Showing : scRNASeq • reset
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scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
RNASeq scRNAseq
27 days ago Bibi • 0
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1
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182
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Can you find the correct transcript in scRNA seq data
scRNAseq RNAseq
updated 9 weeks ago by ★ 4.2k • written 9 weeks ago by • 0
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2
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296
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Non-empty droplets versus good quality cells
CellRanger emptyDrops scRNAseq 10X
12 weeks ago rocanja ▴ 60
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1
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287
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How to select cells that represents more accurately a cluster in a scRNA-seq dataset?
scRNAseq
updated 3 months ago by ★ 4.2k • written 3 months ago by • 0
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1.0k
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ScRNAseq analysis scran :: quickcluster Error
scRNAseq quickcluster scRNA scran
6 months ago ruba-mahmoud • 0
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2
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582
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scRNA analysis : DEG between low and high-expressing cells
scRNAseq
8 months ago Momo • 0
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1
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421
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FALSE error when checking a pre made sample data
Rstudio scRNAseq DESeq2
updated 10 months ago by ★ 4.2k • written 10 months ago by • 0
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5
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929
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Recommendation for large.n in filterByExpr
scRNAseq edgeR SingleCellExperiment
10 months ago duez.tolga • 0
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1.2k
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DESeq2 error after installing BiocManager
scRNAseq RStudio DESeq2
updated 10 months ago by ★ 4.2k • written 10 months ago by • 0
4
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3
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1.1k
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Custom design for scRNA DGE with pseudobulking
scRNAseq scrna paireddesign edgeR pseudobulking
updated 10 months ago by 51k • written 10 months ago by • 0
0
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1
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454
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If highly-expressed genes are upregulated, what happens to genes with lower expression after normalization?
scRNA scRNAseq
updated 10 months ago by ★ 4.2k • written 10 months ago by • 0
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1
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604
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library(topGO) query
topGO scRNAseq
updated 10 months ago by ▴ 780 • written 10 months ago by • 0
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380
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adding noise to scRNA Seq counts
scRNAseq
11 months ago Jiyuan • 0
1
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11
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4.0k
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Error: Bioconductor version cannot be validated; no internet connection?
scRNAseq
updated 7 months ago by • 0 • written 11 months ago by • 0
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3
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1.4k
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P-value histogram of testLinearModel is not uniform
smart-seq2 scRNAseq scran
12 months ago Lluís Revilla Sancho ▴ 730
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549
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News: course - single-cell RNAseq data analysis with R and Bioconductor
Workshop scRNAseq
13 months ago info ▴ 10
0
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1
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608
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scRNAseq Download Errors
scRNAseq
updated 14 months ago by 3.9k • written 14 months ago by ★ 1.5k
2
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0
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1.2k
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How to aggregate pseudobulks: Normalization & Log-Transformation
pseudobulk scRNAseq GSVA
14 months ago Tadeoye ▴ 20
0
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1
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799
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scRNAseq package and cell type annotations
ExperimentHub R ExperimentHubData scRNAseq SingleR
updated 15 months ago by ▴ 740 • written 15 months ago by ▴ 10
4
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5
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1.5k
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Pseudo-bulk celltype comparison across conditions from multiple-sources
DESeq2 edgeR scRNAseq
updated 15 months ago by ▴ 740 • written 15 months ago by ▴ 10
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2
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740
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Could not find function "Standard Chromosomes"
scrna scRNAseq
updated 7 months ago by • 0 • written 15 months ago by • 0
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2
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1.0k
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Single-Cell Data Simulation from Bulk RNA-seq
SingleCell RNASeq RNASeqData scRNAseq
updated 8 weeks ago by • 0 • written 19 months ago by • 0
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1.2k
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What number components should I use if I want to show 2D and 3D UMAP
scater UAMP scRNAseq
20 months ago Guandong Shang ▴ 40
1
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2
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996
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Combine scRNAseq data for bulk analysis using DESeq2
DESeq2 scRNAseq Fluidigm
20 months ago evocanres • 0
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3
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1.1k
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scRNA-seq: RS4' object has no attribute 'T'" in fastMNN R function
scanpy scRNAseq fastmnn r
20 months ago Madiha • 0
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5
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2.5k
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`emptyDrops()` calling 'too many' non-empty droplets
DropletUtils emptyDrops scRNA scRNAseq 10x
22 months ago Peter Hickey ▴ 740
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2
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1.2k
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how to do downstram analysis to cells which are subsetted after MNN batch-correction
batchelor fastMNN scRNAseq
22 months ago Guandong Shang ▴ 40
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4
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2.1k
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how to make the "reconstructed" value in intergated scRNA-seq UMAP plot more readable
scater batchelor scRNAseq fastMNN
updated 22 months ago by ★ 28k • written 22 months ago by ▴ 40
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1.0k
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Job: Scientific Programmer | Altos Labs | San Diego
SpatialData scRNAseq JobPosting
22 months ago peter.kharchenko ▴ 30
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748
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Job: Postdoc position in integrated omics at Karolinska Institute, Stockholm
ATACSeq multiOmicsViz scRNAseq JobPosting
23 months ago Sebastian Lewandowski • 0
1
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4
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1.3k
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Quality control of scRNA-seq data using mitochondrial ratio (drosophila)
Drosophila_melanogaster scRNAseq
23 months ago Chise ▴ 10
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1.0k
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how to calculate similarity between each cluster in scRNA and bulk RNA-seq
SingleR scRNAseq
23 months ago Guandong Shang ▴ 40
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2
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1.9k
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calculateQCMetrics defunct, how to calculate the quality metrics by perCellQCMetrics
scRNAseq
updated 23 months ago by ★ 4.2k • written 23 months ago by • 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 23 months ago by ★ 4.2k • written 23 months ago by • 0
2
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8
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1.6k
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RSEM - tximport; where is effective_length information used? Implications for scRNA?
RSEM tximport scRNAseq DESeq2
24 months ago • updated 23 months ago Kelen ▴ 10
0
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1
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766
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scRNASeq reference at a transcript level
EWCE scRNAseq
updated 2.1 years ago by ▴ 780 • written 2.1 years ago by • 0
1
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2
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1.9k
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unbalanced cell count and unbalanced read count across samples in pseudobulk differential expression analysis using scRNA-seq data
scRNAseq DifferentialExpression DESeq2
2.2 years ago • updated 2.1 years ago Ismail • 0
1
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1
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1.8k
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Can we use 'SCT normalization' to find anchors and 'LogNormalize' for the integration?
Normalization scRNAseq
updated 2.2 years ago by ▴ 740 • written 2.2 years ago by • 0
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2
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1.3k
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scuttle:: librarySizeFactors returning non-finite values
normalizeCounts scran librarySizeFactors scuttle scRNAseq
2.3 years ago behr201 • 0
2
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2
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1.2k
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How to deal with Expression set assembly problem?
deconvolution r scRNAseq bioinformatics
2.4 years ago Hasan Alanya • 0
0
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1
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1.0k
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Aberrant number of cells
CellBarcode DropletUtils emptyDrops() Cellranger scRNAseq
updated 2.1 years ago by ▴ 20 • written 2.4 years ago by • 0
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0
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946
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Job: Postdoc Opening in Bioinformatics or Computational Biology
SpatialData scRNAseq SingleCell Omixer
2.4 years ago Sebastian Lewandowski • 0
0
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3
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1.6k
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NA values for mitochondrial gene percentage
Seurat scRNAseq
2.5 years ago zahra.mesri95 • 0
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0
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660
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scRNA technical replicates in separate runs
SingleCellExperiment scRNAseq
2.5 years ago Núria • 0
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2
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951
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scRNAseq analysis on multiple datasets
scRNAseq
updated 2.7 years ago by ★ 1.4k • written 2.7 years ago by • 0
2
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4
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1.2k
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edgeR output doubts
logFC edgeR DifferentialExpression scRNAseq
2.8 years ago mbenegas ▴ 10
0
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1
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1.1k
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Identify a scRNASeq cell-population using a bulk RNA Seq dataset of that population?
RNASeq rnaseq scRNAseq
updated 2.9 years ago by ★ 28k • written 2.9 years ago by ▴ 10
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814
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Correlation plot using the count data from seurat object
scRNAseq
2.9 years ago Sam • 0
3
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4
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4.1k
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differential expression for Single-cell RNAseq data using edgeR
edgeR single scRNAseq
2.9 years ago • updated 2.8 years ago mbenegas ▴ 10
2
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13
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2.4k
views
Running the DESeq2 "DESeqDataSetFromMatrix" function returns a dimname error
DESeq2 Scrna scRNAseq
2.9 years ago RDoc ▴ 10
50 results • Page 1 of 1
Recent ...
Replies
Comment: gds in GEOmetadb 2023-06-26 version is empty by Frederico Moraes Ferreira ▴ 100
Try axel -n 20 https://gbnci.cancer.gov/geo/GEOmetadb.sqlite.gz
Comment: Most enriched pathway is not expressed when modifying universe parameter by James W. MacDonald 66k
The default for `enrichGO` is to subset to those with a p-value<0.05. You don't adjust that default argument, so you shouldn't have any GO …
Answer: In a 3 group DEG analysis with three batches, can I use 1 group in all three bat by Michael Love 42k
You can compare A and C thanks to the sharing of samples from B across 1, 2 and 3.
Comment: Most enriched pathway is not expressed when modifying universe parameter by adripel • 0
In the enrichGO results we have significant and non-significant enriched terms that are displayed. So why would an enriched term (significa…
Answer: Design formula, numeric contrast, and lfcshrink in deseq2 by Michael Love 42k
For questions about how to construct the correct contrasts correspond to particular hypotheses, I recommend consulting with a local statist…
Votes
Comment: Most enriched pathway is not expressed when modifying universe parameter
Time-course, comparison of two groups
Answer: Behaviour of featureCounts when quantifying multi-mapping reads
Answer: GESA with certain gene list returns no result with human genom, but many result
Answer: Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
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