Showing : scRNAseq • reset
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Single-Cell Data Simulation from Bulk RNA-seq
SingleCell RNASeq RNASeqData scRNAseq
updated 14 days ago by • 0 • written 17 months ago by • 0
0
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1
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131
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Can you find the correct transcript in scRNA seq data
scRNAseq RNAseq
updated 21 days ago by ★ 4.1k • written 23 days ago by • 0
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2
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202
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Non-empty droplets versus good quality cells
CellRanger emptyDrops scRNAseq 10X
6 weeks ago rocanja ▴ 60
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1
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246
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How to select cells that represents more accurately a cluster in a scRNA-seq dataset?
scRNAseq
updated 9 weeks ago by ★ 4.1k • written 9 weeks ago by • 0
1
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2
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795
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ScRNAseq analysis scran :: quickcluster Error
scRNAseq quickcluster scRNA scran
4 months ago ruba-mahmoud • 0
1
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11
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3.5k
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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
0
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2
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678
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Could not find function "Standard Chromosomes"
scrna scRNAseq
updated 6 months ago by • 0 • written 14 months ago by • 0
0
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2
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500
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scRNA analysis : DEG between low and high-expressing cells
scRNAseq
6 months ago Momo • 0
1
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5
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845
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Recommendation for large.n in filterByExpr
scRNAseq edgeR SingleCellExperiment
8 months ago duez.tolga • 0
0
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1
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385
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FALSE error when checking a pre made sample data
Rstudio scRNAseq DESeq2
updated 8 months ago by ★ 4.1k • written 8 months ago by • 0
0
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1
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1.0k
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DESeq2 error after installing BiocManager
scRNAseq RStudio DESeq2
updated 8 months ago by ★ 4.1k • 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 9 months ago by 50k • written 9 months ago by • 0
0
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1
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416
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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
0
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1
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561
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library(topGO) query
topGO scRNAseq
updated 9 months ago by ▴ 780 • written 9 months ago by • 0
0
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350
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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
11 months ago • updated 10 months ago Lluís Revilla Sancho ▴ 730
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477
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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
reply
577
views
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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727
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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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1.4k
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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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2
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960
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Combine scRNAseq data for bulk analysis using DESeq2
DESeq2 scRNAseq Fluidigm
19 months ago • updated 18 months ago evocanres • 0
1
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2
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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
19 months ago Madiha • 0
4
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5
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2.3k
views
`emptyDrops()` calling 'too many' non-empty droplets
DropletUtils emptyDrops scRNA scRNAseq 10x
21 months ago • updated 20 months ago Peter Hickey ▴ 740
4
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2
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1.1k
views
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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2.0k
views
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 21 months ago by ▴ 40
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976
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Job: Scientific Programmer | Altos Labs | San Diego
SpatialData scRNAseq JobPosting
21 months ago peter.kharchenko ▴ 30
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0
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716
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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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0
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963
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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
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 22 months ago by ★ 4.1k • written 22 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
22 months ago Kelen ▴ 10
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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 22 months ago by ★ 4.1k • written 22 months ago by • 0
0
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1
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717
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scRNASeq reference at a transcript level
EWCE scRNAseq
updated 23 months ago by ▴ 780 • written 23 months ago by • 0
0
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1
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967
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Aberrant number of cells
CellBarcode DropletUtils emptyDrops() Cellranger scRNAseq
updated 24 months ago by ▴ 20 • written 2.2 years 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
2.0 years ago Ismail • 0
1
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1
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1.7k
views
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
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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883
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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
views
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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633
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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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916
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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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3.9k
views
differential expression for Single-cell RNAseq data using edgeR
edgeR single scRNAseq
2.8 years ago • updated 2.7 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
reply
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
0
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0
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779
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Correlation plot using the count data from seurat object
scRNAseq
2.8 years ago Sam • 0
2
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13
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2.3k
views
Running the DESeq2 "DESeqDataSetFromMatrix" function returns a dimname error
DESeq2 Scrna scRNAseq
2.8 years ago RDoc ▴ 10
0
votes
1
reply
845
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: log2FoldChange value is way too different when compared with counts(dds) by Michael Love 41k
But just to be clear, this is not the same as regressing out batch from the VST (approx log transformed): ``` limma::removeBatchEffect(cou…
Comment: log2FoldChange value is way too different when compared with counts(dds) by HAK • 0
Thank you for the explanation, probably my brain just needed to accumulate enough info to understand what you are saying, but I finally got…
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call by ATpoint ★ 4.1k
Here the error probably means that you habe genes where expression scross all samples is the same. Rowscaling is value minus mean divided b…
Comment: Store output of matchPWM() by James W. MacDonald 65k
Here's a self contained reproducible example, using part of the example in `?matchPWM` ``` > library(Biostrings) > data(HNF4alpha) > libr…
Comment: DEseq2 coefficient by JKim • 0
Hi Dr. Love, I'm sorry to ask another question to my old post. If the design isn't balanced, the interpretation of coefficients will be…
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SPIA plotP giving error
Answer: Fold change calculation in Diffbind vs. DESEQ2?
C: How to establish a subset from TxDb.Hsapiens.UCSC.hg38.knownGene DB
C: Extremely big genes in annotation TxDb packages
Make custom Txdb class objects from Txdb
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