Showing : scRNASeq • reset
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139
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Can you find the correct transcript in scRNA seq data
scRNAseq RNAseq
updated 25 days ago by ★ 4.1k • written 27 days ago by • 0
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2
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214
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Non-empty droplets versus good quality cells
CellRanger emptyDrops scRNAseq 10X
6 weeks ago rocanja ▴ 60
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1
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253
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How to select cells that represents more accurately a cluster in a scRNA-seq dataset?
scRNAseq
updated 9 weeks ago by ★ 4.1k • written 10 weeks ago by • 0
1
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2
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811
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ScRNAseq analysis scran :: quickcluster Error
scRNAseq quickcluster scRNA scran
5 months ago ruba-mahmoud • 0
0
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2
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512
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scRNA analysis : DEG between low and high-expressing cells
scRNAseq
7 months ago Momo • 0
0
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1
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389
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FALSE error when checking a pre made sample data
Rstudio scRNAseq DESeq2
updated 8 months ago by ★ 4.1k • written 8 months ago by • 0
1
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5
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856
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Recommendation for large.n in filterByExpr
scRNAseq edgeR SingleCellExperiment
9 months ago • updated 8 months ago duez.tolga • 0
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1
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1.0k
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DESeq2 error after installing BiocManager
scRNAseq RStudio DESeq2
updated 9 months ago by ★ 4.1k • written 9 months ago by • 0
4
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3
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1.0k
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Custom design for scRNA DGE with pseudobulking
scRNAseq scrna paireddesign edgeR pseudobulking
updated 9 months ago by 50k • written 9 months ago by • 0
0
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1
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420
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If highly-expressed genes are upregulated, what happens to genes with lower expression after normalization?
scRNA scRNAseq
updated 9 months ago by ★ 4.1k • written 9 months ago by • 0
0
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1
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568
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library(topGO) query
topGO scRNAseq
updated 9 months ago by ▴ 780 • written 9 months ago by • 0
0
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0
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352
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adding noise to scRNA Seq counts
scRNAseq
9 months ago Jiyuan • 0
1
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11
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3.5k
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Error: Bioconductor version cannot be validated; no internet connection?
scRNAseq
updated 6 months ago by • 0 • written 10 months ago by • 0
2
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3
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1.3k
views
P-value histogram of testLinearModel is not uniform
smart-seq2 scRNAseq scran
11 months ago • updated 10 months ago Lluís Revilla Sancho ▴ 730
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484
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News: course - single-cell RNAseq data analysis with R and Bioconductor
Workshop scRNAseq
11 months ago info ▴ 10
0
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1
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580
views
scRNAseq Download Errors
scRNAseq
updated 12 months ago by 3.9k • written 12 months ago by ★ 1.5k
2
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0
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1.1k
views
How to aggregate pseudobulks: Normalization & Log-Transformation
pseudobulk scRNAseq GSVA
12 months ago Tadeoye ▴ 20
0
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1
reply
731
views
scRNAseq package and cell type annotations
ExperimentHub R ExperimentHubData scRNAseq SingleR
updated 13 months ago by ▴ 740 • written 13 months ago by ▴ 10
4
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5
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1.4k
views
Pseudo-bulk celltype comparison across conditions from multiple-sources
DESeq2 edgeR scRNAseq
updated 14 months ago by ▴ 740 • written 14 months ago by ▴ 10
0
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2
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684
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Could not find function "Standard Chromosomes"
scrna scRNAseq
updated 6 months ago by • 0 • written 14 months ago by • 0
0
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2
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918
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Single-Cell Data Simulation from Bulk RNA-seq
SingleCell RNASeq RNASeqData scRNAseq
updated 18 days ago by • 0 • written 17 months ago by • 0
1
vote
2
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1.1k
views
What number components should I use if I want to show 2D and 3D UMAP
scater UAMP scRNAseq
19 months ago • updated 18 months ago Guandong Shang ▴ 40
1
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2
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963
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Combine scRNAseq data for bulk analysis using DESeq2
DESeq2 scRNAseq Fluidigm
19 months ago • updated 18 months ago evocanres • 0
0
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3
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1.0k
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scRNA-seq: RS4' object has no attribute 'T'" in fastMNN R function
scanpy scRNAseq fastmnn r
19 months ago Madiha • 0
4
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5
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2.3k
views
`emptyDrops()` calling 'too many' non-empty droplets
DropletUtils emptyDrops scRNA scRNAseq 10x
21 months ago • updated 20 months ago Peter Hickey ▴ 740
4
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2
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1.1k
views
how to do downstram analysis to cells which are subsetted after MNN batch-correction
batchelor fastMNN scRNAseq
21 months ago Guandong Shang ▴ 40
0
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4
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2.0k
views
how to make the "reconstructed" value in intergated scRNA-seq UMAP plot more readable
scater batchelor scRNAseq fastMNN
updated 21 months ago by ★ 28k • written 21 months ago by ▴ 40
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985
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Job: Scientific Programmer | Altos Labs | San Diego
SpatialData scRNAseq JobPosting
21 months ago peter.kharchenko ▴ 30
0
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0
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720
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Job: Postdoc position in integrated omics at Karolinska Institute, Stockholm
ATACSeq multiOmicsViz scRNAseq JobPosting
21 months ago Sebastian Lewandowski • 0
1
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4
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1.2k
views
Quality control of scRNA-seq data using mitochondrial ratio (drosophila)
Drosophila_melanogaster scRNAseq
21 months ago Chise ▴ 10
0
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0
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967
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how to calculate similarity between each cluster in scRNA and bulk RNA-seq
SingleR scRNAseq
22 months ago Guandong Shang ▴ 40
0
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2
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1.8k
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calculateQCMetrics defunct, how to calculate the quality metrics by perCellQCMetrics
scRNAseq
updated 22 months ago by ★ 4.1k • written 22 months ago by • 0
0
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1
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1.1k
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Error: DESeq(dds , useT = TRUE, minmu = 1e-06, test = "LRT", : likelihood ratio test requires a 'reduced' design, see ?DESeq
scRNAseq DESeq2
updated 22 months ago by ★ 4.1k • written 22 months ago by • 0
2
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8
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1.6k
views
RSEM - tximport; where is effective_length information used? Implications for scRNA?
RSEM tximport scRNAseq DESeq2
22 months ago Kelen ▴ 10
0
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1
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723
views
scRNASeq reference at a transcript level
EWCE scRNAseq
updated 23 months ago by ▴ 780 • written 23 months ago by • 0
1
vote
2
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1.8k
views
unbalanced cell count and unbalanced read count across samples in pseudobulk differential expression analysis using scRNA-seq data
scRNAseq DifferentialExpression DESeq2
2.0 years ago Ismail • 0
1
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1
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1.7k
views
Can we use 'SCT normalization' to find anchors and 'LogNormalize' for the integration?
Normalization scRNAseq
updated 2.1 years ago by ▴ 740 • written 2.1 years ago by • 0
2
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2
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1.2k
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scuttle:: librarySizeFactors returning non-finite values
normalizeCounts scran librarySizeFactors scuttle scRNAseq
2.2 years ago behr201 • 0
2
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2
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1.2k
views
How to deal with Expression set assembly problem?
deconvolution r scRNAseq bioinformatics
2.2 years ago Hasan Alanya • 0
0
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1
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976
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Aberrant number of cells
CellBarcode DropletUtils emptyDrops() Cellranger scRNAseq
updated 2.0 years ago by ▴ 20 • written 2.3 years ago by • 0
0
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0
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891
views
Job: Postdoc Opening in Bioinformatics or Computational Biology
SpatialData scRNAseq SingleCell Omixer
2.3 years ago Sebastian Lewandowski • 0
0
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3
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1.5k
views
NA values for mitochondrial gene percentage
Seurat scRNAseq
2.4 years ago zahra.mesri95 • 0
0
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0
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636
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scRNA technical replicates in separate runs
SingleCellExperiment scRNAseq
2.4 years ago Núria • 0
0
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2
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921
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scRNAseq analysis on multiple datasets
scRNAseq
updated 2.6 years ago by ★ 1.3k • written 2.6 years ago by • 0
2
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4
replies
1.2k
views
edgeR output doubts
logFC edgeR DifferentialExpression scRNAseq
2.7 years ago mbenegas • 0
0
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1
reply
1.0k
views
Identify a scRNASeq cell-population using a bulk RNA Seq dataset of that population?
RNASeq rnaseq scRNAseq
updated 2.7 years ago by ★ 28k • written 2.7 years ago by ▴ 10
0
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0
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781
views
Correlation plot using the count data from seurat object
scRNAseq
2.8 years ago Sam • 0
2
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4
replies
3.9k
views
differential expression for Single-cell RNAseq data using edgeR
edgeR single scRNAseq
2.8 years ago • updated 2.7 years ago mbenegas • 0
2
votes
13
replies
2.3k
views
Running the DESeq2 "DESeqDataSetFromMatrix" function returns a dimname error
DESeq2 Scrna scRNAseq
2.8 years ago RDoc ▴ 10
0
votes
1
reply
849
views
Tool for simulating bulk RNA-Seq from single cell data
scRNAseq
updated 2.9 years ago by 65k • written 2.9 years ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Why does GSEA on edgeR results for randomized samples give highly significant p- by Chris • 0
Intent to delete when going home. Sorry for that!
Comment: Why does GSEA on edgeR results for randomized samples give highly significant p- by Gordon Smyth 50k
Please ask you own question. Inserting your own dataset into someone else's question like this is very impolite. I have already answered m…
Comment: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
limma most certainly is available. It installs in R 4.4.0 and Bioc 3.19 for all platforms without any issues. It has not had any period of …
Comment: package goseq seems to be not available on the latest version of R by Patrycja ▴ 20
limma package also isn't available.Is there any information when these packages will be available?
Comment: Why does GSEA on edgeR results for randomized samples give highly significant p- by Chris • 0
Thanks Gordon for the advice!
Votes
Comment: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Handling multiple differential expression comparisons
Answer: fgsea significant result
Answer: fgsea significant result
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