Showing : scrnaseq • reset
2
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1
reply
108
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Should tSNE from biol. replicates look alike?
scRNAseq SingleCellExperiment batchelor
updated 3 days ago by 67k • written 3 days ago by ▴ 10
0
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0
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260
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Job: Postdoc Opportunity in Bioinformatics at Northwestern University (Research on Human Pregnancy and Autoimmunity)
Bioinformatics scRNAseq
9 weeks ago Damini • 0
1
vote
8
replies
681
views
Advice on appropriateness of an offset in glmGamPoi/edgeR
DESeq2 glmGamPoi offset edgeR scRNAseq
updated 8 weeks ago by 51k • written 10 weeks ago by • 0
0
votes
0
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208
views
scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
RNASeq scRNAseq
3 months ago Bibi • 0
0
votes
1
reply
324
views
Can you find the correct transcript in scRNA seq data
scRNAseq RNAseq
updated 5 months ago by ★ 4.4k • written 5 months ago by • 0
0
votes
2
replies
446
views
Non-empty droplets versus good quality cells
CellRanger emptyDrops scRNAseq 10X
5 months ago rocanja ▴ 60
0
votes
1
reply
380
views
How to select cells that represents more accurately a cluster in a scRNA-seq dataset?
scRNAseq
updated 6 months ago by ★ 4.4k • written 6 months ago by • 0
1
vote
2
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1.3k
views
ScRNAseq analysis scran :: quickcluster Error
scRNAseq quickcluster scRNA scran
9 months ago ruba-mahmoud • 0
0
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2
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757
views
scRNA analysis : DEG between low and high-expressing cells
scRNAseq
11 months ago Momo • 0
0
votes
1
reply
533
views
FALSE error when checking a pre made sample data
Rstudio scRNAseq DESeq2
updated 13 months ago by ★ 4.4k • written 13 months ago by • 0
2
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5
replies
1.2k
views
Recommendation for large.n in filterByExpr
scRNAseq edgeR SingleCellExperiment
13 months ago duez.tolga • 0
0
votes
1
reply
1.5k
views
DESeq2 error after installing BiocManager
scRNAseq RStudio DESeq2
updated 13 months ago by ★ 4.4k • written 13 months ago by • 0
4
votes
3
replies
1.2k
views
Custom design for scRNA DGE with pseudobulking
scRNAseq scrna paireddesign edgeR pseudobulking
updated 13 months ago by 51k • written 13 months ago by • 0
0
votes
1
reply
554
views
If highly-expressed genes are upregulated, what happens to genes with lower expression after normalization?
scRNA scRNAseq
updated 13 months ago by ★ 4.4k • written 13 months ago by • 0
0
votes
1
reply
677
views
library(topGO) query
topGO scRNAseq
updated 13 months ago by ▴ 780 • written 13 months ago by • 0
0
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0
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481
views
adding noise to scRNA Seq counts
scRNAseq
13 months ago Jiyuan • 0
1
vote
11
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4.8k
views
Error: Bioconductor version cannot be validated; no internet connection?
scRNAseq
updated 10 months ago by • 0 • written 14 months ago by • 0
2
votes
3
replies
1.5k
views
P-value histogram of testLinearModel is not uniform
smart-seq2 scRNAseq scran
15 months ago Lluís Revilla Sancho ▴ 730
0
votes
0
replies
661
views
News: course - single-cell RNAseq data analysis with R and Bioconductor
Workshop scRNAseq
15 months ago info ▴ 10
0
votes
1
reply
695
views
scRNAseq Download Errors
scRNAseq
updated 16 months ago by 4.0k • written 16 months ago by ★ 1.5k
2
votes
0
replies
1.5k
views
How to aggregate pseudobulks: Normalization & Log-Transformation
pseudobulk scRNAseq GSVA
17 months ago Tadeoye ▴ 20
0
votes
1
reply
969
views
scRNAseq package and cell type annotations
ExperimentHub R ExperimentHubData scRNAseq SingleR
updated 18 months ago by ▴ 740 • written 18 months ago by ▴ 10
4
votes
5
replies
1.7k
views
Pseudo-bulk celltype comparison across conditions from multiple-sources
DESeq2 edgeR scRNAseq
updated 18 months ago by ▴ 740 • written 18 months ago by ▴ 10
0
votes
2
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895
views
Could not find function "Standard Chromosomes"
scrna scRNAseq
updated 10 months ago by • 0 • written 18 months ago by • 0
0
votes
3
replies
1.3k
views
Single-Cell Data Simulation from Bulk RNA-seq
SingleCell RNASeq RNASeqData scRNAseq
updated 8 weeks ago by • 0 • written 22 months ago by • 0
1
vote
2
replies
1.4k
views
What number components should I use if I want to show 2D and 3D UMAP
scater UAMP scRNAseq
23 months ago Guandong Shang ▴ 40
1
vote
2
replies
1.1k
views
Combine scRNAseq data for bulk analysis using DESeq2
DESeq2 scRNAseq Fluidigm
23 months ago • updated 22 months ago evocanres • 0
0
votes
3
replies
1.2k
views
scRNA-seq: RS4' object has no attribute 'T'" in fastMNN R function
scanpy scRNAseq fastmnn r
23 months ago Madiha • 0
4
votes
5
replies
2.9k
views
`emptyDrops()` calling 'too many' non-empty droplets
DropletUtils emptyDrops scRNA scRNAseq 10x
2.1 years ago Peter Hickey ▴ 740
4
votes
2
replies
1.3k
views
how to do downstram analysis to cells which are subsetted after MNN batch-correction
batchelor fastMNN scRNAseq
2.1 years ago Guandong Shang ▴ 40
0
votes
4
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2.3k
views
how to make the "reconstructed" value in intergated scRNA-seq UMAP plot more readable
scater batchelor scRNAseq fastMNN
updated 2.1 years ago by ★ 28k • written 2.1 years ago by ▴ 40
0
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0
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1.1k
views
Job: Scientific Programmer | Altos Labs | San Diego
SpatialData scRNAseq JobPosting
2.1 years ago peter.kharchenko ▴ 30
0
votes
0
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829
views
Job: Postdoc position in integrated omics at Karolinska Institute, Stockholm
ATACSeq multiOmicsViz scRNAseq JobPosting
2.1 years ago Sebastian Lewandowski • 0
1
vote
4
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1.4k
views
Quality control of scRNA-seq data using mitochondrial ratio (drosophila)
Drosophila_melanogaster scRNAseq
2.1 years ago Chise ▴ 10
0
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0
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1.1k
views
how to calculate similarity between each cluster in scRNA and bulk RNA-seq
SingleR scRNAseq
2.2 years ago Guandong Shang ▴ 40
0
votes
2
replies
2.1k
views
calculateQCMetrics defunct, how to calculate the quality metrics by perCellQCMetrics
scRNAseq
updated 2.2 years ago by ★ 4.4k • written 2.2 years ago by • 0
0
votes
1
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1.3k
views
Error: DESeq(dds , useT = TRUE, minmu = 1e-06, test = "LRT", : likelihood ratio test requires a 'reduced' design, see ?DESeq
scRNAseq DESeq2
updated 2.2 years ago by ★ 4.4k • written 2.2 years ago by • 0
2
votes
8
replies
1.8k
views
RSEM - tximport; where is effective_length information used? Implications for scRNA?
RSEM tximport scRNAseq DESeq2
2.2 years ago Kelen ▴ 10
0
votes
1
reply
867
views
scRNASeq reference at a transcript level
EWCE scRNAseq
updated 2.3 years ago by ▴ 780 • written 2.3 years ago by • 0
1
vote
2
replies
2.1k
views
unbalanced cell count and unbalanced read count across samples in pseudobulk differential expression analysis using scRNA-seq data
scRNAseq DifferentialExpression DESeq2
2.4 years ago Ismail • 0
1
vote
1
reply
2.0k
views
Can we use 'SCT normalization' to find anchors and 'LogNormalize' for the integration?
Normalization scRNAseq
updated 2.4 years ago by ▴ 740 • written 2.4 years ago by • 0
2
votes
2
replies
1.4k
views
scuttle:: librarySizeFactors returning non-finite values
normalizeCounts scran librarySizeFactors scuttle scRNAseq
2.5 years ago behr201 • 0
2
votes
2
replies
1.4k
views
How to deal with Expression set assembly problem?
deconvolution r scRNAseq bioinformatics
2.6 years ago Hasan Alanya • 0
0
votes
1
reply
1.2k
views
Aberrant number of cells
CellBarcode DropletUtils emptyDrops() Cellranger scRNAseq
updated 2.4 years ago by ▴ 20 • written 2.6 years ago by • 0
0
votes
0
replies
1.0k
views
Job: Postdoc Opening in Bioinformatics or Computational Biology
SpatialData scRNAseq SingleCell Omixer
2.6 years ago Sebastian Lewandowski • 0
0
votes
3
replies
1.7k
views
NA values for mitochondrial gene percentage
Seurat scRNAseq
2.8 years ago • updated 2.7 years ago zahra.mesri95 • 0
0
votes
0
replies
722
views
scRNA technical replicates in separate runs
SingleCellExperiment scRNAseq
2.8 years ago Núria • 0
0
votes
2
replies
1.1k
views
scRNAseq analysis on multiple datasets
scRNAseq
updated 2.9 years ago by ★ 1.4k • written 3.0 years ago by • 0
2
votes
4
replies
1.4k
views
edgeR output doubts
logFC edgeR DifferentialExpression scRNAseq
3.1 years ago mbenegas ▴ 10
0
votes
1
reply
1.2k
views
Identify a scRNASeq cell-population using a bulk RNA Seq dataset of that population?
RNASeq rnaseq scRNAseq
updated 3.1 years ago by ★ 28k • written 3.1 years ago by ▴ 10
50 results • Page 1 of 1
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Comment: [DESeq2] Normalization of External Test Dataset for Machine Learning (ML) Applic by Michael Love 42k
I request the post here, so not a problem.
Comment: [DESeq2] Normalization of External Test Dataset for Machine Learning (ML) Applic by micolak0115 • 0
Thanks for the advice Michael. I will try this with my future test datasets.
Comment: [DESeq2] Normalization of External Test Dataset for Machine Learning (ML) Applic by micolak0115 • 0
Hi James, I will try to leave only relevant questions on bioconductor forum hereinafter. Thanks for the note. Cheers, Alan
Comment: SingleR Label.Ont by Stepah • 0
[Aussie Play][1] cares about its Australian players by offering a safe and secure gaming experience where there is never a dull moment. The…
Comment: ensemblVEP deprecation and how to reproduce by Vincent J. Carey, Jr. 6.7k
What aspect of ensemblVEP are you looking for? The vignette https://bioconductor.org/packages/release/bioc/vignettes/VariantAnnotation/in…
Votes
DEXseq: How to do differential exon usage of genes with overlapping exons
A: Moderated F-test followed by moderated t-test in limma
Answer: [DESeq2] Normalization of External Test Dataset for Machine Learning (ML) Applic
Answer: [DESeq2] Normalization of External Test Dataset for Machine Learning (ML) Applic
Answer: [DESeq2] Normalization of External Test Dataset for Machine Learning (ML) Applic
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