Showing : scRNAseq • reset
2
votes
2
replies
322
views
Should tSNE from biol. replicates look alike?
scRNAseq SingleCellExperiment batchelor
written 5 weeks ago by ▴ 10
0
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0
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308
views
Job: Postdoc Opportunity in Bioinformatics at Northwestern University (Research on Human Pregnancy and Autoimmunity)
Bioinformatics scRNAseq
3 months ago Damini • 0
1
vote
8
replies
779
views
Advice on appropriateness of an offset in glmGamPoi/edgeR
DESeq2 glmGamPoi offset edgeR scRNAseq
updated 3 months ago by 51k • written 3 months ago by • 0
0
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0
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244
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scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
RNASeq scRNAseq
4 months ago Bibi • 0
0
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1
reply
406
views
Can you find the correct transcript in scRNA seq data
scRNAseq RNAseq
updated 6 months ago by ★ 4.5k • written 6 months ago by • 0
0
votes
2
replies
510
views
Non-empty droplets versus good quality cells
CellRanger emptyDrops scRNAseq 10X
6 months ago rocanja ▴ 60
0
votes
1
reply
409
views
How to select cells that represents more accurately a cluster in a scRNA-seq dataset?
scRNAseq
updated 7 months ago by ★ 4.5k • written 7 months ago by • 0
1
vote
2
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1.4k
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ScRNAseq analysis scran :: quickcluster Error
scRNAseq quickcluster scRNA scran
10 months ago ruba-mahmoud • 0
0
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2
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833
views
scRNA analysis : DEG between low and high-expressing cells
scRNAseq
12 months ago Momo • 0
0
votes
1
reply
565
views
FALSE error when checking a pre made sample data
Rstudio scRNAseq DESeq2
updated 14 months ago by ★ 4.5k • written 14 months ago by • 0
2
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5
replies
1.2k
views
Recommendation for large.n in filterByExpr
scRNAseq edgeR SingleCellExperiment
14 months ago duez.tolga • 0
0
votes
1
reply
1.6k
views
DESeq2 error after installing BiocManager
scRNAseq RStudio DESeq2
updated 14 months ago by ★ 4.5k • written 14 months ago by • 0
4
votes
3
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1.2k
views
Custom design for scRNA DGE with pseudobulking
scRNAseq scrna paireddesign edgeR pseudobulking
updated 14 months ago by 51k • written 14 months ago by • 0
0
votes
1
reply
602
views
If highly-expressed genes are upregulated, what happens to genes with lower expression after normalization?
scRNA scRNAseq
updated 14 months ago by ★ 4.5k • written 14 months ago by • 0
0
votes
1
reply
707
views
library(topGO) query
topGO scRNAseq
updated 14 months ago by ▴ 780 • written 14 months ago by • 0
0
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0
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520
views
adding noise to scRNA Seq counts
scRNAseq
15 months ago Jiyuan • 0
1
vote
11
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5.3k
views
Error: Bioconductor version cannot be validated; no internet connection?
scRNAseq
updated 11 months ago by • 0 • written 15 months ago by • 0
2
votes
3
replies
1.6k
views
P-value histogram of testLinearModel is not uniform
smart-seq2 scRNAseq scran
16 months ago Lluís Revilla Sancho ▴ 750
0
votes
0
replies
693
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News: course - single-cell RNAseq data analysis with R and Bioconductor
Workshop scRNAseq
17 months ago info ▴ 10
0
votes
1
reply
733
views
scRNAseq Download Errors
scRNAseq
updated 18 months ago by 4.0k • written 18 months ago by ★ 1.5k
2
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0
replies
1.6k
views
How to aggregate pseudobulks: Normalization & Log-Transformation
pseudobulk scRNAseq GSVA
18 months ago Tadeoye ▴ 20
0
votes
1
reply
1.0k
views
scRNAseq package and cell type annotations
ExperimentHub R ExperimentHubData scRNAseq SingleR
updated 19 months ago by ▴ 740 • written 19 months ago by ▴ 10
4
votes
5
replies
1.8k
views
Pseudo-bulk celltype comparison across conditions from multiple-sources
DESeq2 edgeR scRNAseq
updated 19 months ago by ▴ 740 • written 19 months ago by ▴ 10
0
votes
2
replies
961
views
Could not find function "Standard Chromosomes"
scrna scRNAseq
updated 11 months ago by • 0 • written 19 months ago by • 0
0
votes
3
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1.4k
views
Single-Cell Data Simulation from Bulk RNA-seq
SingleCell RNASeq RNASeqData scRNAseq
updated 3 months ago by • 0 • written 23 months ago by • 0
1
vote
2
replies
1.4k
views
What number components should I use if I want to show 2D and 3D UMAP
scater UAMP scRNAseq
2.0 years ago Guandong Shang ▴ 40
1
vote
2
replies
1.1k
views
Combine scRNAseq data for bulk analysis using DESeq2
DESeq2 scRNAseq Fluidigm
2.0 years ago • updated 24 months ago evocanres • 0
0
votes
3
replies
1.3k
views
scRNA-seq: RS4' object has no attribute 'T'" in fastMNN R function
scanpy scRNAseq fastmnn r
2.0 years ago Madiha • 0
4
votes
5
replies
3.0k
views
`emptyDrops()` calling 'too many' non-empty droplets
DropletUtils emptyDrops scRNA scRNAseq 10x
2.2 years ago Peter Hickey ▴ 740
4
votes
2
replies
1.4k
views
how to do downstram analysis to cells which are subsetted after MNN batch-correction
batchelor fastMNN scRNAseq
2.2 years ago Guandong Shang ▴ 40
0
votes
4
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2.4k
views
how to make the "reconstructed" value in intergated scRNA-seq UMAP plot more readable
scater batchelor scRNAseq fastMNN
updated 2.2 years ago by ★ 28k • written 2.2 years ago by ▴ 40
0
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0
replies
1.2k
views
Job: Scientific Programmer | Altos Labs | San Diego
SpatialData scRNAseq JobPosting
2.2 years ago peter.kharchenko ▴ 30
0
votes
0
replies
858
views
Job: Postdoc position in integrated omics at Karolinska Institute, Stockholm
ATACSeq multiOmicsViz scRNAseq JobPosting
2.2 years ago Sebastian Lewandowski • 0
1
vote
4
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1.5k
views
Quality control of scRNA-seq data using mitochondrial ratio (drosophila)
Drosophila_melanogaster scRNAseq
2.2 years ago Chise ▴ 10
0
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0
replies
1.2k
views
how to calculate similarity between each cluster in scRNA and bulk RNA-seq
SingleR scRNAseq
2.3 years ago Guandong Shang ▴ 40
0
votes
2
replies
2.2k
views
calculateQCMetrics defunct, how to calculate the quality metrics by perCellQCMetrics
scRNAseq
updated 2.3 years ago by ★ 4.5k • written 2.3 years ago by • 0
0
votes
1
reply
1.3k
views
Error: DESeq(dds , useT = TRUE, minmu = 1e-06, test = "LRT", : likelihood ratio test requires a 'reduced' design, see ?DESeq
scRNAseq DESeq2
updated 2.3 years ago by ★ 4.5k • written 2.3 years ago by • 0
2
votes
8
replies
1.9k
views
RSEM - tximport; where is effective_length information used? Implications for scRNA?
RSEM tximport scRNAseq DESeq2
2.3 years ago Kelen ▴ 10
0
votes
1
reply
898
views
scRNASeq reference at a transcript level
EWCE scRNAseq
updated 2.4 years ago by ▴ 780 • written 2.4 years ago by • 0
1
vote
2
replies
2.2k
views
unbalanced cell count and unbalanced read count across samples in pseudobulk differential expression analysis using scRNA-seq data
scRNAseq DifferentialExpression DESeq2
2.5 years ago Ismail • 0
1
vote
1
reply
2.1k
views
Can we use 'SCT normalization' to find anchors and 'LogNormalize' for the integration?
Normalization scRNAseq
updated 2.5 years ago by ▴ 740 • written 2.5 years ago by • 0
2
votes
2
replies
1.5k
views
scuttle:: librarySizeFactors returning non-finite values
normalizeCounts scran librarySizeFactors scuttle scRNAseq
2.6 years ago behr201 • 0
2
votes
2
replies
1.4k
views
How to deal with Expression set assembly problem?
deconvolution r scRNAseq bioinformatics
2.7 years ago Hasan Alanya • 0
0
votes
1
reply
1.2k
views
Aberrant number of cells
CellBarcode DropletUtils emptyDrops() Cellranger scRNAseq
updated 2.4 years ago by ▴ 20 • written 2.7 years ago by • 0
0
votes
0
replies
1.1k
views
Job: Postdoc Opening in Bioinformatics or Computational Biology
SpatialData scRNAseq SingleCell Omixer
2.7 years ago Sebastian Lewandowski • 0
0
votes
3
replies
1.8k
views
NA values for mitochondrial gene percentage
Seurat scRNAseq
2.8 years ago zahra.mesri95 • 0
0
votes
0
replies
749
views
scRNA technical replicates in separate runs
SingleCellExperiment scRNAseq
2.9 years ago Núria • 0
0
votes
2
replies
1.1k
views
scRNAseq analysis on multiple datasets
scRNAseq
updated 3.0 years ago by ★ 1.4k • written 3.0 years ago by • 0
2
votes
4
replies
1.5k
views
edgeR output doubts
logFC edgeR DifferentialExpression scRNAseq
3.2 years ago mbenegas ▴ 10
0
votes
1
reply
1.2k
views
Identify a scRNASeq cell-population using a bulk RNA Seq dataset of that population?
RNASeq rnaseq scRNAseq
updated 3.2 years ago by ★ 28k • written 3.2 years ago by ▴ 10
50 results • Page 1 of 1
Recent ...
Replies
Comment: How to reverse complement some elements of a DNAStringSet by Christine Jones • 0
Fantastic, thank you
Comment: When running contrasts, does it use normalized read counts? by Katherine • 0
Ok, so the comment I was given where they said DeSeq2 should be with normalized counts is incorrect. the ```normalized_counts``` variable …
Answer: How to reverse complement some elements of a DNAStringSet by James W. MacDonald 67k
You should always try the vectorized method first, rather than looping. ``` > myFasta[myFasta_rc] <- reverseComplement(myFasta[myFasta_…
Answer: When running contrasts, does it use normalized read counts? by James W. MacDonald 67k
A contrast is a comparison of two or more coefficients. When you run `nbiomWaldTest` you are fitting the GLM and estimating coefficients. T…
Comment: Too much data for Diffbind by Ou, Jianhong ★ 1.3k
Just in case if somebody still want to apply summits greater than 0 and got the same error, you can filter out the peaks with start positio…
Votes
Comment: featureCounts fails to load annotation file
Answer: How to reverse complement some elements of a DNAStringSet
Answer: KEGGgraph result difference
Answer: What should be the normalization protocol for RNA seq data for WGCNA?
What should be the normalization protocol for RNA seq data for WGCNA?
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