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Showing :
scRNAseq
•
reset
4
votes
7
replies
4.4k
views
removing rows from SingleCellExperiment container
sce
singlecellexperiment
scRNAseq
subsetting
updated 5.3 years ago by
Aaron Lun
★ 28k • written 5.3 years ago by
TJ
• 0
3
votes
9
replies
4.1k
views
Why does scran's computeSumFactors produce different size factors for cells with the exact same gene counts?
scran
scater
drop-seq
scrnaseq
updated 7.0 years ago by
Aaron Lun
★ 28k • written 7.0 years ago by
Friederike
▴ 10
2
votes
4
replies
3.8k
views
differential expression for Single-cell RNAseq data using edgeR
edgeR
single
scRNAseq
2.7 years ago • updated 2.6 years ago
mbenegas
• 0
6
votes
12
replies
3.6k
views
Merging RNAseq Datasets of Different Depths
singlecellexperiment
scran
sequencing depth
batch effect
scrnaseq
updated 5.8 years ago by
Aaron Lun
★ 28k • written 5.8 years ago by
liam.salleh
• 0
1
vote
11
replies
3.3k
views
Error: Bioconductor version cannot be validated; no internet connection?
scRNAseq
updated 5 months ago by
Manuel
• 0 • written 9 months ago by
Elham
• 0
7
votes
3
replies
3.1k
views
Estimating cell size factors for single cell RNA-seq data
scrnaseq
rnaseq
normalization
DESeq2
updated 6.7 years ago by
Michael Love
41k • written 6.7 years ago by
gquon
▴ 10
4
votes
5
replies
2.2k
views
`emptyDrops()` calling 'too many' non-empty droplets
DropletUtils
emptyDrops
scRNA
scRNAseq
10x
20 months ago
Peter Hickey
▴ 740
2
votes
13
replies
2.2k
views
Running the DESeq2 "DESeqDataSetFromMatrix" function returns a dimname error
DESeq2
Scrna
scRNAseq
2.8 years ago
RDoc
▴ 10
5
votes
4
replies
2.1k
views
Using DESeq2 with GlmGamPoi
DESeq2
glmGamPoi
scRNAseq
3.1 years ago
tatyana.perlova
• 0
0
votes
4
replies
2.0k
views
how to make the "reconstructed" value in intergated scRNA-seq UMAP plot more readable
scater
batchelor
scRNAseq
fastMNN
updated 20 months ago by
Aaron Lun
★ 28k • written 20 months ago by
Guandong Shang
▴ 40
1
vote
1
reply
2.0k
views
Mean Expression Calculation scRNA-seq (All cells or only Expressed Cells)
scrnaseq
monocle
updated 6.0 years ago by
davide risso
▴ 950 • written 6.0 years ago by
chitsazanalex
▴ 10
0
votes
2
replies
1.8k
views
How to filter cells for scRNA-seq analysis based on expression level of surface marker?
scRNAseq
3.3 years ago • updated 3.2 years ago
Iris Wing To
• 0
4
votes
3
replies
1.8k
views
using SC3 and scater for bulk-RNAseq
sc3
scater
scRNAseq
updated 7.1 years ago by
Vladimir Kiselev
▴ 150 • written 7.1 years ago by
Assa Yeroslaviz
★ 1.5k
1
vote
2
replies
1.8k
views
install celldex in r4. 04
scRNAseq
written 3.1 years ago by
Wenzhong
• 0
0
votes
2
replies
1.8k
views
calculateQCMetrics defunct, how to calculate the quality metrics by perCellQCMetrics
scRNAseq
updated 21 months ago by
ATpoint
★ 4.0k • written 21 months ago by
otieno43
• 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
1
vote
2
replies
1.7k
views
unbalanced cell count and unbalanced read count across samples in pseudobulk differential expression analysis using scRNA-seq data
scRNAseq
DifferentialExpression
DESeq2
2.0 years ago • updated 24 months ago
Ismail
• 0
0
votes
6
replies
1.7k
views
analysis of multiple batches and multiple treatment conditions in scRNA-seq
limma
deseq2
edger
scRNAseq
combat
updated 4.7 years ago by
Andrew_McDavid
▴ 270 • written 4.7 years ago by
Bogdan
▴ 670
1
vote
1
reply
1.7k
views
Can we use 'SCT normalization' to find anchors and 'LogNormalize' for the integration?
Normalization
scRNAseq
updated 2.1 years ago by
Peter Hickey
▴ 740 • written 2.1 years ago by
nitinnarwade1504
• 0
2
votes
6
replies
1.7k
views
Change the number of clusters with scater
scater
scran
scrnaseq
clustering
updated 5.4 years ago by
Aaron Lun
★ 28k • written 5.4 years ago by
shbrief
▴ 20
1
vote
5
replies
1.6k
views
computeSumFactors: warning about cluster size
scrnaseq
scrn
sizefactors
6.7 years ago
sfpacman
• 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
8
votes
2
replies
1.6k
views
how can I annotate my scRNAseq clusters from a Rat experiment?
scRNAseq
Rattus_norvegicus_Data
annotation
updated 3.0 years ago by
ATpoint
★ 4.0k • written 3.0 years ago by
pcantalupo
▴ 10
5
votes
6
replies
1.6k
views
DE Analysis on Scran-Normalized Counts
DifferentialExpression
scRNAseq
scran
updated 3.2 years ago by
Aaron Lun
★ 28k • written 3.2 years ago by
LUCIA
• 0
0
votes
2
replies
1.6k
views
PCA outliers cleaning
scRNAseq
Pipeline
Seurat
SingleCellExperiment
4.4 years ago
albadrs.93
▴ 10
0
votes
5
replies
1.5k
views
analysis of multiple time points * 2 replicates of scRNA-seq
scRNAseq
updated 4.2 years ago by
Aaron Lun
★ 28k • written 4.2 years ago by
Bogdan
▴ 670
4
votes
1
reply
1.5k
views
Best practice for correlating scRNA seq to bulkRNA seq data
seurat
edgeR
spearman
correlation
scRNAseq
updated 4.0 years ago by
Aaron Lun
★ 28k • written 4.0 years ago by
tobias-messmer
▴ 10
2
votes
8
replies
1.5k
views
RSEM - tximport; where is effective_length information used? Implications for scRNA?
RSEM
tximport
scRNAseq
DESeq2
22 months ago • updated 21 months ago
Kelen
▴ 10
0
votes
3
replies
1.5k
views
NA values for mitochondrial gene percentage
Seurat
scRNAseq
2.4 years ago
zahra.mesri95
• 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
1.5k
views
Differential Expression analysis between distinct scRNA-seq datasets
scrna
scrnaseq
differential gene expression
updated 6.5 years ago by
davide risso
▴ 950 • written 6.5 years ago by
d.depledge
• 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
3.4 years ago • updated 3.3 years ago
jirkanov
• 0
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
7
votes
3
replies
1.4k
views
Effect of feature number on adjusted p-values
edgeR
DESeq2
single-cell
scRNAseq
zinbwave
updated 2.9 years ago by
Aaron Lun
★ 28k • written 2.9 years ago by
vincent.croset
▴ 20
1
vote
1
reply
1.4k
views
Question: Removal of mRNA contamination from scRNA-seq data using SoupX: How to proceed when "Extremely high contamination estimated"?
scRNAseq
SoupX
updated 3.5 years ago by
James W. MacDonald
65k • written 3.5 years ago by
AA
▴ 10
4
votes
5
replies
1.3k
views
RNA Seq analysis vs. Single cell RNA seq analysis
rnaseq
scrnaseq
edger
6.5 years ago
fawazfebin
▴ 60
4
votes
5
replies
1.3k
views
Pseudo-bulk celltype comparison across conditions from multiple-sources
DESeq2
edgeR
scRNAseq
updated 13 months ago by
Peter Hickey
▴ 740 • written 13 months ago by
EspressoKris
▴ 10
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
2
votes
3
replies
1.3k
views
P-value histogram of testLinearModel is not uniform
smart-seq2
scRNAseq
scran
10 months ago
Lluís Revilla Sancho
▴ 730
0
votes
2
replies
1.2k
views
BASiCS spike info for single cell RNA sequences or Bayesian statistics help
BASiCS
bayesian
single cell
scrnaseq
updated 6.2 years ago by
CataVallejos
▴ 10 • written 6.2 years ago by
alexandriapinto1
▴ 10
2
votes
2
replies
1.2k
views
scuttle:: librarySizeFactors returning non-finite values
normalizeCounts
scran
librarySizeFactors
scuttle
scRNAseq
2.2 years ago
behr201
• 0
1
vote
4
replies
1.2k
views
Quality control of scRNA-seq data using mitochondrial ratio (drosophila)
Drosophila_melanogaster
scRNAseq
21 months ago
Chise
▴ 10
2
votes
4
replies
1.2k
views
edgeR output doubts
logFC
edgeR
DifferentialExpression
scRNAseq
2.7 years ago
mbenegas
• 0
2
votes
4
replies
1.2k
views
Does hashedDrops support 'imbalanced' combinations of HTOs?
DropletUtils
scRNAseq
updated 3.2 years ago by
Aaron Lun
★ 28k • written 3.2 years ago by
Peter Hickey
▴ 740
2
votes
2
replies
1.1k
views
How to deal with Expression set assembly problem?
deconvolution
r
scRNAseq
bioinformatics
2.2 years ago
Hasan Alanya
• 0
1
vote
2
replies
1.1k
views
What number components should I use if I want to show 2D and 3D UMAP
scater
UAMP
scRNAseq
18 months ago
Guandong Shang
▴ 40
2
votes
0
replies
1.1k
views
How to aggregate pseudobulks: Normalization & Log-Transformation
pseudobulk
scRNAseq
GSVA
12 months ago
Tadeoye
▴ 20
4
votes
2
replies
1.1k
views
how to do downstram analysis to cells which are subsetted after MNN batch-correction
batchelor
fastMNN
scRNAseq
20 months ago
Guandong Shang
▴ 40
0
votes
1
reply
1.0k
views
Identify a scRNASeq cell-population using a bulk RNA Seq dataset of that population?
RNASeq
rnaseq
scRNAseq
updated 2.7 years ago by
Aaron Lun
★ 28k • written 2.7 years ago by
curiousmind007
▴ 10
0
votes
1
reply
1.0k
views
Error: DESeq(dds , useT = TRUE, minmu = 1e-06, test = "LRT", : likelihood ratio test requires a 'reduced' design, see ?DESeq
scRNAseq
DESeq2
updated 22 months ago by
ATpoint
★ 4.0k • written 22 months ago by
abdi.zhr26
• 0
50 results • Page
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Answer: RNAseq:Technical replicates from different batches
by
Gordon Smyth
50k
I am not entirely clear what you mean by "technical" replicates in this case. Are they resequencing of the same RNA samples or are they fre…
Comment: DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, param
by
russ.bainer
▴ 10
Hi, I'm hitting this too. As far as I can tell my DataTrack is fine, but perhaps I am missing something. Notably the same code works on o…
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions
by
Chris
• 0
Hi Robert, If I don't want to use all pathway in c2 gene set but only a few pathways of interested, how can I do that? So we try to get a …
Comment: How to retrieve detailed regression results from deseq2
by
Weiqian
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Hi Michael, thanks for the answer! I'll have a look : )
Comment: DESeq filtering specific to contrasts
by
Michael Love
41k
It will likely not filter it out, but really the per-dataset details would affect the results.
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Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
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