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Showing :
scrnaseq
•
reset
4
votes
7
replies
4.3k
views
removing rows from SingleCellExperiment container
sce
singlecellexperiment
scRNAseq
subsetting
updated 5.2 years ago by
Aaron Lun
★ 28k • written 5.2 years ago by
TJ
• 0
3
votes
9
replies
4.0k
views
Why does scran's computeSumFactors produce different size factors for cells with the exact same gene counts?
scran
scater
drop-seq
scrnaseq
updated 6.9 years ago by
Aaron Lun
★ 28k • written 6.9 years ago by
Friederike
▴ 10
2
votes
4
replies
3.7k
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
3.5k
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
7
votes
3
replies
3.1k
views
Estimating cell size factors for single cell RNA-seq data
scrnaseq
rnaseq
normalization
DESeq2
updated 6.6 years ago by
Michael Love
41k • written 6.6 years ago by
gquon
▴ 10
1
vote
11
replies
3.0k
views
Error: Bioconductor version cannot be validated; no internet connection?
scRNAseq
updated 4 months ago by
Manuel
• 0 • written 9 months ago by
Elham
• 0
2
votes
13
replies
2.2k
views
Running the DESeq2 "DESeqDataSetFromMatrix" function returns a dimname error
DESeq2
Scrna
scRNAseq
2.7 years ago
RDoc
▴ 10
4
votes
5
replies
2.1k
views
`emptyDrops()` calling 'too many' non-empty droplets
DropletUtils
emptyDrops
scRNA
scRNAseq
10x
20 months ago • updated 19 months ago
Peter Hickey
▴ 670
5
votes
4
replies
2.0k
views
Using DESeq2 with GlmGamPoi
DESeq2
glmGamPoi
scRNAseq
3.0 years ago
tatyana.perlova
• 0
0
votes
4
replies
1.9k
views
how to make the "reconstructed" value in intergated scRNA-seq UMAP plot more readable
scater
batchelor
scRNAseq
fastMNN
updated 19 months ago by
Aaron Lun
★ 28k • written 20 months ago by
Guandong Shang
▴ 40
1
vote
1
reply
1.9k
views
Mean Expression Calculation scRNA-seq (All cells or only Expressed Cells)
scrnaseq
monocle
updated 5.9 years ago by
davide risso
▴ 950 • written 5.9 years ago by
chitsazanalex
▴ 10
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
0
votes
2
replies
1.8k
views
How to filter cells for scRNA-seq analysis based on expression level of surface marker?
scRNAseq
3.2 years ago
Iris Wing To
• 0
1
vote
2
replies
1.8k
views
install celldex in r4. 04
scRNAseq
written 3.0 years ago by
Wenzhong
• 0
0
votes
2
replies
1.7k
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
6.6 years ago
Andrew_McDavid
▴ 270
0
votes
6
replies
1.7k
views
analysis of multiple batches and multiple treatment conditions in scRNA-seq
limma
deseq2
edger
scRNAseq
combat
updated 4.6 years ago by
Andrew_McDavid
▴ 270 • written 4.7 years ago by
Bogdan
▴ 670
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
23 months ago
Ismail
• 0
1
vote
1
reply
1.7k
views
Can we use 'SCT normalization' to find anchors and 'LogNormalize' for the integration?
Normalization
scRNAseq
updated 24 months ago by
Peter Hickey
▴ 670 • written 24 months ago by
nitinnarwade1504
• 0
2
votes
6
replies
1.6k
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
6.6 years ago
sfpacman
• 0
0
votes
2
replies
1.5k
views
PCA outliers cleaning
scRNAseq
Pipeline
Seurat
SingleCellExperiment
4.4 years ago
albadrs.93
▴ 10
0
votes
1
reply
1.5k
views
Minimum number of cells required for the MAST
MAST
scRNAseq
differential expression
4.6 years ago
Andrew_McDavid
▴ 270
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
5
votes
6
replies
1.5k
views
DE Analysis on Scran-Normalized Counts
DifferentialExpression
scRNAseq
scran
updated 3.1 years ago by
Aaron Lun
★ 28k • written 3.1 years ago by
LUCIA
• 0
6
votes
2
replies
1.5k
views
how can I annotate my scRNAseq clusters from a Rat experiment?
scRNAseq
Rattus_norvegicus_Data
annotation
updated 2.9 years ago by
ATpoint
★ 4.0k • written 2.9 years ago by
pcantalupo
• 0
4
votes
1
reply
1.5k
views
Best practice for correlating scRNA seq to bulkRNA seq data
seurat
edgeR
spearman
correlation
scRNAseq
updated 3.9 years ago by
Aaron Lun
★ 28k • written 3.9 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
21 months ago
Kelen
▴ 10
0
votes
3
replies
1.5k
views
MAST invalid Hypothesis, class objectORconnection error
R
MAST
scRNASeq
3.6 years ago
TriS
▴ 200
1
vote
3
replies
1.4k
views
Differential Expression analysis between distinct scRNA-seq datasets
scrna
scrnaseq
differential gene expression
updated 6.4 years ago by
davide risso
▴ 950 • written 6.4 years ago by
d.depledge
• 0
0
votes
3
replies
1.4k
views
NA values for mitochondrial gene percentage
Seurat
scRNAseq
2.3 years ago
zahra.mesri95
• 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
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
1.3k
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
4
votes
5
replies
1.3k
views
RNA Seq analysis vs. Single cell RNA seq analysis
rnaseq
scrnaseq
edger
6.5 years ago • updated 6.4 years ago
fawazfebin
▴ 60
1
vote
1
reply
1.3k
views
Question: Removal of mRNA contamination from scRNA-seq data using SoupX: How to proceed when "Extremely high contamination estimated"?
scRNAseq
SoupX
updated 3.4 years ago by
James W. MacDonald
65k • written 3.4 years ago by
AA
▴ 10
0
votes
1
reply
1.3k
views
Removal of batch effects before non-linear clustering for scRNAseq
scrnaseq
MAST
6.9 years ago
Andrew_McDavid
▴ 270
4
votes
5
replies
1.3k
views
Pseudo-bulk celltype comparison across conditions from multiple-sources
DESeq2
edgeR
scRNAseq
updated 12 months ago by
Peter Hickey
▴ 670 • written 12 months ago by
EspressoKris
▴ 10
2
votes
3
replies
1.2k
views
P-value histogram of testLinearModel is not uniform
smart-seq2
scRNAseq
scran
9 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 6.1 years ago by
CataVallejos
▴ 10 • written 6.1 years ago by
alexandriapinto1
▴ 10
2
votes
2
replies
1.2k
views
scuttle:: librarySizeFactors returning non-finite values
normalizeCounts
scran
librarySizeFactors
scuttle
scRNAseq
2.1 years ago
behr201
• 0
1
vote
4
replies
1.2k
views
Quality control of scRNA-seq data using mitochondrial ratio (drosophila)
Drosophila_melanogaster
scRNAseq
20 months ago
Chise
▴ 10
2
votes
4
replies
1.1k
views
edgeR output doubts
logFC
edgeR
DifferentialExpression
scRNAseq
2.6 years ago
mbenegas
• 0
2
votes
4
replies
1.1k
views
Does hashedDrops support 'imbalanced' combinations of HTOs?
DropletUtils
scRNAseq
updated 3.1 years ago by
Aaron Lun
★ 28k • written 3.1 years ago by
Peter Hickey
▴ 670
2
votes
2
replies
1.1k
views
How to deal with Expression set assembly problem?
deconvolution
r
scRNAseq
bioinformatics
2.1 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
17 months ago
Guandong Shang
▴ 40
4
votes
2
replies
1.0k
views
how to do downstram analysis to cells which are subsetted after MNN batch-correction
batchelor
fastMNN
scRNAseq
20 months ago • updated 19 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 2.6 years ago by
Aaron Lun
★ 28k • written 2.6 years ago by
curiousmind007
▴ 10
2
votes
0
replies
1.0k
views
How to aggregate pseudobulks: Normalization & Log-Transformation
pseudobulk
scRNAseq
GSVA
11 months ago
Tadeoye
▴ 20
0
votes
1
reply
986
views
Error: DESeq(dds , useT = TRUE, minmu = 1e-06, test = "LRT", : likelihood ratio test requires a 'reduced' design, see ?DESeq
scRNAseq
DESeq2
updated 21 months ago by
ATpoint
★ 4.0k • written 21 months ago by
abdi.zhr26
• 0
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Answer: WGCNA: analysis of complex trait associations with regressions
by
James W. MacDonald
65k
This support site is meant to help people with questions about Bioconductor packages (WGCNA is not a Bioconductor package). You might try o…
Comment: miRTarRnaseq library
by
mercedeh.movassagh
▴ 10
Yes that is correct
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
by
Gordon Smyth
50k
It is the minimum group size rather than the total number of samples that is relevant. `min.prop` is more a biological parameter rather th…
Answer: Microarray Limma Model fitting and DEG
by
Gordon Smyth
50k
This dataset seems straightforward to analyse using the original MAS expression values on GEO. MAS expression values are known to be noisy …
Answer: Trimming a section of a scaffold from a genome
by
James W. MacDonald
65k
It's undoubtedly possible, but you don't provide enough information to go on. If I assume you are talking about an existing `BSgenome` pack…
Votes
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
DESeq2 normalization vs VST vs rlog
Answer: DESeq2 "Contrast" option
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