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Showing :
scrnaseq
•
reset
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
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
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
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 7.0 years ago by
Aaron Lun
★ 28k • written 7.0 years ago by
Friederike
▴ 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
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
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
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
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
1
vote
5
replies
767
views
Recommendation for large.n in filterByExpr
scRNAseq
edgeR
SingleCellExperiment
7 months ago
duez.tolga
• 0
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
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
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
1
vote
5
replies
1.6k
views
computeSumFactors: warning about cluster size
scrnaseq
scrn
sizefactors
6.6 years ago
sfpacman
• 0
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
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
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
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
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
5
votes
4
replies
2.0k
views
Using DESeq2 with GlmGamPoi
DESeq2
glmGamPoi
scRNAseq
3.0 years ago
tatyana.perlova
• 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
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
3
replies
1.4k
views
NA values for mitochondrial gene percentage
Seurat
scRNAseq
2.3 years ago
zahra.mesri95
• 0
0
votes
3
replies
979
views
scRNA-seq: RS4' object has no attribute 'T'" in fastMNN R function
scanpy
scRNAseq
fastmnn
r
18 months ago • updated 17 months ago
Madiha
• 0
4
votes
3
replies
982
views
Custom design for scRNA DGE with pseudobulking
scRNAseq
scrna
paireddesign
edgeR
pseudobulking
updated 7 months ago by
Gordon Smyth
50k • written 7 months ago by
garcia
• 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
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
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
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
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
0
votes
2
replies
1.5k
views
PCA outliers cleaning
scRNAseq
Pipeline
Seurat
SingleCellExperiment
4.4 years ago
albadrs.93
▴ 10
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
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
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
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
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
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
0
votes
2
replies
434
views
scRNA analysis : DEG between low and high-expressing cells
scRNAseq
5 months ago
Momo
• 0
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
0
votes
2
replies
883
views
scRNAseq analysis on multiple datasets
scRNAseq
updated 2.5 years ago by
swbarnes2
★ 1.3k • written 2.5 years ago by
SG
• 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
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
1
vote
2
replies
628
views
ScRNAseq analysis scran :: quickcluster Error
scRNAseq
quickcluster
scRNA
scran
3 months ago
ruba-mahmoud
• 0
0
votes
2
replies
634
views
Could not find function "Standard Chromosomes"
scrna
scRNAseq
updated 5 months ago by
Gabriella
• 0 • written 12 months ago by
sarah.jobbins
• 0
1
vote
2
replies
912
views
Combine scRNAseq data for bulk analysis using DESeq2
DESeq2
scRNAseq
Fluidigm
17 months ago
evocanres
• 0
0
votes
2
replies
136
views
Non-empty droplets versus good quality cells
CellRanger
emptyDrops
scRNAseq
10X
9 days ago • updated 8 days ago
rocanja
▴ 60
0
votes
1
reply
922
views
Aberrant number of cells
CellBarcode
DropletUtils
emptyDrops()
Cellranger
scRNAseq
updated 23 months ago by
rohitsatyam102
▴ 20 • written 2.2 years ago by
gregoire.destreel
• 0
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Answer: New genes that did not exist in dds object suddenly showed up after degPatterns
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Michael Love
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May be documented by the software you are using? https://github.com/lpantano/DEGreport
Answer: Doing comparison of RNA-seq data using Deseq2
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Take a look at our workflow, this starts from a beginner's level. You could export from Excel using CSV or TSV, then read into R. htt…
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This support site is meant to help people with questions about Bioconductor packages (WGCNA is not a Bioconductor package). You might try o…
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Yes that is correct
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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…
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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
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