Showing : scrnaseq • reset
0
votes
1
reply
93
views
Can you find the correct transcript in scRNA seq data
scRNAseq RNAseq
updated 5 days ago by ★ 4.0k • written 7 days ago by • 0
0
votes
2
replies
181
views
Non-empty droplets versus good quality cells
CellRanger emptyDrops scRNAseq 10X
28 days ago • updated 27 days ago rocanja ▴ 60
0
votes
1
reply
231
views
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
vote
2
replies
720
views
ScRNAseq analysis scran :: quickcluster Error
scRNAseq quickcluster scRNA scran
4 months ago ruba-mahmoud • 0
0
votes
2
replies
466
views
scRNA analysis : DEG between low and high-expressing cells
scRNAseq
6 months ago Momo • 0
0
votes
1
reply
372
views
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
1
vote
5
replies
810
views
Recommendation for large.n in filterByExpr
scRNAseq edgeR SingleCellExperiment
8 months ago duez.tolga • 0
0
votes
1
reply
956
views
DESeq2 error after installing BiocManager
scRNAseq RStudio DESeq2
updated 8 months ago by ★ 4.0k • written 8 months ago by • 0
4
votes
3
replies
1.0k
views
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
votes
1
reply
392
views
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
votes
1
reply
541
views
library(topGO) query
topGO scRNAseq
updated 8 months ago by ▴ 750 • written 8 months ago by • 0
0
votes
0
replies
331
views
adding noise to scRNA Seq counts
scRNAseq
9 months ago Jiyuan • 0
1
vote
11
replies
3.3k
views
Error: Bioconductor version cannot be validated; no internet connection?
scRNAseq
updated 5 months ago by • 0 • written 9 months ago by • 0
2
votes
3
replies
1.3k
views
P-value histogram of testLinearModel is not uniform
smart-seq2 scRNAseq scran
10 months ago Lluís Revilla Sancho ▴ 730
0
votes
0
replies
454
views
News: course - single-cell RNAseq data analysis with R and Bioconductor
Workshop scRNAseq
10 months ago info ▴ 10
0
votes
1
reply
556
views
scRNAseq Download Errors
scRNAseq
updated 12 months ago by 3.8k • written 12 months ago by ★ 1.5k
2
votes
0
replies
1.1k
views
How to aggregate pseudobulks: Normalization & Log-Transformation
pseudobulk scRNAseq GSVA
12 months ago Tadeoye ▴ 20
0
votes
1
reply
707
views
scRNAseq package and cell type annotations
ExperimentHub R ExperimentHubData scRNAseq SingleR
updated 13 months ago by ▴ 690 • written 13 months ago by ▴ 10
4
votes
5
replies
1.3k
views
Pseudo-bulk celltype comparison across conditions from multiple-sources
DESeq2 edgeR scRNAseq
updated 13 months ago by ▴ 690 • written 13 months ago by ▴ 10
0
votes
2
replies
655
views
Could not find function "Standard Chromosomes"
scrna scRNAseq
updated 5 months ago by • 0 • written 13 months ago by • 0
0
votes
1
reply
829
views
Single-Cell Data Simulation from Bulk RNA-seq
SingleCell RNASeq RNASeqData scRNAseq
updated 17 months ago by 50k • written 17 months ago by • 0
1
vote
2
replies
1.1k
views
What number components should I use if I want to show 2D and 3D UMAP
scater UAMP scRNAseq
18 months ago Guandong Shang ▴ 40
1
vote
2
replies
931
views
Combine scRNAseq data for bulk analysis using DESeq2
DESeq2 scRNAseq Fluidigm
18 months ago evocanres • 0
0
votes
3
replies
998
views
scRNA-seq: RS4' object has no attribute 'T'" in fastMNN R function
scanpy scRNAseq fastmnn r
18 months ago Madiha • 0
4
votes
5
replies
2.2k
views
`emptyDrops()` calling 'too many' non-empty droplets
DropletUtils emptyDrops scRNA scRNAseq 10x
20 months ago Peter Hickey ▴ 690
4
votes
2
replies
1.1k
views
how to do downstram analysis to cells which are subsetted after MNN batch-correction
batchelor fastMNN scRNAseq
20 months ago Guandong Shang ▴ 40
0
votes
4
replies
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
0
votes
0
replies
956
views
Job: Scientific Programmer | Altos Labs | San Diego
SpatialData scRNAseq JobPosting
20 months ago peter.kharchenko ▴ 30
0
votes
0
replies
699
views
Job: Postdoc position in integrated omics at Karolinska Institute, Stockholm
ATACSeq multiOmicsViz scRNAseq JobPosting
21 months ago Sebastian Lewandowski • 0
1
vote
4
replies
1.2k
views
Quality control of scRNA-seq data using mitochondrial ratio (drosophila)
Drosophila_melanogaster scRNAseq
21 months ago Chise ▴ 10
0
votes
0
replies
934
views
how to calculate similarity between each cluster in scRNA and bulk RNA-seq
SingleR scRNAseq
21 months ago Guandong Shang ▴ 40
0
votes
2
replies
1.8k
views
calculateQCMetrics defunct, how to calculate the quality metrics by perCellQCMetrics
scRNAseq
updated 21 months ago by ★ 4.0k • written 21 months ago by • 0
0
votes
1
reply
1.0k
views
Error: DESeq(dds , useT = TRUE, minmu = 1e-06, test = "LRT", : likelihood ratio test requires a 'reduced' design, see ?DESeq
scRNAseq DESeq2
updated 21 months ago by ★ 4.0k • written 21 months ago by • 0
2
votes
8
replies
1.5k
views
RSEM - tximport; where is effective_length information used? Implications for scRNA?
RSEM tximport scRNAseq DESeq2
22 months ago • updated 21 months ago Kelen ▴ 10
0
votes
1
reply
698
views
scRNASeq reference at a transcript level
EWCE scRNAseq
updated 23 months ago by ▴ 750 • written 23 months ago by • 0
1
vote
2
replies
1.7k
views
unbalanced cell count and unbalanced read count across samples in pseudobulk differential expression analysis using scRNA-seq data
scRNAseq DifferentialExpression DESeq2
24 months ago Ismail • 0
1
vote
1
reply
1.7k
views
Can we use 'SCT normalization' to find anchors and 'LogNormalize' for the integration?
Normalization scRNAseq
updated 2.0 years ago by ▴ 690 • written 2.0 years ago by • 0
2
votes
2
replies
1.2k
views
scuttle:: librarySizeFactors returning non-finite values
normalizeCounts scran librarySizeFactors scuttle scRNAseq
2.1 years ago behr201 • 0
2
votes
2
replies
1.1k
views
How to deal with Expression set assembly problem?
deconvolution r scRNAseq bioinformatics
2.2 years ago Hasan Alanya • 0
0
votes
1
reply
943
views
Aberrant number of cells
CellBarcode DropletUtils emptyDrops() Cellranger scRNAseq
updated 23 months ago by ▴ 20 • written 2.2 years ago by • 0
0
votes
0
replies
865
views
Job: Postdoc Opening in Bioinformatics or Computational Biology
SpatialData scRNAseq SingleCell Omixer
2.2 years ago Sebastian Lewandowski • 0
0
votes
3
replies
1.5k
views
NA values for mitochondrial gene percentage
Seurat scRNAseq
2.4 years ago • updated 2.3 years ago zahra.mesri95 • 0
0
votes
0
replies
616
views
scRNA technical replicates in separate runs
SingleCellExperiment scRNAseq
2.4 years ago Núria • 0
0
votes
2
replies
906
views
scRNAseq analysis on multiple datasets
scRNAseq
updated 2.5 years ago by ★ 1.3k • written 2.6 years ago by • 0
2
votes
4
replies
1.2k
views
edgeR output doubts
logFC edgeR DifferentialExpression scRNAseq
2.7 years ago mbenegas • 0
0
votes
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
votes
0
replies
760
views
Correlation plot using the count data from seurat object
scRNAseq
2.7 years ago Sam • 0
2
votes
4
replies
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
votes
13
replies
2.2k
views
Running the DESeq2 "DESeqDataSetFromMatrix" function returns a dimname error
DESeq2 Scrna scRNAseq
2.7 years ago RDoc ▴ 10
0
votes
1
reply
832
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
Recent ...
Replies
Comment: Memory errors using read.bismark? by Peter Hickey ▴ 690
If you process serially (i.e. with `BPPARAM = SerialParam()`) then you might be okay. The final object will be on the order of 250 GB in-me…
Answer: blockwiseModule crashes in the end and doesn't generate modules by xaweh28128 • 0
Test your word skills and see if you can crack the code in today's Wordle puzzle. [Nytimes wordle](https://wordlenytimes.net/quordle-game/)…
Comment: Memory errors using read.bismark? by Juan Higareda • 0
Thanks for the answer. Actually, processing one file and keeping it in memory wasn't the problem, is more processing all the 15 files to bu…
Answer: Differentially expressed genes in monocle pseudotime by Gordon Smyth 50k
You might try the methods in this paper: Cheng J, Smyth GK*, Chen Y* (2023). Unraveling the timeline of gene expression: A pseudotempora…
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa by Seyram M. • 0
Thank you Michael for your attention to my question. I am truly grateful. I subsetted the data using lines of codes to include only the g…
Votes
Comment: Not fully paired differential gene expression analysis
Comment: [DiffBind] Obtaining normalization factors
Answer: ComplexHeatmap: add pch to rowAnnotation when the input is a data frame with var
Comment: Not fully paired differential gene expression analysis
Answer: GSVA error
Awards • All
Popular Question to paria.alipour • 0
Popular Question to Eman • 0
Popular Question to James W. MacDonald 65k
Scholar to nhaus ▴ 30
Popular Question to shepherl 3.8k
Locations • All
Switzerland, 3 minutes ago
WEHI, Melbourne, Australia, 6 minutes ago
France, 13 minutes ago
France, 14 minutes ago
Pakistan, 15 minutes ago
Traffic: 827 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6