OSCA
18 months ago
Guandong Shang
▴ 40
0
votes
8
replies
1.1k
views
fail to annotate chromosome data to single cell object
error
SingleCell
annotate
updated 4 months ago by
yw24418
• 0 • written 12 months ago by
sandra.garces.19
• 0
1
vote
4
replies
647
views
Single-cell differential expression analysis with multiple samples
SingleCell
12 months ago
iaradsouza1
• 0
0
votes
1
reply
1.1k
views
Error in .testForValidKeys(x, keys, keytype, fks) :
SingleCell
AnnotationDbi
updated 19 months ago by
James W. MacDonald
65k • written 19 months ago by
techgirl2022
• 0
2
votes
1
reply
707
views
() followed by [] within an argument in singlecell OSCA workflow
SingleCell
R
OSCA
updated 23 months ago by
jeroen.gilis
▴ 90 • written 23 months ago by
BioInfoBeginnerrr
• 0
3
votes
1
reply
694
views
'Seurat' package
singlecell
seurat
updated 10 months ago by
ATpoint
★ 4.0k • written 10 months ago by
Sooni
▴ 10
0
votes
1
reply
2.1k
views
DESeq2 after Seurat analysis on integrated datasets
DESeq2
SingleCell
GeneExpression
Seurat
updated 13 months ago by
ATpoint
★ 4.0k • written 13 months ago by
bio.boi
• 0
2
votes
4
replies
864
views
Summary of library size factor is all equal to one
SingleCell
SingleCellData
SingleCellWorkflow
SingleCellExperiment
18 months ago
Romina
• 0
2
votes
2
replies
737
views
How to detect LacZ tagged cells from single cell
SingleCell
SingleCellExperiment
SingleCellWorkflow
SingleCellData
18 months ago
k1m
▴ 20
1
vote
2
replies
1.3k
views
DESeq2 aggregated single cell data
pseudobulk
SingleCell
DESeq2
20 months ago
fluentin44
• 0
0
votes
1
reply
791
views
Single-Cell Data Simulation from Bulk RNA-seq
SingleCell
RNASeq
RNASeqData
scRNAseq
updated 16 months ago by
Gordon Smyth
50k • written 16 months ago by
irvin.ng
• 0
0
votes
0
replies
507
views
Gene Id duplicated
SingleCell
SingleCellData
updated 18 months ago by
ATpoint
★ 4.0k • written 18 months ago by
Romina
• 0
5
votes
5
replies
1.4k
views
Association analysis between gene expression and Phenotype
rna
singlecell
limma
updated 5.0 years ago by
Aaron Lun
★ 28k • written 5.0 years ago by
hrishi27n
▴ 20
2
votes
1
reply
1.6k
views
Convert AnnotatedDataFrame S4 object from GEO datasets to Seurat Object
biobase
SingleCellData
seurat
SingleCell
updated 2.2 years ago by
James W. MacDonald
65k • written 2.2 years ago by
NGS_enthusiast
• 0
0
votes
1
reply
892
views
Differentially expressed genes across three different conditions
MAST
SingleCell
diffGeneAnalysis
updated 2.7 years ago by
James W. MacDonald
65k • written 2.7 years ago by
sofia.puvogel
• 0
1
vote
2
replies
988
views
Using limma duplicateCorrelation to account for donor/dataset effects in scRNA-Seq pseudobulk counts from multiple sources
limma
SingleCell
2.5 years ago
Andrew Pattison
• 0
0
votes
1
reply
621
views
Choosing the right lower limit for emptyDrops
SingleCell
emptyDrops
10X
updated 10 months ago by
Peter Hickey
▴ 670 • written 10 months ago by
sandra.garces.19
• 0
0
votes
1
reply
718
views
allele count data bioc object
SingleCell
SingleCellMultiModal
allele
updated 17 months ago by
Michael Love
41k • written 17 months ago by
oliver.crook
• 0
1
vote
1
reply
617
views
Pseudobulk running all groups together vs subsetting first
DESeq2
edgeR
SingleCell
updated 13 months ago by
Wolfgang Huber
★ 13k • written 13 months ago by
nhaus
▴ 10
0
votes
0
replies
884
views
Job:
Computational Biologist at Denali Therapeutics
Transcriptomics
SingleCell
JobPosting
3.2 years ago
Steve Lianoglou
★ 13k
0
votes
0
replies
860
views
Job:
Senior Bioinformatician - University of Alabama at Birmingham
JobPosting
Transcriptomics
SingleCell
RNA-seq
2.7 years ago
lianov
• 0
0
votes
1
reply
607
views
Job:
Reopened: 'Omics data analyst for HPCBio, University of Illinois
SingleCell
Spatial
RNA-seq
13 months ago
Jenny Drnevich
★ 2.0k
0
votes
0
replies
791
views
Job:
Postdoctoral Fellow in Epigenomcis/Neurobiology (MGH/Harvard Medical School, Boston)
GenomicVariation
SingleCell
Autism
Neurogenesis
Epigenetics
17 months ago
sudhir.thakurela
• 0
0
votes
0
replies
694
views
Issues geting meaninfull results for single cell DGE using MAST
MAST
SingleCell
2.2 years ago
zroger499
• 0
2
votes
2
replies
1.1k
views
velociraptor preparation
SingleCellExperiment
singlecell
velociraptor
scvelo
updated 2.3 years ago by
ATpoint
★ 4.0k • written 2.3 years ago by
Pietro
▴ 40
0
votes
0
replies
635
views
Differential expression with single cell data: any good two component (hurdle) models recently?
SingleCellWorkflow
DifferentialExpression
SingleCell
SingleCellMultiModal
MAST
21 months ago
Nik Tuzov
▴ 80
0
votes
0
replies
433
views
weighting sample group
monocle
SingleCell
DifferentialExpression
18 months ago
Sogand
• 0
0
votes
0
replies
657
views
Job:
Computational postdoctoral fellow for cancer disparities research (Boston University)
DNASeq
RNASeq
SingleCell
2.6 years ago
camp
• 0
0
votes
1
reply
893
views
Error in running: classifySingleR from SingleR package
SingleR
SingleCell
updated 20 months ago by
ATpoint
★ 4.0k • written 20 months ago by
amit.korngut
• 0
0
votes
0
replies
740
views
Creating a stable batch-corrected scRNA-Seq data with multiple datasets and multiple integrations
scater
singlecell
scran
BatchEffect
3.4 years ago
hamza_karakurt
▴ 50
2
votes
4
replies
3.7k
views
How to convert large gene counts data into matrix?
R
Bioconductor
singlecell
bioinformatics
seurat
updated 6 weeks ago by
Gordon Smyth
50k • written 4.7 years ago by
sambunga094
• 0
0
votes
0
replies
679
views
Spike-In Cells for Normalization?
SpikeIn
SingleCell
2.6 years ago
mb1996
• 0
0
votes
1
reply
626
views
Job:
'Omics data analyst for HPCBio, University of Illinois
SingleCell
rnaseq
methylationArrayAnalysis
Spatial
written 15 months ago by
Jenny Drnevich
★ 2.0k
0
votes
0
replies
146
views
Job:
Bioinformatics Spatial Omics and Proteomics Postdoc (Research Officer / Senior Research Officer) at WEHI (Melbourne, Australia)
Proteomics
JobPosting
SingleCell
Spatial
SpatialExperiment
24 days ago
Peter Hickey
▴ 670
0
votes
2
replies
637
views
Scaling and normalization by deconvolution of SMART-Seq 2 data
scran
Clustering
SingleCell
Normalization
12 months ago
Assa Yeroslaviz
★ 1.5k
0
votes
0
replies
842
views
Job:
Postdoc Opening in Bioinformatics or Computational Biology
SpatialData
scRNAseq
SingleCell
Omixer
2.2 years ago
Sebastian Lewandowski
• 0
0
votes
0
replies
673
views
Performing DGE analysis with MAST on a variable with more than 2 levels
MAST
DEG
SingleCell
22 months ago
zroger499
• 0
50 results • Page
1 of 1
Recent ...
Replies
Comment: limma models out of memory issue on Slurm HPC
by
Jitendra
▴ 10
thanks Gordon, but our methylation epic array input file is quite big and we can't read it in R by just using laptop memory so we need to …
Comment: Doing comparison of RNA-seq data using EdgeR
by
Michael Love
41k
Just to clarify, when I originally posted the title and tags had listed "DESeq2" and then the post was changed after my answer was added. …
Comment: fgsea fork
by
shepherl
3.8k
Not quite sure what you mean by clone or fork the package on latest version of R. Bioconductor runs all builds on the latest version of R.…
Answer: Doing comparison of RNA-seq data using EdgeR
by
Gordon Smyth
50k
It's pretty easy to do a two-group comparison using edgeR, but you seem to be stuck at the initial stage of reading data into R. If you exp…
Answer: Differing results from plotMDS and PCAtools
by
Gordon Smyth
50k
The reason why the two plots are different is that the first plot is a PCA plot while the second is a biplot. Quite different plots. The P…
Votes
transcript name mapping between human and mouse
transcript name mapping between human and mouse
A: Error object and replacement value dimnames differ, when changing column names o
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
Awards
• All
Popular Question
to
Dario Strbenac
★ 1.5k
Popular Question
to
Ankit
▴ 20
Popular Question
to
michael.s
• 0
Popular Question
to
James W. MacDonald
65k
Popular Question
to
Pierre Lindenbaum
▴ 10
Locations
• All
France/Marseille/Inserm,
1 minute ago
Wageningen University, Wageningen, the Netherlands,
2 minutes ago
Switzerland,
11 minutes ago
United States,
11 minutes ago
Toulouse, France,
21 minutes ago
Traffic: 763 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