Showing : scRNASeq • reset
1
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Using DESeq2 on single cell RNA Seq data of same cell type but different conditions that were pseudo bulked
DESeq2 scRNAseq
updated 9 weeks ago by ★ 4.0k • written 5 months ago by • 0
0
votes
1
reply
370
views
Must I do pseudobulk analysis on Cell Surface Protein Labeling data of Single Cell RNA Sequencing
scRNAseq
updated 9 weeks ago by ★ 4.0k • written 10 weeks ago by • 0
0
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1
reply
364
views
Length of 'dimnames' [1] not equal to array extent
SingleCellExperiment singlecelle scRNAseq
updated 9 weeks ago by ★ 4.0k • written 4 months ago by • 0
5
votes
13
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1.5k
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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 4 months ago by • 0
1
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2
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424
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Testing KO vs WT at day4/day14 with interactions in edgeR
scRNAseq
updated 5 months ago by 53k • written 5 months ago by • 0
0
votes
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
5 months ago Peter Hickey ▴ 760
0
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3
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1.1k
views
Differential variance analysis - can i use deseq2
DESeq2 DifferentialExpression RNASeq RNASeqData scRNAseq
updated 11 months ago by 43k • written 11 months ago by • 0
0
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0
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435
views
Help with mouse cell type annotation
annotation SingleR mouse SingleCellData scRNAseq
11 months ago Muhammad • 0
0
votes
3
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1.1k
views
How to compare expression levels of genes between scRNAseq and bulkRNAseq?
Seurat RNASeq DESeq2 scRNAseq
updated 11 months ago by • 0 • written 12 months ago by ▴ 10
2
votes
2
replies
923
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Should tSNE from biol. replicates look alike?
scRNAseq SingleCellExperiment batchelor
written 16 months ago by ▴ 10
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0
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913
views
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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2.0k
views
Advice on appropriateness of an offset in glmGamPoi/edgeR
DESeq2 glmGamPoi offset edgeR scRNAseq
updated 18 months ago by 53k • written 19 months ago by • 0
0
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0
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691
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scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
RNASeq scRNAseq
20 months ago Bibi • 0
0
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1
reply
1.0k
views
Can you find the correct transcript in scRNA seq data
scRNAseq RNAseq
updated 21 months ago by ★ 5.0k • written 21 months ago by • 0
0
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2
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1.2k
views
Non-empty droplets versus good quality cells
CellRanger emptyDrops scRNAseq 10X
22 months ago rocanja ▴ 60
0
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1
reply
814
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How to select cells that represents more accurately a cluster in a scRNA-seq dataset?
scRNAseq
updated 23 months ago by ★ 5.0k • written 23 months ago by • 0
1
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2
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2.1k
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ScRNAseq analysis scran :: quickcluster Error
scRNAseq quickcluster scRNA scran
2.1 years ago ruba-mahmoud • 0
0
votes
2
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1.5k
views
scRNA analysis : DEG between low and high-expressing cells
scRNAseq
2.3 years ago Momo • 0
0
votes
1
reply
922
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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1.9k
views
Recommendation for large.n in filterByExpr
scRNAseq edgeR SingleCellExperiment
2.5 years ago • updated 2.4 years ago duez.tolga • 0
0
votes
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 2.5 years ago by ▴ 780 • written 2.5 years ago by • 0
0
votes
0
replies
833
views
adding noise to scRNA Seq counts
scRNAseq
2.5 years ago Jiyuan • 0
1
vote
11
replies
9.9k
views
Error: Bioconductor version cannot be validated; no internet connection?
scRNAseq
updated 2.2 years ago by • 0 • written 2.6 years ago by • 0
2
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3
replies
2.2k
views
P-value histogram of testLinearModel is not uniform
smart-seq2 scRNAseq scran
2.6 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
votes
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
votes
0
replies
2.7k
views
How to aggregate pseudobulks: Normalization & Log-Transformation
pseudobulk scRNAseq GSVA
2.8 years ago Tadeoye ▴ 20
0
votes
1
reply
1.7k
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
3.2k
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
votes
2
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1.7k
views
Could not find function "Standard Chromosomes"
scrna scRNAseq
updated 2.3 years ago by • 0 • written 2.9 years ago by • 0
0
votes
3
replies
2.5k
views
Single-Cell Data Simulation from Bulk RNA-seq
SingleCell RNASeq RNASeqData scRNAseq
updated 18 months ago by • 0 • written 3.2 years ago by • 0
1
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2
replies
2.1k
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
3.3 years ago evocanres • 0
0
votes
3
replies
1.9k
views
scRNA-seq: RS4' object has no attribute 'T'" in fastMNN R function
scanpy scRNAseq fastmnn r
3.3 years ago Madiha • 0
4
votes
5
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4.8k
views
`emptyDrops()` calling 'too many' non-empty droplets
DropletUtils emptyDrops scRNA scRNAseq 10x
3.5 years ago • updated 3.4 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
votes
4
replies
3.1k
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
votes
0
replies
1.6k
views
Job: Scientific Programmer | Altos Labs | San Diego
SpatialData scRNAseq JobPosting
3.5 years ago peter.kharchenko ▴ 30
0
votes
0
replies
1.2k
views
Job: Postdoc position in integrated omics at Karolinska Institute, Stockholm
ATACSeq multiOmicsViz scRNAseq JobPosting
3.5 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
3.5 years ago Chise ▴ 10
0
votes
0
replies
1.7k
views
how to calculate similarity between each cluster in scRNA and bulk RNA-seq
SingleR scRNAseq
3.5 years ago Guandong Shang ▴ 40
0
votes
2
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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
2.7k
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
1.2k
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
1
vote
1
reply
3.1k
views
Can we use 'SCT normalization' to find anchors and 'LogNormalize' for the integration?
Normalization scRNAseq
updated 3.8 years ago by ▴ 760 • written 3.8 years ago by • 0
96 results • Page 1 of 2
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Replies
Comment: chemmineOB install help by Jeremy • 0
I could install ChemmineOB on my MacBook Pro M1 Max using this procedure **1. Install open-babel and eigen using homebrew and create a cus…
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by Gordon Smyth 53k
The design matrix that I described above is completely general. I imagine that it would be possible to use the same approach to generate fu…
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by chp265 • 0
Cool, glad to hear I wasn't missing some functionality in DESeq2. I don't know that much about the differences between DESeq2 vs edgeR; my …
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by Michael Love 43k
Yes, so for one thing, note that Gordon has provided code for doing what you are asking in edgeR, which you can go ahead and use. You aske…
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by chp265 • 0
I don't think DESeq2 has the ability to do multi-contrast comparisons, at least based on what I can understand of the manual; I can pick mu…
Votes
A: DESeq2: Is it possible to convert read counts to expression values via TPM and r
A: Filtering read counts matrix: how to deal with duplicated gene symbols, differen
Comment: limpa analysis advice
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
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