Showing : scRNAseq • reset
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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 17 days ago by ★ 4.0k • written 3 months ago by • 0
0
votes
1
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200
views
Must I do pseudobulk analysis on Cell Surface Protein Labeling data of Single Cell RNA Sequencing
scRNAseq
updated 20 days ago by ★ 4.0k • written 27 days ago by • 0
0
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1
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287
views
Length of 'dimnames' [1] not equal to array extent
SingleCellExperiment singlecelle scRNAseq
updated 20 days ago by ★ 4.0k • written 3 months ago by • 0
5
votes
13
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1.3k
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Guidance on limma for pseudobulk scRNA-seq with multi-factor design
limma RNASeq scRNAseq
updated 10 weeks ago by 53k • written 12 weeks ago by • 0
1
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2
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354
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Testing KO vs WT at day4/day14 with interactions in edgeR
scRNAseq
updated 3 months ago by 53k • written 4 months ago by • 0
0
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11
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940
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emptyDrops new default alpha = Inf giving far fewer non-empty droplets than under old default of alpha = NULL
scrn 10x scRNAseq emptyDrops DropletUtils
4 months ago • updated 3 months ago Peter Hickey ▴ 760
0
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3
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1.0k
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Differential variance analysis - can i use deseq2
DESeq2 DifferentialExpression RNASeq RNASeqData scRNAseq
updated 9 months ago by 43k • written 9 months ago by • 0
0
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0
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409
views
Help with mouse cell type annotation
annotation SingleR mouse SingleCellData scRNAseq
9 months ago Muhammad • 0
0
votes
3
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871
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How to compare expression levels of genes between scRNAseq and bulkRNAseq?
Seurat RNASeq DESeq2 scRNAseq
updated 10 months ago by • 0 • written 10 months ago by ▴ 10
2
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2
replies
859
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Should tSNE from biol. replicates look alike?
scRNAseq SingleCellExperiment batchelor
written 15 months ago by ▴ 10
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0
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857
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Job: Postdoc Opportunity in Bioinformatics at Northwestern University (Research on Human Pregnancy and Autoimmunity)
Bioinformatics scRNAseq
17 months ago Damini • 0
1
vote
8
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1.9k
views
Advice on appropriateness of an offset in glmGamPoi/edgeR
DESeq2 glmGamPoi offset edgeR scRNAseq
updated 17 months ago by 53k • written 17 months ago by • 0
0
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0
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651
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scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
RNASeq scRNAseq
18 months ago Bibi • 0
0
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1
reply
997
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Can you find the correct transcript in scRNA seq data
scRNAseq RNAseq
updated 20 months ago by ★ 5.0k • written 20 months ago by • 0
0
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2
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1.1k
views
Non-empty droplets versus good quality cells
CellRanger emptyDrops scRNAseq 10X
20 months ago rocanja ▴ 60
0
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1
reply
759
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How to select cells that represents more accurately a cluster in a scRNA-seq dataset?
scRNAseq
updated 21 months ago by ★ 5.0k • written 21 months ago by • 0
1
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2
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2.0k
views
ScRNAseq analysis scran :: quickcluster Error
scRNAseq quickcluster scRNA scran
2.0 years ago ruba-mahmoud • 0
0
votes
2
replies
1.4k
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scRNA analysis : DEG between low and high-expressing cells
scRNAseq
2.2 years ago Momo • 0
0
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1
reply
874
views
FALSE error when checking a pre made sample data
Rstudio scRNAseq DESeq2
updated 2.3 years ago by ★ 5.0k • written 2.3 years ago by • 0
2
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5
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1.8k
views
Recommendation for large.n in filterByExpr
scRNAseq edgeR SingleCellExperiment
2.3 years ago duez.tolga • 0
0
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1
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2.8k
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DESeq2 error after installing BiocManager
scRNAseq RStudio DESeq2
updated 2.3 years ago by ★ 5.0k • written 2.3 years ago by • 0
4
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3
replies
1.7k
views
Custom design for scRNA DGE with pseudobulking
scRNAseq scrna paireddesign edgeR pseudobulking
updated 2.3 years ago by 53k • written 2.4 years ago by • 0
0
votes
1
reply
950
views
If highly-expressed genes are upregulated, what happens to genes with lower expression after normalization?
scRNA scRNAseq
updated 2.4 years ago by ★ 5.0k • written 2.4 years ago by • 0
0
votes
1
reply
998
views
library(topGO) query
topGO scRNAseq
updated 2.4 years ago by ▴ 780 • written 2.4 years ago by • 0
0
votes
0
replies
804
views
adding noise to scRNA Seq counts
scRNAseq
2.4 years ago Jiyuan • 0
1
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11
replies
9.5k
views
Error: Bioconductor version cannot be validated; no internet connection?
scRNAseq
updated 2.1 years ago by • 0 • written 2.4 years ago by • 0
2
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3
replies
2.1k
views
P-value histogram of testLinearModel is not uniform
smart-seq2 scRNAseq scran
2.5 years ago Lluís Revilla Sancho ▴ 760
0
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0
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1.0k
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News: course - single-cell RNAseq data analysis with R and Bioconductor
Workshop scRNAseq
2.6 years ago info ▴ 10
0
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1
reply
1.1k
views
scRNAseq Download Errors
scRNAseq
updated 2.6 years ago by 4.2k • written 2.6 years ago by ★ 1.6k
2
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0
replies
2.6k
views
How to aggregate pseudobulks: Normalization & Log-Transformation
pseudobulk scRNAseq GSVA
2.7 years ago Tadeoye ▴ 20
0
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1
reply
1.6k
views
scRNAseq package and cell type annotations
ExperimentHub R ExperimentHubData scRNAseq SingleR
updated 2.7 years ago by ▴ 760 • written 2.7 years ago by ▴ 10
4
votes
5
replies
2.9k
views
Pseudo-bulk celltype comparison across conditions from multiple-sources
DESeq2 edgeR scRNAseq
updated 2.8 years ago by ▴ 760 • written 2.8 years ago by ▴ 10
0
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2
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1.7k
views
Could not find function "Standard Chromosomes"
scrna scRNAseq
updated 2.1 years ago by • 0 • written 2.8 years ago by • 0
0
votes
3
replies
2.3k
views
Single-Cell Data Simulation from Bulk RNA-seq
SingleCell RNASeq RNASeqData scRNAseq
updated 17 months ago by • 0 • written 3.1 years ago by • 0
1
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2
replies
2.0k
views
What number components should I use if I want to show 2D and 3D UMAP
scater UAMP scRNAseq
3.2 years ago Guandong Shang ▴ 40
1
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2
replies
1.5k
views
Combine scRNAseq data for bulk analysis using DESeq2
DESeq2 scRNAseq Fluidigm
3.2 years ago • updated 3.1 years ago evocanres • 0
0
votes
3
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1.8k
views
scRNA-seq: RS4' object has no attribute 'T'" in fastMNN R function
scanpy scRNAseq fastmnn r
3.2 years ago Madiha • 0
4
votes
5
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4.2k
views
`emptyDrops()` calling 'too many' non-empty droplets
DropletUtils emptyDrops scRNA scRNAseq 10x
3.4 years ago • updated 3.3 years ago Peter Hickey ▴ 760
4
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2
replies
1.9k
views
how to do downstram analysis to cells which are subsetted after MNN batch-correction
batchelor fastMNN scRNAseq
3.3 years ago Guandong Shang ▴ 40
0
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4
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3.0k
views
how to make the "reconstructed" value in intergated scRNA-seq UMAP plot more readable
scater batchelor scRNAseq fastMNN
updated 3.3 years ago by ★ 29k • written 3.4 years ago by ▴ 40
0
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0
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1.5k
views
Job: Scientific Programmer | Altos Labs | San Diego
SpatialData scRNAseq JobPosting
3.4 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
3.4 years ago Sebastian Lewandowski • 0
1
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4
replies
2.0k
views
Quality control of scRNA-seq data using mitochondrial ratio (drosophila)
Drosophila_melanogaster scRNAseq
3.4 years ago Chise ▴ 10
0
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0
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1.7k
views
how to calculate similarity between each cluster in scRNA and bulk RNA-seq
SingleR scRNAseq
3.4 years ago Guandong Shang ▴ 40
0
votes
2
replies
2.7k
views
calculateQCMetrics defunct, how to calculate the quality metrics by perCellQCMetrics
scRNAseq
updated 3.4 years ago by ★ 5.0k • written 3.4 years ago by • 0
0
votes
1
reply
1.8k
views
Error: DESeq(dds , useT = TRUE, minmu = 1e-06, test = "LRT", : likelihood ratio test requires a 'reduced' design, see ?DESeq
scRNAseq DESeq2
updated 3.4 years ago by ★ 5.0k • written 3.4 years ago by • 0
2
votes
8
replies
2.6k
views
RSEM - tximport; where is effective_length information used? Implications for scRNA?
RSEM tximport scRNAseq DESeq2
3.5 years ago • updated 3.4 years ago Kelen ▴ 10
0
votes
1
reply
1.2k
views
scRNASeq reference at a transcript level
EWCE scRNAseq
updated 3.5 years ago by ▴ 780 • written 3.5 years ago by • 0
1
vote
2
replies
3.1k
views
unbalanced cell count and unbalanced read count across samples in pseudobulk differential expression analysis using scRNA-seq data
scRNAseq DifferentialExpression DESeq2
3.6 years ago Ismail • 0
1
vote
1
reply
2.9k
views
Can we use 'SCT normalization' to find anchors and 'LogNormalize' for the integration?
Normalization scRNAseq
updated 3.7 years ago by ▴ 760 • written 3.7 years ago by • 0
96 results • Page 1 of 2
Recent ...
Replies
Comment: DECIPHER DesignProbes unable to design FISH-probes by Erik Wright ▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Answer: PTM analysis in LIMPA by Gordon Smyth 53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR by James W. MacDonald 68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Awards • All
Popular Question to James W. MacDonald 68k
Popular Question to Gordon Smyth 53k
Commentator to sina.nassiri ▴ 130
Popular Question to Hervé Pagès 16k
Popular Question to jared.andrews07 ▴ 30
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