Showing : scRNASeq • reset
0
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3
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2.4k
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PCA outliers cleaning
scRNAseq Pipeline Seurat SingleCellExperiment
written 6.3 years ago by ▴ 10
1
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11
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2.3k
views
Using DESeq2 on single cell RNA Seq data of same cell type but different conditions that were pseudo bulked
DESeq2 scRNAseq
updated 11 weeks ago by ★ 4.0k • written 5 months ago by • 0
0
votes
1
reply
498
views
Must I do pseudobulk analysis on Cell Surface Protein Labeling data of Single Cell RNA Sequencing
scRNAseq
updated 11 weeks ago by ★ 4.0k • written 12 weeks ago by • 0
0
votes
1
reply
375
views
Length of 'dimnames' [1] not equal to array extent
SingleCellExperiment singlecelle scRNAseq
updated 11 weeks ago by ★ 4.0k • written 5 months ago by • 0
5
votes
13
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1.6k
views
Guidance on limma for pseudobulk scRNA-seq with multi-factor design
limma RNASeq scRNAseq
updated 4 months ago by 53k • written 4 months ago by • 0
1
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2
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446
views
Testing KO vs WT at day4/day14 with interactions in edgeR
scRNAseq
updated 6 months ago by 53k • written 6 months ago by • 0
0
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11
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1.1k
views
emptyDrops new default alpha = Inf giving far fewer non-empty droplets than under old default of alpha = NULL
scrn 10x scRNAseq emptyDrops DropletUtils
6 months ago • updated 5 months ago Peter Hickey ▴ 760
0
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3
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1.2k
views
Differential variance analysis - can i use deseq2
DESeq2 DifferentialExpression RNASeq RNASeqData scRNAseq
updated 11 months ago by 43k • written 11 months ago by • 0
0
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0
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449
views
Help with mouse cell type annotation
annotation SingleR mouse SingleCellData scRNAseq
11 months ago Muhammad • 0
0
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3
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1.2k
views
How to compare expression levels of genes between scRNAseq and bulkRNAseq?
Seurat RNASeq DESeq2 scRNAseq
updated 12 months ago by • 0 • written 12 months ago by ▴ 10
2
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2
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943
views
Should tSNE from biol. replicates look alike?
scRNAseq SingleCellExperiment batchelor
written 17 months ago by ▴ 10
0
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0
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931
views
Job: Postdoc Opportunity in Bioinformatics at Northwestern University (Research on Human Pregnancy and Autoimmunity)
Bioinformatics scRNAseq
19 months ago Damini • 0
1
vote
8
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2.1k
views
Advice on appropriateness of an offset in glmGamPoi/edgeR
DESeq2 glmGamPoi offset edgeR scRNAseq
updated 19 months ago by 53k • written 19 months ago by • 0
0
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0
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710
views
scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
RNASeq scRNAseq
20 months ago Bibi • 0
0
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1
reply
1.1k
views
Can you find the correct transcript in scRNA seq data
scRNAseq RNAseq
updated 22 months ago by ★ 5.0k • written 22 months ago by • 0
0
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2
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1.2k
views
Non-empty droplets versus good quality cells
CellRanger emptyDrops scRNAseq 10X
23 months ago rocanja ▴ 60
0
votes
1
reply
833
views
How to select cells that represents more accurately a cluster in a scRNA-seq dataset?
scRNAseq
updated 23 months ago by ★ 5.0k • written 23 months ago by • 0
1
vote
2
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2.1k
views
ScRNAseq analysis scran :: quickcluster Error
scRNAseq quickcluster scRNA scran
2.2 years ago ruba-mahmoud • 0
0
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2
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1.6k
views
scRNA analysis : DEG between low and high-expressing cells
scRNAseq
2.3 years ago Momo • 0
0
votes
1
reply
949
views
FALSE error when checking a pre made sample data
Rstudio scRNAseq DESeq2
updated 2.5 years ago by ★ 5.0k • written 2.5 years ago by • 0
2
votes
5
replies
1.9k
views
Recommendation for large.n in filterByExpr
scRNAseq edgeR SingleCellExperiment
2.5 years ago duez.tolga • 0
0
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1
reply
3.0k
views
DESeq2 error after installing BiocManager
scRNAseq RStudio DESeq2
updated 2.5 years ago by ★ 5.0k • written 2.5 years ago by • 0
4
votes
3
replies
1.8k
views
Custom design for scRNA DGE with pseudobulking
scRNAseq scrna paireddesign edgeR pseudobulking
updated 2.5 years ago by 53k • written 2.5 years ago by • 0
0
votes
1
reply
1.0k
views
If highly-expressed genes are upregulated, what happens to genes with lower expression after normalization?
scRNA scRNAseq
updated 2.5 years ago by ★ 5.0k • written 2.5 years ago by • 0
0
votes
1
reply
1.0k
views
library(topGO) query
topGO scRNAseq
updated 2.5 years ago by ▴ 780 • written 2.6 years ago by • 0
0
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0
replies
845
views
adding noise to scRNA Seq counts
scRNAseq
2.6 years ago Jiyuan • 0
1
vote
11
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10k
views
Error: Bioconductor version cannot be validated; no internet connection?
scRNAseq
updated 2.3 years ago by • 0 • written 2.6 years ago by • 0
2
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3
replies
2.2k
views
P-value histogram of testLinearModel is not uniform
smart-seq2 scRNAseq scran
2.7 years ago Lluís Revilla Sancho ▴ 760
0
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0
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1.1k
views
News: course - single-cell RNAseq data analysis with R and Bioconductor
Workshop scRNAseq
2.7 years ago info ▴ 10
0
votes
1
reply
1.2k
views
scRNAseq Download Errors
scRNAseq
updated 2.8 years ago by 4.3k • written 2.8 years ago by ★ 1.6k
2
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0
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2.8k
views
How to aggregate pseudobulks: Normalization & Log-Transformation
pseudobulk scRNAseq GSVA
2.8 years ago Tadeoye ▴ 20
0
votes
1
reply
1.7k
views
scRNAseq package and cell type annotations
ExperimentHub R ExperimentHubData scRNAseq SingleR
updated 2.9 years ago by ▴ 760 • written 2.9 years ago by ▴ 10
4
votes
5
replies
3.3k
views
Pseudo-bulk celltype comparison across conditions from multiple-sources
DESeq2 edgeR scRNAseq
updated 2.9 years ago by ▴ 760 • written 2.9 years ago by ▴ 10
0
votes
2
replies
1.8k
views
Could not find function "Standard Chromosomes"
scrna scRNAseq
updated 2.3 years ago by • 0 • written 2.9 years ago by • 0
0
votes
3
replies
2.6k
views
Single-Cell Data Simulation from Bulk RNA-seq
SingleCell RNASeq RNASeqData scRNAseq
updated 19 months ago by • 0 • written 3.2 years ago by • 0
1
vote
2
replies
2.2k
views
What number components should I use if I want to show 2D and 3D UMAP
scater UAMP scRNAseq
3.3 years ago Guandong Shang ▴ 40
1
vote
2
replies
1.6k
views
Combine scRNAseq data for bulk analysis using DESeq2
DESeq2 scRNAseq Fluidigm
3.3 years ago evocanres • 0
0
votes
3
replies
1.9k
views
scRNA-seq: RS4' object has no attribute 'T'" in fastMNN R function
scanpy scRNAseq fastmnn r
3.3 years ago Madiha • 0
4
votes
5
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5.0k
views
`emptyDrops()` calling 'too many' non-empty droplets
DropletUtils emptyDrops scRNA scRNAseq 10x
3.5 years ago Peter Hickey ▴ 760
4
votes
2
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2.0k
views
how to do downstram analysis to cells which are subsetted after MNN batch-correction
batchelor fastMNN scRNAseq
3.5 years ago Guandong Shang ▴ 40
0
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4
replies
3.2k
views
how to make the "reconstructed" value in intergated scRNA-seq UMAP plot more readable
scater batchelor scRNAseq fastMNN
updated 3.5 years ago by ★ 29k • written 3.5 years ago by ▴ 40
0
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0
replies
1.6k
views
Job: Scientific Programmer | Altos Labs | San Diego
SpatialData scRNAseq JobPosting
3.5 years ago peter.kharchenko ▴ 30
0
votes
0
replies
1.2k
views
Job: Postdoc position in integrated omics at Karolinska Institute, Stockholm
ATACSeq multiOmicsViz scRNAseq JobPosting
3.5 years ago Sebastian Lewandowski • 0
1
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4
replies
2.1k
views
Quality control of scRNA-seq data using mitochondrial ratio (drosophila)
Drosophila_melanogaster scRNAseq
3.6 years ago Chise ▴ 10
0
votes
0
replies
1.7k
views
how to calculate similarity between each cluster in scRNA and bulk RNA-seq
SingleR scRNAseq
3.6 years ago Guandong Shang ▴ 40
0
votes
2
replies
2.8k
views
calculateQCMetrics defunct, how to calculate the quality metrics by perCellQCMetrics
scRNAseq
updated 3.6 years ago by ★ 5.0k • written 3.6 years ago by • 0
0
votes
1
reply
1.9k
views
Error: DESeq(dds , useT = TRUE, minmu = 1e-06, test = "LRT", : likelihood ratio test requires a 'reduced' design, see ?DESeq
scRNAseq DESeq2
updated 3.6 years ago by ★ 5.0k • written 3.6 years ago by • 0
2
votes
8
replies
2.8k
views
RSEM - tximport; where is effective_length information used? Implications for scRNA?
RSEM tximport scRNAseq DESeq2
3.6 years ago Kelen ▴ 10
0
votes
1
reply
1.3k
views
scRNASeq reference at a transcript level
EWCE scRNAseq
updated 3.7 years ago by ▴ 780 • written 3.7 years ago by • 0
1
vote
2
replies
3.2k
views
unbalanced cell count and unbalanced read count across samples in pseudobulk differential expression analysis using scRNA-seq data
scRNAseq DifferentialExpression DESeq2
3.8 years ago Ismail • 0
96 results • Page 1 of 2
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Comment: GOseq Probability Weight Function bad fit by a2sahaaaq2c • 0
the mobile gaming world offers a different kind of strategic challenge. Many users today are shifting from heavy data processing to lighthe…
Comment: Postdoctoral Fellow (Computational Biology / Bioinformatics) - Neuroepigenetics by mudasarnaeem2020 • 0
Promoting UDISE+ Features on Social Media to Increase Awareness https://udisseplus.com/[enter link description here][1] [1]: https://ud…
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To resolve technical errors like installation failures or login issues, first ensure your device allows in the security settings and that…
Comment: soGGi error by shepherl 4.3k
We have tried to contact the soGGi maintainer to have them update the package to the newer version of gglot2 but they have so far been unre…
Comment: using limma trend workflow in CAMERA by Gordon Smyth 53k
No, `trend.var=TRUE` and `trend=TRUE` are not needed in any voom pipeline, because the trend is already incorporated into the voom weights.
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Answer: DiffBind differential analysis
Answer: Limma-voom sample weights and impact on DEG numbers
C: Why limma, edgeR, and DESeq did not implement fold change moderation first?
Comment: using limma trend workflow in CAMERA
C: z-score with DESeq2?
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