Showing : scRNAseq • reset
0
votes
1
reply
152
views
Can you find the correct transcript in scRNA seq data
scRNAseq RNAseq
updated 5 weeks ago by ★ 4.1k • written 5 weeks ago by • 0
0
votes
2
replies
240
views
Non-empty droplets versus good quality cells
CellRanger emptyDrops scRNAseq 10X
8 weeks ago rocanja ▴ 60
0
votes
1
reply
263
views
How to select cells that represents more accurately a cluster in a scRNA-seq dataset?
scRNAseq
updated 11 weeks ago by ★ 4.1k • written 11 weeks ago by • 0
1
vote
2
replies
883
views
ScRNAseq analysis scran :: quickcluster Error
scRNAseq quickcluster scRNA scran
5 months ago ruba-mahmoud • 0
0
votes
2
replies
536
views
scRNA analysis : DEG between low and high-expressing cells
scRNAseq
7 months ago Momo • 0
0
votes
1
reply
392
views
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
vote
5
replies
881
views
Recommendation for large.n in filterByExpr
scRNAseq edgeR SingleCellExperiment
9 months ago duez.tolga • 0
0
votes
1
reply
1.1k
views
DESeq2 error after installing BiocManager
scRNAseq RStudio DESeq2
updated 9 months ago by ★ 4.1k • written 9 months ago by • 0
4
votes
3
replies
1.1k
views
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
votes
1
reply
426
views
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
votes
1
reply
582
views
library(topGO) query
topGO scRNAseq
updated 9 months ago by ▴ 780 • written 9 months ago by • 0
0
votes
0
replies
365
views
adding noise to scRNA Seq counts
scRNAseq
10 months ago Jiyuan • 0
1
vote
11
replies
3.6k
views
Error: Bioconductor version cannot be validated; no internet connection?
scRNAseq
updated 6 months ago by • 0 • written 10 months ago by • 0
2
votes
3
replies
1.3k
views
P-value histogram of testLinearModel is not uniform
smart-seq2 scRNAseq scran
11 months ago Lluís Revilla Sancho ▴ 730
0
votes
0
replies
506
views
News: course - single-cell RNAseq data analysis with R and Bioconductor
Workshop scRNAseq
12 months ago info ▴ 10
0
votes
1
reply
586
views
scRNAseq Download Errors
scRNAseq
updated 13 months ago by 3.9k • written 13 months ago by ★ 1.5k
2
votes
0
replies
1.1k
views
How to aggregate pseudobulks: Normalization & Log-Transformation
pseudobulk scRNAseq GSVA
13 months ago Tadeoye ▴ 20
0
votes
1
reply
749
views
scRNAseq package and cell type annotations
ExperimentHub R ExperimentHubData scRNAseq SingleR
updated 14 months ago by ▴ 740 • written 14 months ago by ▴ 10
4
votes
5
replies
1.4k
views
Pseudo-bulk celltype comparison across conditions from multiple-sources
DESeq2 edgeR scRNAseq
updated 14 months ago by ▴ 740 • written 14 months ago by ▴ 10
0
votes
2
replies
693
views
Could not find function "Standard Chromosomes"
scrna scRNAseq
updated 6 months ago by • 0 • written 14 months ago by • 0
0
votes
2
replies
949
views
Single-Cell Data Simulation from Bulk RNA-seq
SingleCell RNASeq RNASeqData scRNAseq
updated 29 days ago by • 0 • written 18 months ago by • 0
1
vote
2
replies
1.2k
views
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
vote
2
replies
969
views
Combine scRNAseq data for bulk analysis using DESeq2
DESeq2 scRNAseq Fluidigm
19 months ago evocanres • 0
0
votes
3
replies
1.0k
views
scRNA-seq: RS4' object has no attribute 'T'" in fastMNN R function
scanpy scRNAseq fastmnn r
19 months ago Madiha • 0
4
votes
5
replies
2.4k
views
`emptyDrops()` calling 'too many' non-empty droplets
DropletUtils emptyDrops scRNA scRNAseq 10x
21 months ago Peter Hickey ▴ 740
4
votes
2
replies
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
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 21 months ago by ★ 28k • written 21 months ago by ▴ 40
0
votes
0
replies
1.0k
views
Job: Scientific Programmer | Altos Labs | San Diego
SpatialData scRNAseq JobPosting
21 months ago peter.kharchenko ▴ 30
0
votes
0
replies
728
views
Job: Postdoc position in integrated omics at Karolinska Institute, Stockholm
ATACSeq multiOmicsViz scRNAseq JobPosting
22 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
22 months ago Chise ▴ 10
0
votes
0
replies
982
views
how to calculate similarity between each cluster in scRNA and bulk RNA-seq
SingleR scRNAseq
22 months ago Guandong Shang ▴ 40
0
votes
2
replies
1.8k
views
calculateQCMetrics defunct, how to calculate the quality metrics by perCellQCMetrics
scRNAseq
updated 22 months ago by ★ 4.1k • written 22 months ago by • 0
0
votes
1
reply
1.1k
views
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
2
votes
8
replies
1.6k
views
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
votes
1
reply
732
views
scRNASeq reference at a transcript level
EWCE scRNAseq
updated 24 months ago by ▴ 780 • written 24 months ago by • 0
1
vote
2
replies
1.8k
views
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
vote
1
reply
1.8k
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
votes
2
replies
1.2k
views
scuttle:: librarySizeFactors returning non-finite values
normalizeCounts scran librarySizeFactors scuttle scRNAseq
2.2 years ago behr201 • 0
2
votes
2
replies
1.2k
views
How to deal with Expression set assembly problem?
deconvolution r scRNAseq bioinformatics
2.3 years ago Hasan Alanya • 0
0
votes
1
reply
987
views
Aberrant number of cells
CellBarcode DropletUtils emptyDrops() Cellranger scRNAseq
updated 2.0 years ago by ▴ 20 • written 2.3 years ago by • 0
0
votes
0
replies
903
views
Job: Postdoc Opening in Bioinformatics or Computational Biology
SpatialData scRNAseq SingleCell Omixer
2.3 years ago Sebastian Lewandowski • 0
0
votes
3
replies
1.5k
views
NA values for mitochondrial gene percentage
Seurat scRNAseq
2.4 years ago zahra.mesri95 • 0
0
votes
0
replies
640
views
scRNA technical replicates in separate runs
SingleCellExperiment scRNAseq
2.5 years ago Núria • 0
0
votes
2
replies
929
views
scRNAseq analysis on multiple datasets
scRNAseq
updated 2.6 years ago by ★ 1.4k • written 2.6 years ago by • 0
2
votes
4
replies
1.2k
views
edgeR output doubts
logFC edgeR DifferentialExpression scRNAseq
2.8 years ago mbenegas ▴ 10
0
votes
1
reply
1.1k
views
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
0
votes
0
replies
790
views
Correlation plot using the count data from seurat object
scRNAseq
2.8 years ago Sam • 0
3
votes
4
replies
4.0k
views
differential expression for Single-cell RNAseq data using edgeR
edgeR single scRNAseq
2.8 years ago • updated 2.7 years ago mbenegas ▴ 10
2
votes
13
replies
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
859
views
Tool for simulating bulk RNA-Seq from single cell data
scRNAseq
updated 2.9 years ago by 65k • written 2.9 years ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Ensembl plants at annotationHub? by Daniele • 0
Dear Johannes, Would it be possible to create the EnsDb for Triticum aestivum (IWGSC)? Thank you very much, Daniele
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools by BioinfGuru ▴ 30
Figured it out with ?eigencorplot, thanks Michael. I was trying to pass 10 PCs when I only had 8, and I was including metadata columns that…
Answer: DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set by makala • 0
Thanks a lot!
Comment: DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set by Erik Wright ▴ 150
Thanks for notifying us of this broken link. It should be fixed on the Downloads page now. [1] [1]: http://www2.decipher.codes/Classificat…
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa by Matthew Thornton ▴ 360
So it turns out that if the count and the size are the same in 'GOstats", the odds ratio is 'inf'. These are causing the issue. Thank you!!
Votes
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
Comment: Can DESeq2 rlog normalized matrix reflects time course result directly?
Awards • All
Popular Question to Chris ▴ 10
Popular Question to Guido Hooiveld ★ 4.0k
Scholar to Michael Love 42k
Popular Question to Vincent J. Carey, Jr. 6.7k
Popular Question to boczniak767 ▴ 720
Locations • All
Melbourne, Australia, 4 minutes ago
United States, 1 hour ago
The Netherlands, 2 hours ago
India, 2 hours ago
Germany, 2 hours ago
Traffic: 395 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