Showing : scRNAseq • reset
0
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3
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2.5k
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PCA outliers cleaning
scRNAseq Pipeline Seurat SingleCellExperiment
written 6.3 years ago by ▴ 10
1
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11
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2.4k
views
Using DESeq2 on single cell RNA Seq data of same cell type but different conditions that were pseudo bulked
DESeq2 scRNAseq
updated 12 weeks ago by ★ 4.0k • written 5 months ago by • 0
0
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1
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557
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Must I do pseudobulk analysis on Cell Surface Protein Labeling data of Single Cell RNA Sequencing
scRNAseq
updated 12 weeks ago by ★ 4.0k • written 3 months ago by • 0
0
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1
reply
386
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Length of 'dimnames' [1] not equal to array extent
SingleCellExperiment singlecelle scRNAseq
updated 12 weeks ago by ★ 4.0k • written 5 months ago by • 0
5
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13
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1.6k
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Guidance on limma for pseudobulk scRNA-seq with multi-factor design
limma RNASeq scRNAseq
updated 4 months ago by 53k • written 5 months ago by • 0
1
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2
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458
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Testing KO vs WT at day4/day14 with interactions in edgeR
scRNAseq
updated 6 months ago by 53k • written 6 months ago by • 0
0
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11
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1.1k
views
emptyDrops new default alpha = Inf giving far fewer non-empty droplets than under old default of alpha = NULL
scrn 10x scRNAseq emptyDrops DropletUtils
6 months ago Peter Hickey ▴ 760
0
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3
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1.2k
views
Differential variance analysis - can i use deseq2
DESeq2 DifferentialExpression RNASeq RNASeqData scRNAseq
updated 11 months ago by 43k • written 12 months ago by • 0
0
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0
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456
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Help with mouse cell type annotation
annotation SingleR mouse SingleCellData scRNAseq
12 months ago Muhammad • 0
0
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3
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1.2k
views
How to compare expression levels of genes between scRNAseq and bulkRNAseq?
Seurat RNASeq DESeq2 scRNAseq
updated 12 months ago by • 0 • written 12 months ago by ▴ 10
2
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2
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947
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Should tSNE from biol. replicates look alike?
scRNAseq SingleCellExperiment batchelor
written 17 months ago by ▴ 10
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0
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938
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Job: Postdoc Opportunity in Bioinformatics at Northwestern University (Research on Human Pregnancy and Autoimmunity)
Bioinformatics scRNAseq
19 months ago Damini • 0
1
vote
8
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2.1k
views
Advice on appropriateness of an offset in glmGamPoi/edgeR
DESeq2 glmGamPoi offset edgeR scRNAseq
updated 19 months ago by 53k • written 19 months ago by • 0
0
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0
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721
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scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
RNASeq scRNAseq
21 months ago Bibi • 0
0
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1
reply
1.1k
views
Can you find the correct transcript in scRNA seq data
scRNAseq RNAseq
updated 22 months ago by ★ 5.0k • written 22 months ago by • 0
0
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2
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1.3k
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Non-empty droplets versus good quality cells
CellRanger emptyDrops scRNAseq 10X
23 months ago rocanja ▴ 60
0
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1
reply
838
views
How to select cells that represents more accurately a cluster in a scRNA-seq dataset?
scRNAseq
updated 23 months ago by ★ 5.0k • written 24 months ago by • 0
1
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2
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2.1k
views
ScRNAseq analysis scran :: quickcluster Error
scRNAseq quickcluster scRNA scran
2.2 years ago ruba-mahmoud • 0
0
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2
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1.6k
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scRNA analysis : DEG between low and high-expressing cells
scRNAseq
2.4 years ago Momo • 0
0
votes
1
reply
960
views
FALSE error when checking a pre made sample data
Rstudio scRNAseq DESeq2
updated 2.5 years ago by ★ 5.0k • written 2.5 years ago by • 0
2
votes
5
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2.0k
views
Recommendation for large.n in filterByExpr
scRNAseq edgeR SingleCellExperiment
2.5 years ago duez.tolga • 0
0
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1
reply
3.0k
views
DESeq2 error after installing BiocManager
scRNAseq RStudio DESeq2
updated 2.5 years ago by ★ 5.0k • written 2.5 years ago by • 0
4
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3
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1.8k
views
Custom design for scRNA DGE with pseudobulking
scRNAseq scrna paireddesign edgeR pseudobulking
updated 2.5 years ago by 53k • written 2.5 years ago by • 0
0
votes
1
reply
1.0k
views
If highly-expressed genes are upregulated, what happens to genes with lower expression after normalization?
scRNA scRNAseq
updated 2.5 years ago by ★ 5.0k • written 2.5 years ago by • 0
0
votes
1
reply
1.0k
views
library(topGO) query
topGO scRNAseq
updated 2.6 years ago by ▴ 780 • written 2.6 years ago by • 0
0
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0
replies
850
views
adding noise to scRNA Seq counts
scRNAseq
2.6 years ago Jiyuan • 0
1
vote
11
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10k
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Error: Bioconductor version cannot be validated; no internet connection?
scRNAseq
updated 2.3 years ago by • 0 • written 2.6 years ago by • 0
2
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3
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2.2k
views
P-value histogram of testLinearModel is not uniform
smart-seq2 scRNAseq scran
2.7 years ago Lluís Revilla Sancho ▴ 760
0
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0
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1.1k
views
News: course - single-cell RNAseq data analysis with R and Bioconductor
Workshop scRNAseq
2.7 years ago info ▴ 10
0
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1
reply
1.2k
views
scRNAseq Download Errors
scRNAseq
updated 2.8 years ago by 4.3k • written 2.8 years ago by ★ 1.6k
2
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0
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2.9k
views
How to aggregate pseudobulks: Normalization & Log-Transformation
pseudobulk scRNAseq GSVA
2.8 years ago Tadeoye ▴ 20
0
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1
reply
1.8k
views
scRNAseq package and cell type annotations
ExperimentHub R ExperimentHubData scRNAseq SingleR
updated 2.9 years ago by ▴ 760 • written 2.9 years ago by ▴ 10
4
votes
5
replies
3.3k
views
Pseudo-bulk celltype comparison across conditions from multiple-sources
DESeq2 edgeR scRNAseq
updated 2.9 years ago by ▴ 760 • written 2.9 years ago by ▴ 10
0
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2
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1.8k
views
Could not find function "Standard Chromosomes"
scrna scRNAseq
updated 2.3 years ago by • 0 • written 2.9 years ago by • 0
0
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3
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2.6k
views
Single-Cell Data Simulation from Bulk RNA-seq
SingleCell RNASeq RNASeqData scRNAseq
updated 19 months ago by • 0 • written 3.2 years ago by • 0
1
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2
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2.2k
views
What number components should I use if I want to show 2D and 3D UMAP
scater UAMP scRNAseq
3.3 years ago Guandong Shang ▴ 40
1
vote
2
replies
1.6k
views
Combine scRNAseq data for bulk analysis using DESeq2
DESeq2 scRNAseq Fluidigm
3.4 years ago • updated 3.3 years ago evocanres • 0
0
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3
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1.9k
views
scRNA-seq: RS4' object has no attribute 'T'" in fastMNN R function
scanpy scRNAseq fastmnn r
3.4 years ago Madiha • 0
4
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5
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5.1k
views
`emptyDrops()` calling 'too many' non-empty droplets
DropletUtils emptyDrops scRNA scRNAseq 10x
3.5 years ago Peter Hickey ▴ 760
4
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2
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2.0k
views
how to do downstram analysis to cells which are subsetted after MNN batch-correction
batchelor fastMNN scRNAseq
3.5 years ago Guandong Shang ▴ 40
0
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4
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3.2k
views
how to make the "reconstructed" value in intergated scRNA-seq UMAP plot more readable
scater batchelor scRNAseq fastMNN
updated 3.5 years ago by ★ 29k • written 3.5 years ago by ▴ 40
0
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0
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1.6k
views
Job: Scientific Programmer | Altos Labs | San Diego
SpatialData scRNAseq JobPosting
3.5 years ago peter.kharchenko ▴ 30
0
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0
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1.2k
views
Job: Postdoc position in integrated omics at Karolinska Institute, Stockholm
ATACSeq multiOmicsViz scRNAseq JobPosting
3.6 years ago Sebastian Lewandowski • 0
1
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4
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2.1k
views
Quality control of scRNA-seq data using mitochondrial ratio (drosophila)
Drosophila_melanogaster scRNAseq
3.6 years ago Chise ▴ 10
0
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0
replies
1.8k
views
how to calculate similarity between each cluster in scRNA and bulk RNA-seq
SingleR scRNAseq
3.6 years ago Guandong Shang ▴ 40
0
votes
2
replies
2.8k
views
calculateQCMetrics defunct, how to calculate the quality metrics by perCellQCMetrics
scRNAseq
updated 3.6 years ago by ★ 5.0k • written 3.6 years ago by • 0
0
votes
1
reply
1.9k
views
Error: DESeq(dds , useT = TRUE, minmu = 1e-06, test = "LRT", : likelihood ratio test requires a 'reduced' design, see ?DESeq
scRNAseq DESeq2
updated 3.6 years ago by ★ 5.0k • written 3.6 years ago by • 0
2
votes
8
replies
2.8k
views
RSEM - tximport; where is effective_length information used? Implications for scRNA?
RSEM tximport scRNAseq DESeq2
3.6 years ago Kelen ▴ 10
0
votes
1
reply
1.3k
views
scRNASeq reference at a transcript level
EWCE scRNAseq
updated 3.7 years ago by ▴ 780 • written 3.7 years ago by • 0
1
vote
2
replies
3.2k
views
unbalanced cell count and unbalanced read count across samples in pseudobulk differential expression analysis using scRNA-seq data
scRNAseq DifferentialExpression DESeq2
3.8 years ago Ismail • 0
96 results • Page 1 of 2
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Comment: Which preprocessing steps are needed before running limpa? by miro165sabo • 0
Hi @gordonsmyth, thank you a lot for very fast and valuable response. I edited the question to provide more details.
Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ? by Gordon Smyth 53k
I tend to use dpcCN(), because it more robust than dpc() to experiments with lots of samples and big differences between samples. You coul…
Answer: Which preprocessing steps are needed before running limpa? by Gordon Smyth 53k
Please see the example limpa analyses given at <http://github.com/smythlab/limpa>, especially the kidney cancer case study. limpa does not…
Comment: Why does IDTaxa trainingSet for SILVA contain "_2" suffixes in the taxonomy name by Korneel • 0
Thanks for the quick reply! If I understand correctly, I think if I keep track of the full lineage, I shouldn't have any risk of collapsin…
Comment: Pathway abundance data from Curatedmetagenomics by yesquokkan • 0
Hello, I was also wondering about the same issue. Did you figure it out?
Votes
Answer: Which preprocessing steps are needed before running limpa?
Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ?
Answer: Which preprocessing steps are needed before running limpa?
Answer: Which preprocessing steps are needed before running limpa?
Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ?
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