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Showing :
scRNAseq
•
reset
1
vote
2
replies
110
views
unbalanced cell count and unbalanced read count across samples in pseudobulk differential expression analysis using scRNA-seq data
scRNAseq
DifferentialExpression
DESeq2
25 days ago • updated 20 days ago
Ismail
• 0
1
vote
1
reply
96
views
Can we use 'SCT normalization' to find anchors and 'LogNormalize' for the integration?
Normalization
scRNAseq
updated 6 weeks ago by
Peter Hickey
▴ 550 • written 6 weeks ago by
nitinnarwade1504
• 0
2
votes
2
replies
229
views
scuttle:: librarySizeFactors returning non-finite values
normalizeCounts
scran
librarySizeFactors
scuttle
scRNAseq
11 weeks ago
behr201
• 0
2
votes
2
replies
245
views
How to deal with Expression set assembly problem?
deconvolution
r
scRNAseq
bioinformatics
3 months ago
Hasan Alanya
• 0
0
votes
1
reply
145
views
Aberrant number of cells
CellBarcode
DropletUtils
emptyDrops()
Cellranger
scRNAseq
updated 11 days ago by
rohitsatyam102
▴ 20 • written 3 months ago by
gregoire.destreel
• 0
0
votes
0
replies
229
views
Job:
Postdoc Opening in Bioinformatics or Computational Biology
SpatialData
scRNAseq
SingleCell
Omixer
3 months ago
Sebastian Lewandowski
• 0
0
votes
3
replies
304
views
NA values for mitochondrial gene percentage
Seurat
scRNAseq
5 months ago
zahra.mesri95
• 0
0
votes
0
replies
120
views
scRNA technical replicates in separate runs
SingleCellExperiment
scRNAseq
5 months ago
Núria
• 0
0
votes
2
replies
233
views
scRNAseq analysis on multiple datasets
scRNAseq
updated 7 months ago by
swbarnes2
★ 1.0k • written 7 months ago by
SG
• 0
2
votes
4
replies
375
views
edgeR output doubts
logFC
edgeR
DifferentialExpression
scRNAseq
9 months ago
mbenegas
• 0
0
votes
1
reply
374
views
Identify a scRNASeq cell-population using a bulk RNA Seq dataset of that population?
RNASeq
rnaseq
scRNAseq
updated 9 months ago by
Aaron Lun
★ 27k • written 9 months ago by
curiousmind007
• 0
0
votes
0
replies
167
views
Correlation plot using the count data from seurat object
scRNAseq
9 months ago
Sam
• 0
2
votes
4
replies
778
views
differential expression for Single-cell RNAseq data using edgeR
edgeR
single
scRNAseq
9 months ago • updated 8 months ago
mbenegas
• 0
2
votes
13
replies
668
views
Running the DESeq2 "DESeqDataSetFromMatrix" function returns a dimname error
DESeq2
Scrna
scRNAseq
9 months ago
RDoc
▴ 10
0
votes
1
reply
277
views
Tool for simulating bulk RNA-Seq from single cell data
scRNAseq
updated 10 months ago by
James W. MacDonald
59k • written 10 months ago by
mpatino2799
• 0
0
votes
0
replies
174
views
Using csClassify on a SeuratObject
scRNAseq
csClassify
Seurat
updated 11 months ago by
ATpoint
★ 1.2k • written 12 months ago by
curiousmind007
• 0
4
votes
3
replies
451
views
Effect of feature number on adjusted p-values
edgeR
DESeq2
single-cell
scRNAseq
zinbwave
updated 12 months ago by
Aaron Lun
★ 27k • written 12 months ago by
vincent.croset
▴ 20
6
votes
2
replies
451
views
how can I annotate my scRNAseq clusters from a Rat experiment?
scRNAseq
Rattus_norvegicus_Data
annotation
updated 12 months ago by
ATpoint
★ 1.2k • written 12 months ago by
pcantalupo
• 0
1
vote
2
replies
720
views
install celldex in r4. 04
scRNAseq
written 14 months ago by
Wenzhong
• 0
5
votes
4
replies
637
views
Using DESeq2 with GlmGamPoi
DESeq2
glmGamPoi
scRNAseq
14 months ago
tatyana.perlova
• 0
2
votes
4
replies
428
views
Does hashedDrops support 'imbalanced' combinations of HTOs?
DropletUtils
scRNAseq
updated 14 months ago by
Aaron Lun
★ 27k • written 15 months ago by
Peter Hickey
▴ 550
5
votes
6
replies
613
views
DE Analysis on Scran-Normalized Counts
DifferentialExpression
scRNAseq
scran
updated 15 months ago by
Aaron Lun
★ 27k • written 15 months ago by
LUCIA
• 0
0
votes
2
replies
404
views
How to filter cells for scRNA-seq analysis based on expression level of surface marker?
scRNAseq
16 months ago • updated 15 months ago
Iris Wing To
• 0
0
votes
2
replies
522
views
Removal of cell cycle effect using batchelor::regressBatches() and proper usage of corrected UMI matrix
scRNAseq
batchelor
SingleCell
SingleCellExperiment
scran
17 months ago
jirkanov
• 0
1
vote
1
reply
406
views
Combining treatment and control batches for analysis
scRNAseq
scRNA
batchelor
BatchEffect
updated 18 months ago by
Aaron Lun
★ 27k • written 18 months ago by
Adrien
• 0
1
vote
1
reply
454
views
Question: Removal of mRNA contamination from scRNA-seq data using SoupX: How to proceed when "Extremely high contamination estimated"?
scRNAseq
SoupX
updated 18 months ago by
James W. MacDonald
59k • written 18 months ago by
AA
▴ 10
0
votes
3
replies
766
views
MAST invalid Hypothesis, class objectORconnection error
R
MAST
scRNASeq
21 months ago
TriS
▴ 200
4
votes
1
reply
475
views
Best practice for correlating scRNA seq to bulkRNA seq data
seurat
edgeR
spearman
correlation
scRNAseq
updated 2.1 years ago by
Aaron Lun
★ 27k • written 2.1 years ago by
tobias-messmer
▴ 10
1
vote
0
replies
419
views
News:
News: Bioinformatics Summer School - July 2020 - UCLouvain (Belgium)
rnaseq
course
proteomics
transcriptomics
scrnaseq
News
2.3 years ago
Laurent Gatto
1.5k
0
votes
5
replies
843
views
analysis of multiple time points * 2 replicates of scRNA-seq
scRNAseq
updated 2.3 years ago by
Aaron Lun
★ 27k • written 2.3 years ago by
Bogdan
▴ 640
0
votes
2
replies
522
views
PCA outliers cleaning
scRNAseq
Pipeline
Seurat
SingleCellExperiment
2.5 years ago
albadrs.93
▴ 10
0
votes
1
reply
578
views
Minimum number of cells required for the MAST
MAST
scRNAseq
differential expression
2.7 years ago
Andrew_McDavid
▴ 260
0
votes
6
replies
980
views
analysis of multiple batches and multiple treatment conditions in scRNA-seq
limma
deseq2
edger
scRNAseq
combat
updated 2.8 years ago by
Andrew_McDavid
▴ 260 • written 2.8 years ago by
Bogdan
▴ 640
4
votes
7
replies
1.7k
views
removing rows from SingleCellExperiment container
sce
singlecellexperiment
scRNAseq
subsetting
updated 3.4 years ago by
Aaron Lun
★ 27k • written 3.4 years ago by
TJ
• 0
2
votes
6
replies
779
views
Change the number of clusters with scater
scater
scran
scrnaseq
clustering
updated 3.5 years ago by
Aaron Lun
★ 27k • written 3.5 years ago by
shbrief
▴ 20
0
votes
1
reply
579
views
RNAseq scater error in plotQC()
scater
plotQC
scRNAseq
updated 3.8 years ago by
Aaron Lun
★ 27k • written 3.8 years ago by
Vladimir Krasikov
▴ 90
6
votes
12
replies
2.2k
views
Merging RNAseq Datasets of Different Depths
singlecellexperiment
scran
sequencing depth
batch effect
scrnaseq
updated 3.9 years ago by
Aaron Lun
★ 27k • written 3.9 years ago by
liam.salleh
• 0
1
vote
1
reply
718
views
Mean Expression Calculation scRNA-seq (All cells or only Expressed Cells)
scrnaseq
monocle
updated 4.0 years ago by
davide risso
▴ 890 • written 4.0 years ago by
chitsazanalex
▴ 10
0
votes
2
replies
651
views
BASiCS spike info for single cell RNA sequences or Bayesian statistics help
BASiCS
bayesian
single cell
scrnaseq
updated 4.3 years ago by
CataVallejos
▴ 10 • written 4.3 years ago by
alexandriapinto1
▴ 10
4
votes
5
replies
782
views
RNA Seq analysis vs. Single cell RNA seq analysis
rnaseq
scrnaseq
edger
4.6 years ago • updated 4.5 years ago
fawazfebin
▴ 30
1
vote
3
replies
741
views
Differential Expression analysis between distinct scRNA-seq datasets
scrna
scrnaseq
differential gene expression
updated 4.5 years ago by
davide risso
▴ 890 • written 4.5 years ago by
d.depledge
• 0
4
votes
1
reply
1.1k
views
NAs in continuous coefficient and fold change in `zlm`
scrnaseq
MAST
differential gene expression
4.8 years ago
Andrew_McDavid
▴ 260
1
vote
5
replies
1.1k
views
computeSumFactors: warning about cluster size
scrnaseq
scrn
sizefactors
4.8 years ago
sfpacman
• 0
7
votes
3
replies
2.2k
views
Estimating cell size factors for single cell RNA-seq data
scrnaseq
rnaseq
normalization
DESeq2
updated 4.8 years ago by
Michael Love
36k • written 4.8 years ago by
gquon
▴ 10
0
votes
3
replies
794
views
Modeling Dose-response data in MAST
MAST
sc-rnaseq
scrnaseq
updated 4.8 years ago by
Andrew_McDavid
▴ 260 • written 4.8 years ago by
eleanorahowe
• 0
0
votes
1
reply
770
views
Removal of batch effects before non-linear clustering for scRNAseq
scrnaseq
MAST
5.0 years ago
Andrew_McDavid
▴ 260
3
votes
9
replies
2.6k
views
Why does scran's computeSumFactors produce different size factors for cells with the exact same gene counts?
scran
scater
drop-seq
scrnaseq
updated 5.1 years ago by
Aaron Lun
★ 27k • written 5.1 years ago by
Friederike
▴ 10
4
votes
3
replies
1.3k
views
using SC3 and scater for bulk-RNAseq
sc3
scater
scRNAseq
updated 5.2 years ago by
Vladimir Kiselev
▴ 150 • written 5.2 years ago by
Assa Yeroslaviz
★ 1.5k
48 results • Page
1 of 1
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by
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• 0
Hi Johannes, Could I request the same EnsDb creation for Medicago truncatula? Thank you very much, Karen
Answer: EnrichGO not working with db created from annotationhub
by
Guido Hooiveld
★ 3.2k
Did you notice the first message that was returned after you ran `enrichGO()`? Thus: `--> No gene can be mapped....` This basically means…
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by
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• 0
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by
Wei Shi
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Yes we are currently working on generating a small example for cellCounts.
Comment: Separate exogenous from endogenous transcripts using Salmon RNAseq DTU
by
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• 0
Hi Dr Sudbery, yes I found looking at the coverage in IGV helps a lot. I did find some differences between CDS and UTR and between samples.…
Votes
Comment: Separate exogenous from endogenous transcripts using Salmon RNAseq DTU
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Answer: Handling NA values in limma's voom design matrix
Answer: Handling NA values in limma's voom design matrix
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