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 24 days ago by ★ 4.0k • written 3 months ago by • 0
0
votes
1
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214
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Must I do pseudobulk analysis on Cell Surface Protein Labeling data of Single Cell RNA Sequencing
scRNAseq
updated 27 days ago by ★ 4.0k • written 4 weeks ago by • 0
0
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1
reply
314
views
Length of 'dimnames' [1] not equal to array extent
SingleCellExperiment singlecelle scRNAseq
updated 27 days ago by ★ 4.0k • written 3 months ago by • 0
5
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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 11 weeks ago by 53k • written 3 months ago by • 0
1
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2
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362
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Testing KO vs WT at day4/day14 with interactions in edgeR
scRNAseq
updated 4 months ago by 53k • written 4 months ago by • 0
0
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11
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951
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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 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 10 months ago by • 0
0
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0
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415
views
Help with mouse cell type annotation
annotation SingleR mouse SingleCellData scRNAseq
10 months ago Muhammad • 0
0
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3
replies
883
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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
867
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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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867
views
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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657
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scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
RNASeq scRNAseq
19 months ago Bibi • 0
0
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1
reply
1.0k
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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
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Non-empty droplets versus good quality cells
CellRanger emptyDrops scRNAseq 10X
21 months ago rocanja ▴ 60
0
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1
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766
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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 22 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
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2
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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
885
views
FALSE error when checking a pre made sample data
Rstudio scRNAseq DESeq2
updated 2.4 years ago by ★ 5.0k • written 2.4 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
2.4 years ago • updated 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 2.4 years ago by ★ 5.0k • written 2.4 years ago by • 0
4
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3
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1.7k
views
Custom design for scRNA DGE with pseudobulking
scRNAseq scrna paireddesign edgeR pseudobulking
updated 2.4 years ago by 53k • written 2.4 years ago by • 0
0
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1
reply
955
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
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1
reply
1.0k
views
library(topGO) query
topGO scRNAseq
updated 2.4 years ago by ▴ 780 • written 2.4 years ago by • 0
0
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0
replies
815
views
adding noise to scRNA Seq counts
scRNAseq
2.4 years ago Jiyuan • 0
1
vote
11
replies
9.6k
views
Error: Bioconductor version cannot be validated; no internet connection?
scRNAseq
updated 2.1 years ago by • 0 • written 2.5 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 2.7 years ago by 4.2k • written 2.7 years ago by ★ 1.6k
2
votes
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 2.8 years ago by ▴ 760 • written 2.8 years ago by ▴ 10
4
votes
5
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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
2.1k
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
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Combine scRNAseq data for bulk analysis using DESeq2
DESeq2 scRNAseq Fluidigm
3.2 years ago evocanres • 0
0
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3
replies
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
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1.9k
views
how to do downstram analysis to cells which are subsetted after MNN batch-correction
batchelor fastMNN scRNAseq
3.4 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 3.4 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
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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
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2
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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
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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 3.5 years ago by ★ 5.0k • written 3.5 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 Kelen ▴ 10
0
votes
1
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1.2k
views
scRNASeq reference at a transcript level
EWCE scRNAseq
updated 3.6 years ago by ▴ 780 • written 3.6 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
3.7 years ago • updated 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
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Answer: NUPOP usage by shepherl 4.2k
You should read the documentation in the package especially the package vignette https://bioconductor.org/packages/release/bioc/html/NuPoP.…
Comment: How can I correctly use phyloseq with Docker? by fnfgame • 0
In a rocker image, this error usually means the Bioconductor install happened as root but the runtime library paths used by the shiny user …
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…
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
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