Showing : scRNAseq • reset
8
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2
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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 ★ 4.1k • written 3.0 years ago by ▴ 10
7
votes
3
replies
1.4k
views
Effect of feature number on adjusted p-values
edgeR DESeq2 single-cell scRNAseq zinbwave
updated 3.0 years ago by ★ 28k • written 3.0 years ago by ▴ 20
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 41k • written 6.7 years ago by ▴ 10
6
votes
12
replies
3.6k
views
Merging RNAseq Datasets of Different Depths
singlecellexperiment scran sequencing depth batch effect scrnaseq
updated 5.9 years ago by ★ 28k • written 5.9 years ago by • 0
5
votes
4
replies
2.1k
views
Using DESeq2 with GlmGamPoi
DESeq2 glmGamPoi scRNAseq
3.1 years ago tatyana.perlova • 0
5
votes
6
replies
1.6k
views
DE Analysis on Scran-Normalized Counts
DifferentialExpression scRNAseq scran
updated 3.2 years ago by ★ 28k • written 3.2 years ago by • 0
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 ★ 28k • written 4.0 years ago by ▴ 10
4
votes
5
replies
1.4k
views
Pseudo-bulk celltype comparison across conditions from multiple-sources
DESeq2 edgeR scRNAseq
updated 13 months ago by ▴ 740 • written 13 months ago by ▴ 10
4
votes
3
replies
1.0k
views
Custom design for scRNA DGE with pseudobulking
scRNAseq scrna paireddesign edgeR pseudobulking
updated 9 months ago by 50k • written 9 months ago by • 0
4
votes
7
replies
4.5k
views
removing rows from SingleCellExperiment container
sce singlecellexperiment scRNAseq subsetting
updated 5.3 years ago by ★ 28k • written 5.3 years ago by • 0
4
votes
3
replies
1.8k
views
using SC3 and scater for bulk-RNAseq
sc3 scater scRNAseq
updated 7.1 years ago by ▴ 150 • written 7.1 years ago by ★ 1.5k
4
votes
1
reply
1.8k
views
NAs in continuous coefficient and fold change in `zlm`
scrnaseq MAST differential gene expression
6.7 years ago Andrew_McDavid ▴ 270
4
votes
2
replies
1.1k
views
how to do downstram analysis to cells which are subsetted after MNN batch-correction
batchelor fastMNN scRNAseq
21 months ago Guandong Shang ▴ 40
4
votes
5
replies
1.4k
views
RNA Seq analysis vs. Single cell RNA seq analysis
rnaseq scrnaseq edger
6.6 years ago • updated 6.5 years ago fawazfebin ▴ 60
4
votes
5
replies
2.3k
views
`emptyDrops()` calling 'too many' non-empty droplets
DropletUtils emptyDrops scRNA scRNAseq 10x
21 months ago • updated 20 months ago Peter Hickey ▴ 740
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 ★ 28k • written 7.0 years ago by ▴ 10
2
votes
6
replies
1.7k
views
Change the number of clusters with scater
scater scran scrnaseq clustering
updated 5.4 years ago by ★ 28k • written 5.4 years ago by ▴ 20
2
votes
2
replies
1.2k
views
How to deal with Expression set assembly problem?
deconvolution r scRNAseq bioinformatics
2.2 years ago Hasan Alanya • 0
2
votes
0
replies
1.1k
views
How to aggregate pseudobulks: Normalization & Log-Transformation
pseudobulk scRNAseq GSVA
12 months ago Tadeoye ▴ 20
2
votes
4
replies
1.2k
views
edgeR output doubts
logFC edgeR DifferentialExpression scRNAseq
2.7 years ago mbenegas • 0
2
votes
13
replies
2.3k
views
Running the DESeq2 "DESeqDataSetFromMatrix" function returns a dimname error
DESeq2 Scrna scRNAseq
2.8 years ago RDoc ▴ 10
2
votes
4
replies
1.2k
views
Does hashedDrops support 'imbalanced' combinations of HTOs?
DropletUtils scRNAseq
updated 3.2 years ago by ★ 28k • written 3.2 years ago by ▴ 740
2
votes
4
replies
3.9k
views
differential expression for Single-cell RNAseq data using edgeR
edgeR single scRNAseq
2.8 years ago • updated 2.7 years ago mbenegas • 0
2
votes
8
replies
1.6k
views
RSEM - tximport; where is effective_length information used? Implications for scRNA?
RSEM tximport scRNAseq DESeq2
22 months ago Kelen ▴ 10
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
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
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 ▴ 950 • written 6.0 years ago by ▴ 10
1
vote
11
replies
3.4k
views
Error: Bioconductor version cannot be validated; no internet connection?
scRNAseq
updated 5 months ago by • 0 • written 10 months ago by • 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
1
vote
1
reply
1.0k
views
Combining treatment and control batches for analysis
scRNAseq scRNA batchelor BatchEffect
updated 3.5 years ago by ★ 28k • written 3.5 years ago by • 0
1
vote
5
replies
844
views
Recommendation for large.n in filterByExpr
scRNAseq edgeR SingleCellExperiment
8 months ago duez.tolga • 0
1
vote
2
replies
1.8k
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 Ismail • 0
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 65k • written 3.5 years ago by ▴ 10
1
vote
0
replies
959
views
News: News: Bioinformatics Summer School - July 2020 - UCLouvain (Belgium)
rnaseq course proteomics transcriptomics scrnaseq News
4.2 years ago Laurent Gatto 1.6k
1
vote
5
replies
1.6k
views
computeSumFactors: warning about cluster size
scrnaseq scrn sizefactors
6.7 years ago sfpacman • 0
1
vote
2
replies
959
views
Combine scRNAseq data for bulk analysis using DESeq2
DESeq2 scRNAseq Fluidigm
19 months ago • updated 18 months ago evocanres • 0
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 ▴ 740 • written 2.1 years ago by • 0
1
vote
2
replies
1.8k
views
install celldex in r4. 04
scRNAseq
written 3.1 years ago by • 0
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 ▴ 950 • written 6.5 years ago by • 0
1
vote
2
replies
792
views
ScRNAseq analysis scran :: quickcluster Error
scRNAseq quickcluster scRNA scran
4 months ago ruba-mahmoud • 0
0
votes
3
replies
1.5k
views
MAST invalid Hypothesis, class objectORconnection error
R MAST scRNASeq
3.7 years ago TriS ▴ 200
0
votes
2
replies
201
views
Non-empty droplets versus good quality cells
CellRanger emptyDrops scRNAseq 10X
6 weeks ago • updated 5 weeks ago rocanja ▴ 60
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
0
votes
3
replies
1.4k
views
Modeling Dose-response data in MAST
MAST sc-rnaseq scrnaseq
updated 6.8 years ago by ▴ 270 • written 6.8 years ago by • 0
0
votes
2
replies
1.3k
views
BASiCS spike info for single cell RNA sequences or Bayesian statistics help
BASiCS bayesian single cell scrnaseq
updated 6.2 years ago by ▴ 10 • written 6.2 years ago by ▴ 10
0
votes
1
reply
991
views
RNAseq scater error in plotQC()
scater plotQC scRNAseq
updated 5.8 years ago by ★ 28k • written 5.8 years ago by ▴ 90
0
votes
6
replies
1.8k
views
analysis of multiple batches and multiple treatment conditions in scRNA-seq
limma deseq2 edger scRNAseq combat
updated 4.7 years ago by ▴ 270 • written 4.7 years ago by ▴ 670
0
votes
1
reply
1.6k
views
Minimum number of cells required for the MAST
MAST scRNAseq differential expression
4.7 years ago Andrew_McDavid ▴ 270
0
votes
2
replies
1.6k
views
PCA outliers cleaning
scRNAseq Pipeline Seurat SingleCellExperiment
4.5 years ago albadrs.93 ▴ 10
50 results • Page 1 of 1
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Comment: Help with error using camera() in limma by Chris • 0
Thanks James! I fixed the error. I try gene symbol instead of entrez and it worked.
Comment: limma for gene expression analysis with big and unbalanced sample size by XW • 0
Could you explain more about the comment "there are no problems with using limma for unbalanced data sets" ? thanks.
Comment: Limma, eBayes different sample size of groups and adjustment by XW • 0
Could you explain more about how the analysis self-correct the different sample sizes when calling DEGs in limma? Thanks
Answer: How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy) by James W. MacDonald 65k
The section of the vignette that is *directly above the one you quote* says that you can use the HMMcopy utils to do all three things. And …
Comment: Help with error using camera() in limma by James W. MacDonald 65k
Again, this is where you need to read the help page and try to diagnose. It says ``` index: an index vector or a list of index vectors. …
Votes
C: How to establish a subset from TxDb.Hsapiens.UCSC.hg38.knownGene DB
C: Extremely big genes in annotation TxDb packages
Make custom Txdb class objects from Txdb
Comment: Help with error using camera() in limma
Answer: Help with error using camera() in limma
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