Showing : scRNAseq • reset
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scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
RNASeq scRNAseq
1 day ago Bibi • 0
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1
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155
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Can you find the correct transcript in scRNA seq data
scRNAseq RNAseq
updated 5 weeks ago by ★ 4.1k • written 6 weeks ago by • 0
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2
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256
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Non-empty droplets versus good quality cells
CellRanger emptyDrops scRNAseq 10X
9 weeks ago • updated 8 weeks ago rocanja ▴ 60
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1
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268
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How to select cells that represents more accurately a cluster in a scRNA-seq dataset?
scRNAseq
updated 12 weeks ago by ★ 4.1k • written 12 weeks ago by • 0
1
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916
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ScRNAseq analysis scran :: quickcluster Error
scRNAseq quickcluster scRNA scran
5 months ago ruba-mahmoud • 0
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2
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544
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scRNA analysis : DEG between low and high-expressing cells
scRNAseq
7 months ago Momo • 0
0
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1
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399
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FALSE error when checking a pre made sample data
Rstudio scRNAseq DESeq2
updated 9 months ago by ★ 4.1k • written 9 months ago by • 0
1
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5
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889
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Recommendation for large.n in filterByExpr
scRNAseq edgeR SingleCellExperiment
9 months ago duez.tolga • 0
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1
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1.1k
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DESeq2 error after installing BiocManager
scRNAseq RStudio DESeq2
updated 9 months ago by ★ 4.1k • written 9 months ago by • 0
4
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3
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1.1k
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Custom design for scRNA DGE with pseudobulking
scRNAseq scrna paireddesign edgeR pseudobulking
updated 9 months ago by 50k • written 9 months ago by • 0
0
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1
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428
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If highly-expressed genes are upregulated, what happens to genes with lower expression after normalization?
scRNA scRNAseq
updated 9 months ago by ★ 4.1k • written 9 months ago by • 0
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1
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585
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library(topGO) query
topGO scRNAseq
updated 10 months ago by ▴ 780 • written 10 months ago by • 0
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368
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adding noise to scRNA Seq counts
scRNAseq
10 months ago Jiyuan • 0
1
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11
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3.7k
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Error: Bioconductor version cannot be validated; no internet connection?
scRNAseq
updated 6 months ago by • 0 • written 10 months ago by • 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
11 months ago Lluís Revilla Sancho ▴ 730
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511
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News: course - single-cell RNAseq data analysis with R and Bioconductor
Workshop scRNAseq
12 months ago info ▴ 10
0
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1
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590
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scRNAseq Download Errors
scRNAseq
updated 13 months ago by 3.9k • written 13 months ago by ★ 1.5k
2
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0
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1.2k
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How to aggregate pseudobulks: Normalization & Log-Transformation
pseudobulk scRNAseq GSVA
13 months ago Tadeoye ▴ 20
0
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1
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756
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scRNAseq package and cell type annotations
ExperimentHub R ExperimentHubData scRNAseq SingleR
updated 14 months ago by ▴ 740 • written 14 months ago by ▴ 10
4
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5
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1.4k
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Pseudo-bulk celltype comparison across conditions from multiple-sources
DESeq2 edgeR scRNAseq
updated 14 months ago by ▴ 740 • written 14 months ago by ▴ 10
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2
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701
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Could not find function "Standard Chromosomes"
scrna scRNAseq
updated 7 months ago by • 0 • written 14 months ago by • 0
0
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2
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958
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Single-Cell Data Simulation from Bulk RNA-seq
SingleCell RNASeq RNASeqData scRNAseq
updated 4 weeks ago by • 0 • written 18 months ago by • 0
1
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2
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1.2k
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What number components should I use if I want to show 2D and 3D UMAP
scater UAMP scRNAseq
19 months ago Guandong Shang ▴ 40
1
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2
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974
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Combine scRNAseq data for bulk analysis using DESeq2
DESeq2 scRNAseq Fluidigm
19 months ago evocanres • 0
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3
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1.1k
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scRNA-seq: RS4' object has no attribute 'T'" in fastMNN R function
scanpy scRNAseq fastmnn r
19 months ago Madiha • 0
4
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5
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2.4k
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`emptyDrops()` calling 'too many' non-empty droplets
DropletUtils emptyDrops scRNA scRNAseq 10x
21 months ago Peter Hickey ▴ 740
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2
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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
21 months ago Guandong Shang ▴ 40
0
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4
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2.1k
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how to make the "reconstructed" value in intergated scRNA-seq UMAP plot more readable
scater batchelor scRNAseq fastMNN
updated 21 months ago by ★ 28k • written 22 months ago by ▴ 40
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1.0k
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Job: Scientific Programmer | Altos Labs | San Diego
SpatialData scRNAseq JobPosting
22 months ago • updated 21 months ago peter.kharchenko ▴ 30
0
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734
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Job: Postdoc position in integrated omics at Karolinska Institute, Stockholm
ATACSeq multiOmicsViz scRNAseq JobPosting
22 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
22 months ago Chise ▴ 10
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986
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how to calculate similarity between each cluster in scRNA and bulk RNA-seq
SingleR scRNAseq
22 months ago Guandong Shang ▴ 40
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2
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1.9k
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calculateQCMetrics defunct, how to calculate the quality metrics by perCellQCMetrics
scRNAseq
updated 22 months ago by ★ 4.1k • written 22 months ago by • 0
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1
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1.1k
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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 23 months ago by ★ 4.1k • written 23 months ago by • 0
2
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8
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1.6k
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RSEM - tximport; where is effective_length information used? Implications for scRNA?
RSEM tximport scRNAseq DESeq2
23 months ago • updated 22 months ago Kelen ▴ 10
0
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1
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737
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scRNASeq reference at a transcript level
EWCE scRNAseq
updated 24 months ago by ▴ 780 • written 24 months ago by • 0
1
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2
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1.8k
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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
2.1 years ago Ismail • 0
1
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1
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1.8k
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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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1.2k
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How to deal with Expression set assembly problem?
deconvolution r scRNAseq bioinformatics
2.3 years ago Hasan Alanya • 0
0
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1
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992
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Aberrant number of cells
CellBarcode DropletUtils emptyDrops() Cellranger scRNAseq
updated 2.0 years ago by ▴ 20 • written 2.3 years ago by • 0
0
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0
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916
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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
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644
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scRNA technical replicates in separate runs
SingleCellExperiment scRNAseq
2.5 years ago Núria • 0
0
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2
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932
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scRNAseq analysis on multiple datasets
scRNAseq
updated 2.6 years ago by ★ 1.4k • written 2.6 years ago by • 0
2
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4
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1.2k
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edgeR output doubts
logFC edgeR DifferentialExpression scRNAseq
2.8 years ago mbenegas ▴ 10
0
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1
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1.1k
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Identify a scRNASeq cell-population using a bulk RNA Seq dataset of that population?
RNASeq rnaseq scRNAseq
updated 2.8 years ago by ★ 28k • written 2.8 years ago by ▴ 10
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0
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795
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Correlation plot using the count data from seurat object
scRNAseq
2.8 years ago Sam • 0
3
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4
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4.0k
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differential expression for Single-cell RNAseq data using edgeR
edgeR single scRNAseq
2.8 years ago • updated 2.7 years ago mbenegas ▴ 10
2
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13
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2.3k
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Running the DESeq2 "DESeqDataSetFromMatrix" function returns a dimname error
DESeq2 Scrna scRNAseq
2.8 years ago RDoc ▴ 10
50 results • Page 1 of 1
Recent ...
Replies
Comment: Ensembl plants at annotationHub? by Johannes Rainer ★ 2.0k
You can get the `EnsDb` EnsDb.Taestivum.v112.sqlite (for Ensembl 112/ ensemblgenomes 59) [here](https://www.dropbox.com/sh/msic0luivbldmb7/…
Comment: Errors in chromosome annotation-biomaRt by blackwidowzzz • 0
I recommend using a different dataset specific to your rat genome assembly version 8. You can search for available datasets within Ensembl …
Answer: Errors in chromosome annotation-biomaRt by James W. MacDonald 66k
If you are just using HGNC symbols for the lookup, and you are trying to get NCBI IDs, then I wouldn't use `biomaRt` because it's based on …
Comment: Help with ENmix readidat by James W. MacDonald 66k
Please don't add to posts from two years ago. Instead make a new post. Also, please read the help page for `readidat`. The only reason to …
Comment: LRT, more than two conditions and pairwise comparisons by James W. MacDonald 66k
In that case, probably easiest to subset to the groups being compared.
Votes
Answer: Error retrieving ensembl gene id using biomaRt...
Comment: LRT, more than two conditions and pairwise comparisons
Answer: Control group between 2 batches have different expression in RNAseq data
Answer: How to remove batch effect to combine RNAseq data from 2 different experiments?
Comment: DESeq2- Mysterious interaction suppresses DEGs
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