Showing : scrnaseq • reset
0
votes
3
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617
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Differential variance analysis - can i use deseq2
DESeq2 DifferentialExpression RNASeq RNASeqData scRNAseq
updated 9 weeks ago by 43k • written 9 weeks ago by • 0
0
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0
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145
views
Help with mouse cell type annotation
annotation SingleR mouse SingleCellData scRNAseq
10 weeks ago Muhammad • 0
0
votes
3
replies
506
views
How to compare expression levels of genes between scRNAseq and bulkRNAseq?
Seurat RNASeq DESeq2 scRNAseq
updated 11 weeks ago by • 0 • written 3 months ago by ▴ 10
2
votes
2
replies
599
views
Should tSNE from biol. replicates look alike?
scRNAseq SingleCellExperiment batchelor
written 7 months ago by ▴ 10
0
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0
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526
views
Job: Postdoc Opportunity in Bioinformatics at Northwestern University (Research on Human Pregnancy and Autoimmunity)
Bioinformatics scRNAseq
10 months ago Damini • 0
1
vote
8
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1.4k
views
Advice on appropriateness of an offset in glmGamPoi/edgeR
DESeq2 glmGamPoi offset edgeR scRNAseq
updated 9 months ago by 52k • written 10 months ago by • 0
0
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0
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433
views
scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
RNASeq scRNAseq
11 months ago Bibi • 0
0
votes
1
reply
760
views
Can you find the correct transcript in scRNA seq data
scRNAseq RNAseq
updated 12 months ago by ★ 4.8k • written 12 months ago by • 0
0
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2
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798
views
Non-empty droplets versus good quality cells
CellRanger emptyDrops scRNAseq 10X
13 months ago rocanja ▴ 60
0
votes
1
reply
577
views
How to select cells that represents more accurately a cluster in a scRNA-seq dataset?
scRNAseq
updated 14 months ago by ★ 4.8k • written 14 months ago by • 0
1
vote
2
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1.7k
views
ScRNAseq analysis scran :: quickcluster Error
scRNAseq quickcluster scRNA scran
16 months ago ruba-mahmoud • 0
0
votes
2
replies
1.1k
views
scRNA analysis : DEG between low and high-expressing cells
scRNAseq
19 months ago • updated 18 months ago Momo • 0
0
votes
1
reply
683
views
FALSE error when checking a pre made sample data
Rstudio scRNAseq DESeq2
updated 20 months ago by ★ 4.8k • written 20 months ago by • 0
2
votes
5
replies
1.5k
views
Recommendation for large.n in filterByExpr
scRNAseq edgeR SingleCellExperiment
20 months ago duez.tolga • 0
0
votes
1
reply
2.4k
views
DESeq2 error after installing BiocManager
scRNAseq RStudio DESeq2
updated 20 months ago by ★ 4.8k • written 20 months ago by • 0
4
votes
3
replies
1.4k
views
Custom design for scRNA DGE with pseudobulking
scRNAseq scrna paireddesign edgeR pseudobulking
updated 21 months ago by 52k • written 21 months ago by • 0
0
votes
1
reply
747
views
If highly-expressed genes are upregulated, what happens to genes with lower expression after normalization?
scRNA scRNAseq
updated 21 months ago by ★ 4.8k • written 21 months ago by • 0
0
votes
1
reply
822
views
library(topGO) query
topGO scRNAseq
updated 21 months ago by ▴ 780 • written 21 months ago by • 0
0
votes
0
replies
663
views
adding noise to scRNA Seq counts
scRNAseq
21 months ago Jiyuan • 0
1
vote
11
replies
8.0k
views
Error: Bioconductor version cannot be validated; no internet connection?
scRNAseq
updated 18 months ago by • 0 • written 22 months ago by • 0
2
votes
3
replies
1.9k
views
P-value histogram of testLinearModel is not uniform
smart-seq2 scRNAseq scran
23 months ago • updated 22 months ago Lluís Revilla Sancho ▴ 760
0
votes
0
replies
860
views
News: course - single-cell RNAseq data analysis with R and Bioconductor
Workshop scRNAseq
23 months ago info ▴ 10
0
votes
1
reply
934
views
scRNAseq Download Errors
scRNAseq
updated 2.0 years ago by 4.1k • written 2.0 years ago by ★ 1.6k
2
votes
0
replies
2.2k
views
How to aggregate pseudobulks: Normalization & Log-Transformation
pseudobulk scRNAseq GSVA
2.0 years ago Tadeoye ▴ 20
0
votes
1
reply
1.3k
views
scRNAseq package and cell type annotations
ExperimentHub R ExperimentHubData scRNAseq SingleR
updated 2.1 years ago by ▴ 750 • written 2.1 years ago by ▴ 10
4
votes
5
replies
2.5k
views
Pseudo-bulk celltype comparison across conditions from multiple-sources
DESeq2 edgeR scRNAseq
updated 2.1 years ago by ▴ 750 • written 2.1 years ago by ▴ 10
0
votes
2
replies
1.3k
views
Could not find function "Standard Chromosomes"
scrna scRNAseq
updated 18 months ago by • 0 • written 2.1 years ago by • 0
0
votes
3
replies
1.9k
views
Single-Cell Data Simulation from Bulk RNA-seq
SingleCell RNASeq RNASeqData scRNAseq
updated 9 months ago by • 0 • written 2.4 years ago by • 0
1
vote
2
replies
1.8k
views
What number components should I use if I want to show 2D and 3D UMAP
scater UAMP scRNAseq
2.5 years ago Guandong Shang ▴ 40
1
vote
2
replies
1.3k
views
Combine scRNAseq data for bulk analysis using DESeq2
DESeq2 scRNAseq Fluidigm
2.6 years ago • updated 2.5 years ago evocanres • 0
0
votes
3
replies
1.5k
views
scRNA-seq: RS4' object has no attribute 'T'" in fastMNN R function
scanpy scRNAseq fastmnn r
2.6 years ago Madiha • 0
4
votes
5
replies
3.7k
views
`emptyDrops()` calling 'too many' non-empty droplets
DropletUtils emptyDrops scRNA scRNAseq 10x
2.7 years ago Peter Hickey ▴ 750
4
votes
2
replies
1.6k
views
how to do downstram analysis to cells which are subsetted after MNN batch-correction
batchelor fastMNN scRNAseq
2.7 years ago Guandong Shang ▴ 40
0
votes
4
replies
2.7k
views
how to make the "reconstructed" value in intergated scRNA-seq UMAP plot more readable
scater batchelor scRNAseq fastMNN
updated 2.7 years ago by ★ 28k • written 2.7 years ago by ▴ 40
0
votes
0
replies
1.3k
views
Job: Scientific Programmer | Altos Labs | San Diego
SpatialData scRNAseq JobPosting
2.7 years ago peter.kharchenko ▴ 30
0
votes
0
replies
979
views
Job: Postdoc position in integrated omics at Karolinska Institute, Stockholm
ATACSeq multiOmicsViz scRNAseq JobPosting
2.8 years ago Sebastian Lewandowski • 0
1
vote
4
replies
1.7k
views
Quality control of scRNA-seq data using mitochondrial ratio (drosophila)
Drosophila_melanogaster scRNAseq
2.8 years ago Chise ▴ 10
0
votes
0
replies
1.5k
views
how to calculate similarity between each cluster in scRNA and bulk RNA-seq
SingleR scRNAseq
2.8 years ago Guandong Shang ▴ 40
0
votes
2
replies
2.5k
views
calculateQCMetrics defunct, how to calculate the quality metrics by perCellQCMetrics
scRNAseq
updated 2.8 years ago by ★ 4.8k • written 2.8 years ago by • 0
0
votes
1
reply
1.6k
views
Error: DESeq(dds , useT = TRUE, minmu = 1e-06, test = "LRT", : likelihood ratio test requires a 'reduced' design, see ?DESeq
scRNAseq DESeq2
updated 2.8 years ago by ★ 4.8k • written 2.8 years ago by • 0
2
votes
8
replies
2.2k
views
RSEM - tximport; where is effective_length information used? Implications for scRNA?
RSEM tximport scRNAseq DESeq2
2.8 years ago Kelen ▴ 10
0
votes
1
reply
1.0k
views
scRNASeq reference at a transcript level
EWCE scRNAseq
updated 2.9 years ago by ▴ 780 • written 2.9 years ago by • 0
1
vote
2
replies
2.7k
views
unbalanced cell count and unbalanced read count across samples in pseudobulk differential expression analysis using scRNA-seq data
scRNAseq DifferentialExpression DESeq2
3.0 years ago Ismail • 0
1
vote
1
reply
2.6k
views
Can we use 'SCT normalization' to find anchors and 'LogNormalize' for the integration?
Normalization scRNAseq
updated 3.1 years ago by ▴ 750 • written 3.1 years ago by • 0
2
votes
2
replies
1.8k
views
scuttle:: librarySizeFactors returning non-finite values
normalizeCounts scran librarySizeFactors scuttle scRNAseq
3.2 years ago behr201 • 0
2
votes
2
replies
1.8k
views
How to deal with Expression set assembly problem?
deconvolution r scRNAseq bioinformatics
3.2 years ago Hasan Alanya • 0
0
votes
1
reply
1.4k
views
Aberrant number of cells
CellBarcode DropletUtils emptyDrops() Cellranger scRNAseq
updated 3.0 years ago by ▴ 20 • written 3.2 years ago by • 0
0
votes
0
replies
1.2k
views
Job: Postdoc Opening in Bioinformatics or Computational Biology
SpatialData scRNAseq SingleCell Omixer
3.3 years ago Sebastian Lewandowski • 0
0
votes
3
replies
2.0k
views
NA values for mitochondrial gene percentage
Seurat scRNAseq
3.4 years ago zahra.mesri95 • 0
0
votes
0
replies
872
views
scRNA technical replicates in separate runs
SingleCellExperiment scRNAseq
3.4 years ago Núria • 0
50 results • Page 1 of 1
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Comment: Filtering after DESeq by ATpoint ★ 4.8k
The problem is that your prefilter is not group-aware so the behaviour of seeing these sorts of outliers is expected. This is why I always …
Comment: GSEA preranked analysis downstream of DEseq2 by ATpoint ★ 4.8k
All due respect, this is what people do since pvalues exist, so this paper is not a reference, not is this a special score that merits a na…
Comment: Check removeBatchEffect effectiveness by ATpoint ★ 4.8k
> insert size, mean GC, etc... This is not a classical "batch" in the common sense, at least I've never seen this to be corrected for expl…
Answer: Check removeBatchEffect effectiveness by Gordon Smyth 52k
Your call to removeBatchEffect() is not correct because that function does not have an argument called `batch3`, meaning that the batch fac…
Comment: Intepretation of results by Tom • 0
[Locksmith Wombwell][1] I have been interested in using AUCell as a way to determine significantly enriched pathways in my single cell spat…
Votes
Answer: DiffBind; Error: No sites have activity greater than filter value
DiffBind; Error: No sites have activity greater than filter value
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
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