Showing : scRNAseq • reset
8
votes
2
replies
1.6k
views
how can I annotate my scRNAseq clusters from a Rat experiment?
scRNAseq Rattus_norvegicus_Data annotation
updated 2.9 years ago by ★ 4.0k • written 3.0 years ago by ▴ 10
7
votes
3
replies
1.4k
views
Effect of feature number on adjusted p-values
edgeR DESeq2 single-cell scRNAseq zinbwave
updated 2.9 years ago by ★ 28k • written 2.9 years ago by ▴ 20
7
votes
3
replies
3.1k
views
Estimating cell size factors for single cell RNA-seq data
scrnaseq rnaseq normalization DESeq2
updated 6.7 years ago by 41k • written 6.7 years ago by ▴ 10
6
votes
12
replies
3.6k
views
Merging RNAseq Datasets of Different Depths
singlecellexperiment scran sequencing depth batch effect scrnaseq
updated 5.8 years ago by ★ 28k • written 5.8 years ago by • 0
5
votes
4
replies
2.1k
views
Using DESeq2 with GlmGamPoi
DESeq2 glmGamPoi scRNAseq
3.1 years ago tatyana.perlova • 0
5
votes
6
replies
1.6k
views
DE Analysis on Scran-Normalized Counts
DifferentialExpression scRNAseq scran
updated 3.2 years ago by ★ 28k • written 3.2 years ago by • 0
4
votes
1
reply
1.5k
views
Best practice for correlating scRNA seq to bulkRNA seq data
seurat edgeR spearman correlation scRNAseq
updated 4.0 years ago by ★ 28k • written 4.0 years 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 ▴ 710 • written 13 months ago by ▴ 10
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
4
votes
7
replies
4.4k
views
removing rows from SingleCellExperiment container
sce singlecellexperiment scRNAseq subsetting
updated 5.3 years ago by ★ 28k • written 5.3 years ago by • 0
4
votes
3
replies
1.8k
views
using SC3 and scater for bulk-RNAseq
sc3 scater scRNAseq
updated 7.1 years ago by ▴ 150 • written 7.1 years ago by ★ 1.5k
4
votes
1
reply
1.7k
views
NAs in continuous coefficient and fold change in `zlm`
scrnaseq MAST differential gene expression
6.7 years ago Andrew_McDavid ▴ 270
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
4
votes
5
replies
1.3k
views
RNA Seq analysis vs. Single cell RNA seq analysis
rnaseq scrnaseq edger
6.5 years ago fawazfebin ▴ 60
4
votes
5
replies
2.2k
views
`emptyDrops()` calling 'too many' non-empty droplets
DropletUtils emptyDrops scRNA scRNAseq 10x
20 months ago Peter Hickey ▴ 710
3
votes
9
replies
4.1k
views
Why does scran's computeSumFactors produce different size factors for cells with the exact same gene counts?
scran scater drop-seq scrnaseq
updated 7.0 years ago by ★ 28k • written 7.0 years ago by ▴ 10
2
votes
6
replies
1.7k
views
Change the number of clusters with scater
scater scran scrnaseq clustering
updated 5.4 years ago by ★ 28k • written 5.4 years ago by ▴ 20
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
2
votes
0
replies
1.1k
views
How to aggregate pseudobulks: Normalization & Log-Transformation
pseudobulk scRNAseq GSVA
12 months ago Tadeoye ▴ 20
2
votes
4
replies
1.2k
views
edgeR output doubts
logFC edgeR DifferentialExpression scRNAseq
2.7 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
2
votes
4
replies
1.2k
views
Does hashedDrops support 'imbalanced' combinations of HTOs?
DropletUtils scRNAseq
updated 3.2 years ago by ★ 28k • written 3.2 years ago by ▴ 710
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
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
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
2
votes
2
replies
1.2k
views
scuttle:: librarySizeFactors returning non-finite values
normalizeCounts scran librarySizeFactors scuttle scRNAseq
2.2 years ago • updated 2.1 years ago behr201 • 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
1
vote
1
reply
2.0k
views
Mean Expression Calculation scRNA-seq (All cells or only Expressed Cells)
scrnaseq monocle
updated 5.9 years ago by ▴ 950 • written 6.0 years ago by ▴ 10
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
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
1
reply
983
views
Combining treatment and control batches for analysis
scRNAseq scRNA batchelor BatchEffect
updated 3.4 years ago by ★ 28k • written 3.4 years ago by • 0
1
vote
5
replies
816
views
Recommendation for large.n in filterByExpr
scRNAseq edgeR SingleCellExperiment
8 months ago duez.tolga • 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
1.3k
views
Question: Removal of mRNA contamination from scRNA-seq data using SoupX: How to proceed when "Extremely high contamination estimated"?
scRNAseq SoupX
updated 3.5 years ago by 65k • written 3.5 years ago by ▴ 10
1
vote
0
replies
944
views
News: News: Bioinformatics Summer School - July 2020 - UCLouvain (Belgium)
rnaseq course proteomics transcriptomics scrnaseq News
4.2 years ago Laurent Gatto 1.6k
1
vote
5
replies
1.6k
views
computeSumFactors: warning about cluster size
scrnaseq scrn sizefactors
6.7 years ago sfpacman • 0
1
vote
2
replies
934
views
Combine scRNAseq data for bulk analysis using DESeq2
DESeq2 scRNAseq Fluidigm
18 months ago evocanres • 0
1
vote
1
reply
1.7k
views
Can we use 'SCT normalization' to find anchors and 'LogNormalize' for the integration?
Normalization scRNAseq
updated 2.1 years ago by ▴ 710 • written 2.1 years ago by • 0
1
vote
2
replies
1.8k
views
install celldex in r4. 04
scRNAseq
written 3.1 years ago by • 0
1
vote
3
replies
1.5k
views
Differential Expression analysis between distinct scRNA-seq datasets
scrna scrnaseq differential gene expression
updated 6.5 years ago by ▴ 950 • written 6.5 years ago by • 0
1
vote
2
replies
731
views
ScRNAseq analysis scran :: quickcluster Error
scRNAseq quickcluster scRNA scran
4 months ago ruba-mahmoud • 0
0
votes
3
replies
1.5k
views
MAST invalid Hypothesis, class objectORconnection error
R MAST scRNASeq
3.7 years ago TriS ▴ 200
0
votes
2
replies
182
views
Non-empty droplets versus good quality cells
CellRanger emptyDrops scRNAseq 10X
29 days ago • updated 28 days ago rocanja ▴ 60
0
votes
1
reply
1.3k
views
Removal of batch effects before non-linear clustering for scRNAseq
scrnaseq MAST
7.0 years ago Andrew_McDavid ▴ 270
0
votes
3
replies
1.4k
views
Modeling Dose-response data in MAST
MAST sc-rnaseq scrnaseq
updated 6.7 years ago by ▴ 270 • written 6.7 years ago by • 0
0
votes
2
replies
1.2k
views
BASiCS spike info for single cell RNA sequences or Bayesian statistics help
BASiCS bayesian single cell scrnaseq
updated 6.2 years ago by ▴ 10 • written 6.2 years ago by ▴ 10
0
votes
1
reply
982
views
RNAseq scater error in plotQC()
scater plotQC scRNAseq
updated 5.7 years ago by ★ 28k • written 5.7 years ago by ▴ 90
0
votes
6
replies
1.7k
views
analysis of multiple batches and multiple treatment conditions in scRNA-seq
limma deseq2 edger scRNAseq combat
updated 4.7 years ago by ▴ 270 • written 4.7 years ago by ▴ 670
0
votes
1
reply
1.6k
views
Minimum number of cells required for the MAST
MAST scRNAseq differential expression
4.6 years ago Andrew_McDavid ▴ 270
0
votes
2
replies
1.6k
views
PCA outliers cleaning
scRNAseq Pipeline Seurat SingleCellExperiment
4.4 years ago albadrs.93 ▴ 10
50 results • Page 1 of 1
Recent ...
Replies
Comment: FilterByExpr low counts with small sample size by Gordon Smyth 50k
As always, it always helps to see code. Are you running `voom` or `voomLmFit`? Did you run `normLibSizes()` in edgeR? Are you starting with…
Comment: Batch correction and repeated measures by Gordon Smyth 50k
In your code, it was clear that `expr.mat` was a matrix rather than a DGEList, so it has to be a count matrix. If you have a DGEList object…
Comment: Methylation Analysis experiment design using Limma by Gordon Smyth 50k
I don't analyse methylation arrays so cannot advise on specific limma settings for that type of data. Please follow the advice of the methy…
Comment: Light difference when using coef vs omit a group when compare 3 groups. by Chris • 0
Hi Gordon, thank you so much for further guidance! I discussed this issue with doctor know about Alzheimer and they don't expect significan…
Comment: Single-Cell Data Simulation from Bulk RNA-seq by wichaidi • 0
Hi - I am wondering what you decided to do. I am currently in a similar condition where I need to create a toy scRNAseq data from bulk.
Votes
Answer: How many of my genes from my gene list are in each KEGG pathway?
Comment: Light difference when using coef vs omit a group when compare 3 groups.
DESeq2 variance transformation error and plot dispersion Estimate
A: DESeq2 variance transformation error and plot dispersion Estimate
ensembl to hgnc symbols creates duplicates
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
United States, 10 minutes ago
France, 11 minutes ago
United States, 42 minutes ago
WEHI, Melbourne, Australia, 46 minutes ago
United States, 1 hour ago
Traffic: 434 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