Showing : scrnaseq • reset
2
votes
2
replies
446
views
Should tSNE from biol. replicates look alike?
scRNAseq SingleCellExperiment batchelor
written 4 months ago by ▴ 10
0
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0
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413
views
Job: Postdoc Opportunity in Bioinformatics at Northwestern University (Research on Human Pregnancy and Autoimmunity)
Bioinformatics scRNAseq
6 months ago Damini • 0
1
vote
8
replies
1.1k
views
Advice on appropriateness of an offset in glmGamPoi/edgeR
DESeq2 glmGamPoi offset edgeR scRNAseq
updated 6 months ago by 52k • written 6 months ago by • 0
0
votes
0
replies
327
views
scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
RNASeq scRNAseq
8 months ago Bibi • 0
0
votes
1
reply
585
views
Can you find the correct transcript in scRNA seq data
scRNAseq RNAseq
updated 9 months ago by ★ 4.6k • written 9 months ago by • 0
0
votes
2
replies
668
views
Non-empty droplets versus good quality cells
CellRanger emptyDrops scRNAseq 10X
10 months ago rocanja ▴ 60
0
votes
1
reply
477
views
How to select cells that represents more accurately a cluster in a scRNA-seq dataset?
scRNAseq
updated 10 months ago by ★ 4.6k • written 11 months ago by • 0
1
vote
2
replies
1.5k
views
ScRNAseq analysis scran :: quickcluster Error
scRNAseq quickcluster scRNA scran
13 months ago ruba-mahmoud • 0
0
votes
2
replies
941
views
scRNA analysis : DEG between low and high-expressing cells
scRNAseq
15 months ago Momo • 0
0
votes
1
reply
613
views
FALSE error when checking a pre made sample data
Rstudio scRNAseq DESeq2
updated 17 months ago by ★ 4.6k • written 17 months ago by • 0
2
votes
5
replies
1.4k
views
Recommendation for large.n in filterByExpr
scRNAseq edgeR SingleCellExperiment
17 months ago duez.tolga • 0
0
votes
1
reply
1.9k
views
DESeq2 error after installing BiocManager
scRNAseq RStudio DESeq2
updated 17 months ago by ★ 4.6k • written 17 months ago by • 0
4
votes
3
replies
1.3k
views
Custom design for scRNA DGE with pseudobulking
scRNAseq scrna paireddesign edgeR pseudobulking
updated 17 months ago by 52k • written 17 months ago by • 0
0
votes
1
reply
665
views
If highly-expressed genes are upregulated, what happens to genes with lower expression after normalization?
scRNA scRNAseq
updated 17 months ago by ★ 4.6k • written 17 months ago by • 0
0
votes
1
reply
751
views
library(topGO) query
topGO scRNAseq
updated 18 months ago by ▴ 780 • written 18 months ago by • 0
0
votes
0
replies
588
views
adding noise to scRNA Seq counts
scRNAseq
18 months ago Jiyuan • 0
1
vote
11
replies
6.8k
views
Error: Bioconductor version cannot be validated; no internet connection?
scRNAseq
updated 14 months ago by • 0 • written 19 months ago by • 0
2
votes
3
replies
1.7k
views
P-value histogram of testLinearModel is not uniform
smart-seq2 scRNAseq scran
19 months ago Lluís Revilla Sancho ▴ 760
0
votes
0
replies
766
views
News: course - single-cell RNAseq data analysis with R and Bioconductor
Workshop scRNAseq
20 months ago info ▴ 10
0
votes
1
reply
823
views
scRNAseq Download Errors
scRNAseq
updated 21 months ago by 4.1k • written 21 months ago by ★ 1.5k
2
votes
0
replies
1.9k
views
How to aggregate pseudobulks: Normalization & Log-Transformation
pseudobulk scRNAseq GSVA
21 months ago Tadeoye ▴ 20
0
votes
1
reply
1.1k
views
scRNAseq package and cell type annotations
ExperimentHub R ExperimentHubData scRNAseq SingleR
updated 22 months ago by ▴ 740 • written 22 months ago by ▴ 10
4
votes
5
replies
2.0k
views
Pseudo-bulk celltype comparison across conditions from multiple-sources
DESeq2 edgeR scRNAseq
updated 22 months ago by ▴ 740 • written 22 months ago by ▴ 10
0
votes
2
replies
1.1k
views
Could not find function "Standard Chromosomes"
scrna scRNAseq
updated 15 months ago by • 0 • written 22 months ago by • 0
0
votes
3
replies
1.6k
views
Single-Cell Data Simulation from Bulk RNA-seq
SingleCell RNASeq RNASeqData scRNAseq
updated 6 months ago by • 0 • written 2.2 years ago by • 0
1
vote
2
replies
1.5k
views
What number components should I use if I want to show 2D and 3D UMAP
scater UAMP scRNAseq
2.3 years ago Guandong Shang ▴ 40
1
vote
2
replies
1.2k
views
Combine scRNAseq data for bulk analysis using DESeq2
DESeq2 scRNAseq Fluidigm
2.3 years ago evocanres • 0
0
votes
3
replies
1.4k
views
scRNA-seq: RS4' object has no attribute 'T'" in fastMNN R function
scanpy scRNAseq fastmnn r
2.3 years ago Madiha • 0
4
votes
5
replies
3.3k
views
`emptyDrops()` calling 'too many' non-empty droplets
DropletUtils emptyDrops scRNA scRNAseq 10x
2.5 years ago • updated 2.4 years ago Peter Hickey ▴ 740
4
votes
2
replies
1.5k
views
how to do downstram analysis to cells which are subsetted after MNN batch-correction
batchelor fastMNN scRNAseq
2.5 years ago Guandong Shang ▴ 40
0
votes
4
replies
2.5k
views
how to make the "reconstructed" value in intergated scRNA-seq UMAP plot more readable
scater batchelor scRNAseq fastMNN
updated 2.5 years ago by ★ 28k • written 2.5 years ago by ▴ 40
0
votes
0
replies
1.2k
views
Job: Scientific Programmer | Altos Labs | San Diego
SpatialData scRNAseq JobPosting
2.5 years ago peter.kharchenko ▴ 30
0
votes
0
replies
914
views
Job: Postdoc position in integrated omics at Karolinska Institute, Stockholm
ATACSeq multiOmicsViz scRNAseq JobPosting
2.5 years ago Sebastian Lewandowski • 0
1
vote
4
replies
1.6k
views
Quality control of scRNA-seq data using mitochondrial ratio (drosophila)
Drosophila_melanogaster scRNAseq
2.5 years ago Chise ▴ 10
0
votes
0
replies
1.3k
views
how to calculate similarity between each cluster in scRNA and bulk RNA-seq
SingleR scRNAseq
2.5 years ago Guandong Shang ▴ 40
0
votes
2
replies
2.3k
views
calculateQCMetrics defunct, how to calculate the quality metrics by perCellQCMetrics
scRNAseq
updated 2.5 years ago by ★ 4.6k • written 2.5 years ago by • 0
0
votes
1
reply
1.5k
views
Error: DESeq(dds , useT = TRUE, minmu = 1e-06, test = "LRT", : likelihood ratio test requires a 'reduced' design, see ?DESeq
scRNAseq DESeq2
updated 2.6 years ago by ★ 4.6k • written 2.6 years ago by • 0
2
votes
8
replies
2.0k
views
RSEM - tximport; where is effective_length information used? Implications for scRNA?
RSEM tximport scRNAseq DESeq2
2.6 years ago Kelen ▴ 10
0
votes
1
reply
954
views
scRNASeq reference at a transcript level
EWCE scRNAseq
updated 2.7 years ago by ▴ 780 • written 2.7 years ago by • 0
1
vote
2
replies
2.4k
views
unbalanced cell count and unbalanced read count across samples in pseudobulk differential expression analysis using scRNA-seq data
scRNAseq DifferentialExpression DESeq2
2.8 years ago • updated 2.7 years ago Ismail • 0
1
vote
1
reply
2.2k
views
Can we use 'SCT normalization' to find anchors and 'LogNormalize' for the integration?
Normalization scRNAseq
updated 2.8 years ago by ▴ 740 • written 2.8 years ago by • 0
2
votes
2
replies
1.6k
views
scuttle:: librarySizeFactors returning non-finite values
normalizeCounts scran librarySizeFactors scuttle scRNAseq
2.9 years ago behr201 • 0
2
votes
2
replies
1.6k
views
How to deal with Expression set assembly problem?
deconvolution r scRNAseq bioinformatics
3.0 years ago Hasan Alanya • 0
0
votes
1
reply
1.3k
views
Aberrant number of cells
CellBarcode DropletUtils emptyDrops() Cellranger scRNAseq
updated 2.7 years ago by ▴ 20 • written 3.0 years ago by • 0
0
votes
0
replies
1.1k
views
Job: Postdoc Opening in Bioinformatics or Computational Biology
SpatialData scRNAseq SingleCell Omixer
3.0 years ago Sebastian Lewandowski • 0
0
votes
3
replies
1.8k
views
NA values for mitochondrial gene percentage
Seurat scRNAseq
3.1 years ago zahra.mesri95 • 0
0
votes
0
replies
794
views
scRNA technical replicates in separate runs
SingleCellExperiment scRNAseq
3.1 years ago Núria • 0
0
votes
2
replies
1.2k
views
scRNAseq analysis on multiple datasets
scRNAseq
updated 3.3 years ago by ★ 1.4k • written 3.3 years ago by • 0
2
votes
4
replies
1.6k
views
edgeR output doubts
logFC edgeR DifferentialExpression scRNAseq
3.4 years ago mbenegas ▴ 10
0
votes
1
reply
1.3k
views
Identify a scRNASeq cell-population using a bulk RNA Seq dataset of that population?
RNASeq rnaseq scRNAseq
updated 3.5 years ago by ★ 28k • written 3.5 years ago by ▴ 10
50 results • Page 1 of 1
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Replies
Comment: contrast matrix design for a continuous variable by dtzhu337 • 0
Hi Gordon, Thank you very much for your answer. Actually the variable X is the age, which I am also interested in. Somehow, age and V1 are…
Answer: SingleCellExperiment convenience function for metadata+expression? by Peter Hickey ▴ 740
Hi Sarah, `scuttle::makePerCellDF()` / `scuttle::makePerFeatureDF()` and `scater::ggcells()` / `scater::ggfeatures()`, which build upon th…
Comment: How to sort negative log2FC or FC in RNAseq for GSEA? by QN ▴ 10
Thank you ATpoint for your response! In the result of GSEA, like you indicated, there will be gene sets that have positive NES and gene se…
Comment: EdgeR Biological CVs by ATpoint ★ 4.6k
"Joseph" is a spam bot...
Answer: How to sort negative log2FC or FC in RNAseq for GSEA? by ATpoint ★ 4.6k
GSEA asks whether there are general shifts in gene expression towards certain terms. Hence, you would not split your results tables but ord…
Votes
How to correct for tumor purity using DESeq2 to analyze TCGA tumor sample expression.
Answer: EdgeR Biological CVs
Answer: Error in download.file for TCGAutils::symbolsToRanges
Answer: Error in download.file for TCGAutils::symbolsToRanges
Answer: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
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