Showing : scrnaseq • reset
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Single-Cell Data Simulation from Bulk RNA-seq
SingleCell RNASeq RNASeqData scRNAseq
updated 2 days ago by • 0 • written 17 months ago by • 0
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1
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106
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Can you find the correct transcript in scRNA seq data
scRNAseq RNAseq
updated 9 days ago by ★ 4.0k • written 11 days ago by • 0
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2
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190
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Non-empty droplets versus good quality cells
CellRanger emptyDrops scRNAseq 10X
4 weeks ago rocanja ▴ 60
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233
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How to select cells that represents more accurately a cluster in a scRNA-seq dataset?
scRNAseq
updated 7 weeks ago by ★ 4.0k • written 7 weeks ago by • 0
1
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ScRNAseq analysis scran :: quickcluster Error
scRNAseq quickcluster scRNA scran
4 months ago ruba-mahmoud • 0
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Error: Bioconductor version cannot be validated; no internet connection?
scRNAseq
updated 5 months ago by • 0 • written 9 months ago by • 0
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2
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661
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Could not find function "Standard Chromosomes"
scrna scRNAseq
updated 5 months ago by • 0 • written 13 months ago by • 0
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472
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scRNA analysis : DEG between low and high-expressing cells
scRNAseq
6 months ago Momo • 0
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5
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823
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Recommendation for large.n in filterByExpr
scRNAseq edgeR SingleCellExperiment
8 months ago duez.tolga • 0
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376
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FALSE error when checking a pre made sample data
Rstudio scRNAseq DESeq2
updated 8 months ago by ★ 4.0k • written 8 months ago by • 0
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965
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DESeq2 error after installing BiocManager
scRNAseq RStudio DESeq2
updated 8 months ago by ★ 4.0k • written 8 months ago by • 0
4
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3
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1.0k
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Custom design for scRNA DGE with pseudobulking
scRNAseq scrna paireddesign edgeR pseudobulking
updated 8 months ago by 50k • written 8 months ago by • 0
0
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402
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If highly-expressed genes are upregulated, what happens to genes with lower expression after normalization?
scRNA scRNAseq
updated 8 months ago by ★ 4.0k • written 8 months ago by • 0
0
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544
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library(topGO) query
topGO scRNAseq
updated 9 months ago by ▴ 770 • written 9 months ago by • 0
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340
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adding noise to scRNA Seq counts
scRNAseq
9 months ago Jiyuan • 0
2
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3
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1.3k
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P-value histogram of testLinearModel is not uniform
smart-seq2 scRNAseq scran
10 months ago Lluís Revilla Sancho ▴ 730
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457
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News: course - single-cell RNAseq data analysis with R and Bioconductor
Workshop scRNAseq
11 months ago info ▴ 10
0
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1
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560
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scRNAseq Download Errors
scRNAseq
updated 12 months ago by 3.8k • written 12 months ago by ★ 1.5k
2
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0
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1.1k
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How to aggregate pseudobulks: Normalization & Log-Transformation
pseudobulk scRNAseq GSVA
12 months ago Tadeoye ▴ 20
0
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1
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710
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scRNAseq package and cell type annotations
ExperimentHub R ExperimentHubData scRNAseq SingleR
updated 13 months ago by ▴ 740 • written 13 months ago by ▴ 10
4
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5
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1.3k
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Pseudo-bulk celltype comparison across conditions from multiple-sources
DESeq2 edgeR scRNAseq
updated 13 months ago by ▴ 740 • written 13 months ago by ▴ 10
1
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934
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Combine scRNAseq data for bulk analysis using DESeq2
DESeq2 scRNAseq Fluidigm
18 months ago evocanres • 0
1
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1.1k
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What number components should I use if I want to show 2D and 3D UMAP
scater UAMP scRNAseq
18 months ago Guandong Shang ▴ 40
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3
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1.0k
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scRNA-seq: RS4' object has no attribute 'T'" in fastMNN R function
scanpy scRNAseq fastmnn r
18 months ago Madiha • 0
4
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2.2k
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`emptyDrops()` calling 'too many' non-empty droplets
DropletUtils emptyDrops scRNA scRNAseq 10x
20 months ago Peter Hickey ▴ 740
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1.1k
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how to do downstram analysis to cells which are subsetted after MNN batch-correction
batchelor fastMNN scRNAseq
20 months ago Guandong Shang ▴ 40
0
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4
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2.0k
views
how to make the "reconstructed" value in intergated scRNA-seq UMAP plot more readable
scater batchelor scRNAseq fastMNN
updated 20 months ago by ★ 28k • written 20 months ago by ▴ 40
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959
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Job: Scientific Programmer | Altos Labs | San Diego
SpatialData scRNAseq JobPosting
20 months ago peter.kharchenko ▴ 30
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702
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Job: Postdoc position in integrated omics at Karolinska Institute, Stockholm
ATACSeq multiOmicsViz scRNAseq JobPosting
21 months ago Sebastian Lewandowski • 0
1
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4
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1.2k
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Quality control of scRNA-seq data using mitochondrial ratio (drosophila)
Drosophila_melanogaster scRNAseq
21 months ago Chise ▴ 10
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942
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how to calculate similarity between each cluster in scRNA and bulk RNA-seq
SingleR scRNAseq
21 months ago Guandong Shang ▴ 40
0
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2
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1.8k
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calculateQCMetrics defunct, how to calculate the quality metrics by perCellQCMetrics
scRNAseq
updated 21 months ago by ★ 4.0k • written 21 months ago by • 0
2
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8
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1.5k
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RSEM - tximport; where is effective_length information used? Implications for scRNA?
RSEM tximport scRNAseq DESeq2
22 months ago • updated 21 months ago Kelen ▴ 10
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1.0k
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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 22 months ago by ★ 4.0k • written 22 months ago by • 0
0
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1
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700
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scRNASeq reference at a transcript level
EWCE scRNAseq
updated 23 months ago by ▴ 770 • written 23 months ago by • 0
0
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1
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949
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Aberrant number of cells
CellBarcode DropletUtils emptyDrops() Cellranger scRNAseq
updated 23 months ago by ▴ 20 • written 2.2 years ago by • 0
1
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2
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1.7k
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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
2.0 years ago • updated 24 months ago Ismail • 0
1
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1
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1.7k
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Can we use 'SCT normalization' to find anchors and 'LogNormalize' for the integration?
Normalization scRNAseq
updated 2.1 years ago by ▴ 740 • written 2.1 years ago by • 0
2
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2
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1.2k
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scuttle:: librarySizeFactors returning non-finite values
normalizeCounts scran librarySizeFactors scuttle scRNAseq
2.2 years ago behr201 • 0
2
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2
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1.1k
views
How to deal with Expression set assembly problem?
deconvolution r scRNAseq bioinformatics
2.2 years ago Hasan Alanya • 0
0
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0
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869
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Job: Postdoc Opening in Bioinformatics or Computational Biology
SpatialData scRNAseq SingleCell Omixer
2.3 years ago Sebastian Lewandowski • 0
0
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3
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1.5k
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NA values for mitochondrial gene percentage
Seurat scRNAseq
2.4 years ago zahra.mesri95 • 0
0
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0
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624
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scRNA technical replicates in separate runs
SingleCellExperiment scRNAseq
2.4 years ago Núria • 0
0
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2
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908
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scRNAseq analysis on multiple datasets
scRNAseq
updated 2.6 years ago by ★ 1.3k • written 2.6 years ago by • 0
2
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4
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3.8k
views
differential expression for Single-cell RNAseq data using edgeR
edgeR single scRNAseq
2.7 years ago • updated 2.6 years ago mbenegas • 0
2
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4
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1.2k
views
edgeR output doubts
logFC edgeR DifferentialExpression scRNAseq
2.7 years ago mbenegas • 0
0
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1
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1.0k
views
Identify a scRNASeq cell-population using a bulk RNA Seq dataset of that population?
RNASeq rnaseq scRNAseq
updated 2.7 years ago by ★ 28k • written 2.7 years ago by ▴ 10
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762
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Correlation plot using the count data from seurat object
scRNAseq
2.7 years ago Sam • 0
2
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13
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2.2k
views
Running the DESeq2 "DESeqDataSetFromMatrix" function returns a dimname error
DESeq2 Scrna scRNAseq
2.8 years ago • updated 2.7 years ago RDoc ▴ 10
0
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1
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836
views
Tool for simulating bulk RNA-Seq from single cell data
scRNAseq
updated 2.8 years ago by 65k • written 2.8 years ago by • 0
50 results • Page 1 of 1
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Comment: DESeq filtering specific to contrasts by Michael Love 41k
It will likely not filter it out, but really the per-dataset details would affect the results.
Comment: DESeq filtering specific to contrasts by Carlin95 • 0
Thanks for clarifying. Could I ask maybe one more thing for my sanity? Let's say you had a multi-factor experiment with contrasts including…
Comment: FilterByExpr low counts with small sample size by Jonathan ▴ 10
Thank you for your answer; However, I have some follow-up questions. Following up in In your [1-2-3 article][1], you say that > "... the…
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa by Seyram M. • 0
Thank you very much for your reply! I will do so. Kind regards, Seyram
Comment: Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0` by isaac.vock • 0
Thank you for your response. I can confirm that setting `-t exon` and/or removing `-s 1` and adding `-O` has no impact on the number of suc…
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Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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