Showing : scRNAseq • reset
0
votes
3
replies
613
views
Differential variance analysis - can i use deseq2
DESeq2 DifferentialExpression RNASeq RNASeqData scRNAseq
updated 8 weeks ago by 43k • written 9 weeks ago by • 0
0
votes
0
replies
139
views
Help with mouse cell type annotation
annotation SingleR mouse SingleCellData scRNAseq
9 weeks ago Muhammad • 0
0
votes
3
replies
488
views
How to compare expression levels of genes between scRNAseq and bulkRNAseq?
Seurat RNASeq DESeq2 scRNAseq
updated 11 weeks ago by • 0 • written 12 weeks ago by ▴ 10
2
votes
2
replies
593
views
Should tSNE from biol. replicates look alike?
scRNAseq SingleCellExperiment batchelor
written 7 months ago by ▴ 10
0
votes
0
replies
521
views
Job: Postdoc Opportunity in Bioinformatics at Northwestern University (Research on Human Pregnancy and Autoimmunity)
Bioinformatics scRNAseq
9 months ago Damini • 0
1
vote
8
replies
1.4k
views
Advice on appropriateness of an offset in glmGamPoi/edgeR
DESeq2 glmGamPoi offset edgeR scRNAseq
updated 9 months ago by 52k • written 10 months ago by • 0
0
votes
0
replies
423
views
scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
RNASeq scRNAseq
11 months ago Bibi • 0
0
votes
1
reply
757
views
Can you find the correct transcript in scRNA seq data
scRNAseq RNAseq
updated 12 months ago by ★ 4.8k • written 12 months ago by • 0
0
votes
2
replies
792
views
Non-empty droplets versus good quality cells
CellRanger emptyDrops scRNAseq 10X
13 months ago rocanja ▴ 60
0
votes
1
reply
572
views
How to select cells that represents more accurately a cluster in a scRNA-seq dataset?
scRNAseq
updated 14 months ago by ★ 4.8k • written 14 months ago by • 0
1
vote
2
replies
1.7k
views
ScRNAseq analysis scran :: quickcluster Error
scRNAseq quickcluster scRNA scran
16 months ago ruba-mahmoud • 0
0
votes
2
replies
1.1k
views
scRNA analysis : DEG between low and high-expressing cells
scRNAseq
18 months ago Momo • 0
0
votes
1
reply
678
views
FALSE error when checking a pre made sample data
Rstudio scRNAseq DESeq2
updated 20 months ago by ★ 4.8k • written 20 months ago by • 0
2
votes
5
replies
1.5k
views
Recommendation for large.n in filterByExpr
scRNAseq edgeR SingleCellExperiment
20 months ago duez.tolga • 0
0
votes
1
reply
2.3k
views
DESeq2 error after installing BiocManager
scRNAseq RStudio DESeq2
updated 20 months ago by ★ 4.8k • written 20 months ago by • 0
4
votes
3
replies
1.4k
views
Custom design for scRNA DGE with pseudobulking
scRNAseq scrna paireddesign edgeR pseudobulking
updated 20 months ago by 52k • written 21 months ago by • 0
0
votes
1
reply
741
views
If highly-expressed genes are upregulated, what happens to genes with lower expression after normalization?
scRNA scRNAseq
updated 21 months ago by ★ 4.8k • written 21 months ago by • 0
0
votes
1
reply
819
views
library(topGO) query
topGO scRNAseq
updated 21 months ago by ▴ 780 • written 21 months ago by • 0
0
votes
0
replies
657
views
adding noise to scRNA Seq counts
scRNAseq
21 months ago Jiyuan • 0
1
vote
11
replies
8.0k
views
Error: Bioconductor version cannot be validated; no internet connection?
scRNAseq
updated 17 months ago by • 0 • written 22 months ago by • 0
2
votes
3
replies
1.9k
views
P-value histogram of testLinearModel is not uniform
smart-seq2 scRNAseq scran
22 months ago Lluís Revilla Sancho ▴ 760
0
votes
0
replies
859
views
News: course - single-cell RNAseq data analysis with R and Bioconductor
Workshop scRNAseq
23 months ago info ▴ 10
0
votes
1
reply
929
views
scRNAseq Download Errors
scRNAseq
updated 2.0 years ago by 4.1k • written 2.0 years ago by ★ 1.6k
2
votes
0
replies
2.2k
views
How to aggregate pseudobulks: Normalization & Log-Transformation
pseudobulk scRNAseq GSVA
2.0 years ago Tadeoye ▴ 20
0
votes
1
reply
1.3k
views
scRNAseq package and cell type annotations
ExperimentHub R ExperimentHubData scRNAseq SingleR
updated 2.1 years ago by ▴ 750 • written 2.1 years ago by ▴ 10
4
votes
5
replies
2.5k
views
Pseudo-bulk celltype comparison across conditions from multiple-sources
DESeq2 edgeR scRNAseq
updated 2.1 years ago by ▴ 750 • written 2.1 years ago by ▴ 10
0
votes
2
replies
1.3k
views
Could not find function "Standard Chromosomes"
scrna scRNAseq
updated 18 months ago by • 0 • written 2.1 years ago by • 0
0
votes
3
replies
1.9k
views
Single-Cell Data Simulation from Bulk RNA-seq
SingleCell RNASeq RNASeqData scRNAseq
updated 9 months ago by • 0 • written 2.4 years ago by • 0
1
vote
2
replies
1.7k
views
What number components should I use if I want to show 2D and 3D UMAP
scater UAMP scRNAseq
2.5 years ago Guandong Shang ▴ 40
1
vote
2
replies
1.3k
views
Combine scRNAseq data for bulk analysis using DESeq2
DESeq2 scRNAseq Fluidigm
2.5 years ago evocanres • 0
0
votes
3
replies
1.5k
views
scRNA-seq: RS4' object has no attribute 'T'" in fastMNN R function
scanpy scRNAseq fastmnn r
2.5 years ago Madiha • 0
4
votes
5
replies
3.7k
views
`emptyDrops()` calling 'too many' non-empty droplets
DropletUtils emptyDrops scRNA scRNAseq 10x
2.7 years ago Peter Hickey ▴ 750
4
votes
2
replies
1.6k
views
how to do downstram analysis to cells which are subsetted after MNN batch-correction
batchelor fastMNN scRNAseq
2.7 years ago Guandong Shang ▴ 40
0
votes
4
replies
2.7k
views
how to make the "reconstructed" value in intergated scRNA-seq UMAP plot more readable
scater batchelor scRNAseq fastMNN
updated 2.7 years ago by ★ 28k • written 2.7 years ago by ▴ 40
0
votes
0
replies
1.3k
views
Job: Scientific Programmer | Altos Labs | San Diego
SpatialData scRNAseq JobPosting
2.7 years ago peter.kharchenko ▴ 30
0
votes
0
replies
976
views
Job: Postdoc position in integrated omics at Karolinska Institute, Stockholm
ATACSeq multiOmicsViz scRNAseq JobPosting
2.8 years ago Sebastian Lewandowski • 0
1
vote
4
replies
1.7k
views
Quality control of scRNA-seq data using mitochondrial ratio (drosophila)
Drosophila_melanogaster scRNAseq
2.8 years ago Chise ▴ 10
0
votes
0
replies
1.5k
views
how to calculate similarity between each cluster in scRNA and bulk RNA-seq
SingleR scRNAseq
2.8 years ago Guandong Shang ▴ 40
0
votes
2
replies
2.5k
views
calculateQCMetrics defunct, how to calculate the quality metrics by perCellQCMetrics
scRNAseq
updated 2.8 years ago by ★ 4.8k • written 2.8 years ago by • 0
0
votes
1
reply
1.6k
views
Error: DESeq(dds , useT = TRUE, minmu = 1e-06, test = "LRT", : likelihood ratio test requires a 'reduced' design, see ?DESeq
scRNAseq DESeq2
updated 2.8 years ago by ★ 4.8k • written 2.8 years ago by • 0
2
votes
8
replies
2.2k
views
RSEM - tximport; where is effective_length information used? Implications for scRNA?
RSEM tximport scRNAseq DESeq2
2.8 years ago Kelen ▴ 10
0
votes
1
reply
1.0k
views
scRNASeq reference at a transcript level
EWCE scRNAseq
updated 2.9 years ago by ▴ 780 • written 2.9 years ago by • 0
1
vote
2
replies
2.7k
views
unbalanced cell count and unbalanced read count across samples in pseudobulk differential expression analysis using scRNA-seq data
scRNAseq DifferentialExpression DESeq2
3.0 years ago Ismail • 0
1
vote
1
reply
2.5k
views
Can we use 'SCT normalization' to find anchors and 'LogNormalize' for the integration?
Normalization scRNAseq
updated 3.1 years ago by ▴ 750 • written 3.1 years ago by • 0
2
votes
2
replies
1.8k
views
scuttle:: librarySizeFactors returning non-finite values
normalizeCounts scran librarySizeFactors scuttle scRNAseq
3.2 years ago behr201 • 0
2
votes
2
replies
1.7k
views
How to deal with Expression set assembly problem?
deconvolution r scRNAseq bioinformatics
3.2 years ago Hasan Alanya • 0
0
votes
1
reply
1.4k
views
Aberrant number of cells
CellBarcode DropletUtils emptyDrops() Cellranger scRNAseq
updated 3.0 years ago by ▴ 20 • written 3.2 years ago by • 0
0
votes
0
replies
1.2k
views
Job: Postdoc Opening in Bioinformatics or Computational Biology
SpatialData scRNAseq SingleCell Omixer
3.3 years ago Sebastian Lewandowski • 0
0
votes
3
replies
2.0k
views
NA values for mitochondrial gene percentage
Seurat scRNAseq
3.4 years ago zahra.mesri95 • 0
0
votes
0
replies
871
views
scRNA technical replicates in separate runs
SingleCellExperiment scRNAseq
3.4 years ago Núria • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: How to convert transcript counts to gene counts in R? by ben • 0
Simply summing transcripts by gene is sufficient for use with DESeq2. [sprunki clicker][1] [1]: https://sprunkiclicker.com/
Answer: EuroBioC2024 abstract submission is open! by Ali • 0
[Promo products][1] are a smart way to boost visibility, especially with exciting updates like *News: EuroBioC2024 abstract submission is o…
Answer: ROAST for small sets by Gordon Smyth 52k
The p-values from `mroast` will be the same (up to sampling variability associated with random rotations) regardless of whether you test al…
Comment: FlowSOM library requires igraph but igraph does not install by Szabolcs • 0
The R/igraph Installation FAQ covers most issues: https://r.igraph.org/articles/installation-troubleshooting.html
Comment: edgeR::cpm() results in negative values from raw counts of 0 by Kinnary ▴ 20
Thank you very much for the vis suggestion!
Votes
Answer: ROAST for small sets
Answer: ROAST for small sets
A: conceptual question about FDR, FDR adjusted p-value and q-value
Comment: edgeR::cpm() results in negative values from raw counts of 0
Comment: edgeR::cpm() results in negative values from raw counts of 0
Awards • All
Scholar to Gordon Smyth 52k
Popular Question to shepherl 4.1k
Popular Question to Szabolcs • 0
Popular Question to Mengjun • 0
Popular Question to James W. MacDonald 68k
Locations • All
United States, 20 minutes ago
Kazakhstan, 24 minutes ago
United Kingdom, 25 minutes ago
Canada, 34 minutes ago
United States, 36 minutes ago
Traffic: 1182 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6