Showing : scRNAseq • reset
0
votes
3
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551
views
Differential variance analysis - can i use deseq2
DESeq2 DifferentialExpression RNASeq RNASeqData scRNAseq
updated 29 days ago by 43k • written 4 weeks ago by • 0
0
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0
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102
views
Help with mouse cell type annotation
annotation SingleR mouse SingleCellData scRNAseq
5 weeks ago Muhammad • 0
0
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3
replies
415
views
How to compare expression levels of genes between scRNAseq and bulkRNAseq?
Seurat RNASeq DESeq2 scRNAseq
updated 6 weeks ago by • 0 • written 8 weeks ago by ▴ 10
2
votes
2
replies
555
views
Should tSNE from biol. replicates look alike?
scRNAseq SingleCellExperiment batchelor
written 6 months ago by ▴ 10
0
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0
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496
views
Job: Postdoc Opportunity in Bioinformatics at Northwestern University (Research on Human Pregnancy and Autoimmunity)
Bioinformatics scRNAseq
8 months ago Damini • 0
1
vote
8
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1.3k
views
Advice on appropriateness of an offset in glmGamPoi/edgeR
DESeq2 glmGamPoi offset edgeR scRNAseq
updated 8 months ago by 52k • written 8 months ago by • 0
0
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0
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394
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scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
RNASeq scRNAseq
10 months ago Bibi • 0
0
votes
1
reply
700
views
Can you find the correct transcript in scRNA seq data
scRNAseq RNAseq
updated 11 months ago by ★ 4.7k • written 11 months ago by • 0
0
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2
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757
views
Non-empty droplets versus good quality cells
CellRanger emptyDrops scRNAseq 10X
12 months ago rocanja ▴ 60
0
votes
1
reply
543
views
How to select cells that represents more accurately a cluster in a scRNA-seq dataset?
scRNAseq
updated 13 months ago by ★ 4.7k • written 13 months ago by • 0
1
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2
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1.6k
views
ScRNAseq analysis scran :: quickcluster Error
scRNAseq quickcluster scRNA scran
15 months ago ruba-mahmoud • 0
0
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2
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1.1k
views
scRNA analysis : DEG between low and high-expressing cells
scRNAseq
17 months ago Momo • 0
0
votes
1
reply
662
views
FALSE error when checking a pre made sample data
Rstudio scRNAseq DESeq2
updated 19 months ago by ★ 4.7k • written 19 months ago by • 0
2
votes
5
replies
1.5k
views
Recommendation for large.n in filterByExpr
scRNAseq edgeR SingleCellExperiment
19 months ago duez.tolga • 0
0
votes
1
reply
2.2k
views
DESeq2 error after installing BiocManager
scRNAseq RStudio DESeq2
updated 19 months ago by ★ 4.7k • written 19 months ago by • 0
4
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3
replies
1.4k
views
Custom design for scRNA DGE with pseudobulking
scRNAseq scrna paireddesign edgeR pseudobulking
updated 19 months ago by 52k • written 19 months ago by • 0
0
votes
1
reply
724
views
If highly-expressed genes are upregulated, what happens to genes with lower expression after normalization?
scRNA scRNAseq
updated 20 months ago by ★ 4.7k • written 20 months ago by • 0
0
votes
1
reply
800
views
library(topGO) query
topGO scRNAseq
updated 20 months ago by ▴ 780 • written 20 months ago by • 0
0
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0
replies
637
views
adding noise to scRNA Seq counts
scRNAseq
20 months ago Jiyuan • 0
1
vote
11
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7.6k
views
Error: Bioconductor version cannot be validated; no internet connection?
scRNAseq
updated 16 months ago by • 0 • written 21 months ago by • 0
2
votes
3
replies
1.8k
views
P-value histogram of testLinearModel is not uniform
smart-seq2 scRNAseq scran
21 months ago Lluís Revilla Sancho ▴ 760
0
votes
0
replies
833
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News: course - single-cell RNAseq data analysis with R and Bioconductor
Workshop scRNAseq
22 months ago info ▴ 10
0
votes
1
reply
895
views
scRNAseq Download Errors
scRNAseq
updated 23 months ago by 4.1k • written 23 months ago by ★ 1.6k
2
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0
replies
2.1k
views
How to aggregate pseudobulks: Normalization & Log-Transformation
pseudobulk scRNAseq GSVA
23 months ago Tadeoye ▴ 20
0
votes
1
reply
1.3k
views
scRNAseq package and cell type annotations
ExperimentHub R ExperimentHubData scRNAseq SingleR
updated 2.0 years ago by ▴ 750 • written 2.0 years ago by ▴ 10
4
votes
5
replies
2.3k
views
Pseudo-bulk celltype comparison across conditions from multiple-sources
DESeq2 edgeR scRNAseq
updated 2.0 years ago by ▴ 750 • written 2.0 years ago by ▴ 10
0
votes
2
replies
1.3k
views
Could not find function "Standard Chromosomes"
scrna scRNAseq
updated 17 months ago by • 0 • written 2.0 years ago by • 0
0
votes
3
replies
1.8k
views
Single-Cell Data Simulation from Bulk RNA-seq
SingleCell RNASeq RNASeqData scRNAseq
updated 8 months ago by • 0 • written 2.3 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
2.4 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 • updated 2.4 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
3.6k
views
`emptyDrops()` calling 'too many' non-empty droplets
DropletUtils emptyDrops scRNA scRNAseq 10x
2.6 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
2.6 years ago Guandong Shang ▴ 40
0
votes
4
replies
2.6k
views
how to make the "reconstructed" value in intergated scRNA-seq UMAP plot more readable
scater batchelor scRNAseq fastMNN
updated 2.6 years ago by ★ 28k • written 2.6 years ago by ▴ 40
0
votes
0
replies
1.3k
views
Job: Scientific Programmer | Altos Labs | San Diego
SpatialData scRNAseq JobPosting
2.6 years ago peter.kharchenko ▴ 30
0
votes
0
replies
964
views
Job: Postdoc position in integrated omics at Karolinska Institute, Stockholm
ATACSeq multiOmicsViz scRNAseq JobPosting
2.7 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
2.7 years ago Chise ▴ 10
0
votes
0
replies
1.4k
views
how to calculate similarity between each cluster in scRNA and bulk RNA-seq
SingleR scRNAseq
2.7 years ago Guandong Shang ▴ 40
0
votes
2
replies
2.4k
views
calculateQCMetrics defunct, how to calculate the quality metrics by perCellQCMetrics
scRNAseq
updated 2.7 years ago by ★ 4.7k • written 2.7 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 2.7 years ago by ★ 4.7k • written 2.7 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
2.7 years ago Kelen ▴ 10
0
votes
1
reply
998
views
scRNASeq reference at a transcript level
EWCE scRNAseq
updated 2.8 years ago by ▴ 780 • written 2.8 years ago by • 0
1
vote
2
replies
2.6k
views
unbalanced cell count and unbalanced read count across samples in pseudobulk differential expression analysis using scRNA-seq data
scRNAseq DifferentialExpression DESeq2
2.9 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 3.0 years ago by ▴ 750 • written 3.0 years ago by • 0
2
votes
2
replies
1.7k
views
scuttle:: librarySizeFactors returning non-finite values
normalizeCounts scran librarySizeFactors scuttle scRNAseq
3.1 years ago behr201 • 0
2
votes
2
replies
1.7k
views
How to deal with Expression set assembly problem?
deconvolution r scRNAseq bioinformatics
3.1 years ago Hasan Alanya • 0
0
votes
1
reply
1.4k
views
Aberrant number of cells
CellBarcode DropletUtils emptyDrops() Cellranger scRNAseq
updated 2.9 years ago by ▴ 20 • written 3.1 years ago by • 0
0
votes
0
replies
1.2k
views
Job: Postdoc Opening in Bioinformatics or Computational Biology
SpatialData scRNAseq SingleCell Omixer
3.2 years ago Sebastian Lewandowski • 0
0
votes
3
replies
1.9k
views
NA values for mitochondrial gene percentage
Seurat scRNAseq
3.3 years ago zahra.mesri95 • 0
0
votes
0
replies
852
views
scRNA technical replicates in separate runs
SingleCellExperiment scRNAseq
3.3 years ago Núria • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: DiffBind custom normalization factor by Abbie • 0
Hello! Thanks so much for adding dba.normalize and all the documentation in the manual! I'm hoping I can ask a follow-up question here. I…
Answer: CpGs with genomic positions greater than the chromosome size in EPICv2? by James W. MacDonald 68k
All of the annotation packages provided by Bioconductor are simply repackaging of existing data from one or more sources. In this case, the…
Comment: Using TPM from tximport of Salmon output for singscore by Kent • 0
Thank you for the suggestions Michael. Would you say that after filtering out the low count genes, `rlog(counts, blind = T)` is doing the s…
Comment: Using TPM from tximport of Salmon output for singscore by Michael Love 43k
For clustering generally we recommend `vst()` see the workflow for example. For working with individual samples, I can see how a scaling/t…
Comment: DESeq2 model - How to test case/control time course model when taking account wi by Michael Love 43k
I'd recommend working with a local statistician or someone familiar with linear models in R. I have to reserve my time on the support site …
Votes
clusterProfiler-GO enrichment Error
A: Machine learning in R book
Data preparation and Machine learning on time course RNAseq data
Data preparation and Machine learning on time course RNAseq data
Answer: Use of org.Rn.eg.db with GRCr8 reference genome
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