Showing : scRNAseq • reset
7
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3
replies
3.1k
views
Estimating cell size factors for single cell RNA-seq data
scrnaseq rnaseq normalization DESeq2
updated 6.8 years ago by 42k • written 6.8 years ago by ▴ 10
4
votes
3
replies
1.9k
views
using SC3 and scater for bulk-RNAseq
sc3 scater scRNAseq
updated 7.2 years ago by ▴ 150 • written 7.2 years ago by ★ 1.5k
1
vote
5
replies
889
views
Recommendation for large.n in filterByExpr
scRNAseq edgeR SingleCellExperiment
9 months ago duez.tolga • 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
8
votes
2
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1.7k
views
how can I annotate my scRNAseq clusters from a Rat experiment?
scRNAseq Rattus_norvegicus_Data annotation
updated 3.0 years ago by ★ 4.1k • written 3.0 years ago by ▴ 10
4
votes
5
replies
1.4k
views
RNA Seq analysis vs. Single cell RNA seq analysis
rnaseq scrnaseq edger
6.6 years ago • updated 6.5 years ago fawazfebin ▴ 60
3
votes
4
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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
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
0
votes
2
replies
702
views
Could not find function "Standard Chromosomes"
scrna scRNAseq
updated 7 months ago by • 0 • written 14 months ago by • 0
0
votes
1
reply
1.6k
views
Minimum number of cells required for the MAST
MAST scRNAseq differential expression
4.7 years ago Andrew_McDavid ▴ 270
0
votes
1
reply
401
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
0
votes
1
reply
428
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
2
replies
1.6k
views
PCA outliers cleaning
scRNAseq Pipeline Seurat SingleCellExperiment
4.5 years ago albadrs.93 ▴ 10
1
vote
2
replies
975
views
Combine scRNAseq data for bulk analysis using DESeq2
DESeq2 scRNAseq Fluidigm
19 months ago evocanres • 0
0
votes
5
replies
1.6k
views
analysis of multiple time points * 2 replicates of scRNA-seq
scRNAseq
updated 4.3 years ago by ★ 28k • written 4.3 years ago by ▴ 670
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
156
views
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
0
votes
2
replies
257
views
Non-empty droplets versus good quality cells
CellRanger emptyDrops scRNAseq 10X
9 weeks ago • updated 8 weeks ago rocanja ▴ 60
4
votes
1
reply
1.6k
views
Best practice for correlating scRNA seq to bulkRNA seq data
seurat edgeR spearman correlation scRNAseq
updated 4.1 years ago by ★ 28k • written 4.1 years ago by ▴ 10
1
vote
1
reply
1.4k
views
Question: Removal of mRNA contamination from scRNA-seq data using SoupX: How to proceed when "Extremely high contamination estimated"?
scRNAseq SoupX
updated 3.6 years ago by 66k • written 3.6 years ago by ▴ 10
1
vote
1
reply
1.0k
views
Combining treatment and control batches for analysis
scRNAseq scRNA batchelor BatchEffect
updated 3.5 years ago by ★ 28k • written 3.5 years ago by • 0
0
votes
2
replies
1.5k
views
Removal of cell cycle effect using batchelor::regressBatches() and proper usage of corrected UMI matrix
scRNAseq batchelor SingleCell SingleCellExperiment scran
3.4 years ago jirkanov • 0
0
votes
2
replies
1.9k
views
How to filter cells for scRNA-seq analysis based on expression level of surface marker?
scRNAseq
3.3 years ago Iris Wing To • 0
5
votes
6
replies
1.7k
views
DE Analysis on Scran-Normalized Counts
DifferentialExpression scRNAseq scran
updated 3.3 years ago by ★ 28k • written 3.3 years ago by • 0
2
votes
4
replies
1.2k
views
Does hashedDrops support 'imbalanced' combinations of HTOs?
DropletUtils scRNAseq
updated 3.2 years ago by ★ 28k • written 3.3 years ago by ▴ 740
5
votes
4
replies
2.2k
views
Using DESeq2 with GlmGamPoi
DESeq2 glmGamPoi scRNAseq
3.2 years ago tatyana.perlova • 0
1
vote
2
replies
1.9k
views
install celldex in r4. 04
scRNAseq
written 3.2 years ago by • 0
3
votes
9
replies
4.2k
views
Why does scran's computeSumFactors produce different size factors for cells with the exact same gene counts?
scran scater drop-seq scrnaseq
updated 7.1 years ago by ★ 28k • written 7.1 years ago by ▴ 10
0
votes
1
reply
1.3k
views
Removal of batch effects before non-linear clustering for scRNAseq
scrnaseq MAST
7.1 years ago Andrew_McDavid ▴ 270
0
votes
3
replies
1.4k
views
Modeling Dose-response data in MAST
MAST sc-rnaseq scrnaseq
updated 6.8 years ago by ▴ 270 • written 6.8 years 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
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
1
vote
5
replies
1.6k
views
computeSumFactors: warning about cluster size
scrnaseq scrn sizefactors
6.8 years ago sfpacman • 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
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
4
votes
1
reply
1.8k
views
NAs in continuous coefficient and fold change in `zlm`
scrnaseq MAST differential gene expression
6.8 years ago Andrew_McDavid ▴ 270
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
7
votes
3
replies
1.4k
views
Effect of feature number on adjusted p-values
edgeR DESeq2 single-cell scRNAseq zinbwave
updated 3.0 years ago by ★ 28k • written 3.0 years ago by ▴ 20
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
1
reply
586
views
library(topGO) query
topGO scRNAseq
updated 10 months ago by ▴ 780 • written 10 months ago by • 0
0
votes
3
replies
1.5k
views
NA values for mitochondrial gene percentage
Seurat scRNAseq
2.4 years ago zahra.mesri95 • 0
1
vote
3
replies
1.5k
views
Differential Expression analysis between distinct scRNA-seq datasets
scrna scrnaseq differential gene expression
updated 6.6 years ago by ▴ 950 • written 6.6 years ago by • 0
0
votes
2
replies
546
views
scRNA analysis : DEG between low and high-expressing cells
scRNAseq
7 months ago Momo • 0
0
votes
2
replies
960
views
Single-Cell Data Simulation from Bulk RNA-seq
SingleCell RNASeq RNASeqData scRNAseq
updated 4 weeks ago by • 0 • written 18 months ago by • 0
0
votes
2
replies
1.3k
views
BASiCS spike info for single cell RNA sequences or Bayesian statistics help
BASiCS bayesian single cell scrnaseq
updated 6.3 years ago by ▴ 10 • written 6.3 years ago by ▴ 10
0
votes
1
reply
862
views
Tool for simulating bulk RNA-Seq from single cell data
scRNAseq
updated 2.9 years ago by 66k • written 2.9 years ago by • 0
1
vote
11
replies
3.7k
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
2
replies
1.2k
views
How to deal with Expression set assembly problem?
deconvolution r scRNAseq bioinformatics
2.3 years ago Hasan Alanya • 0
1
vote
1
reply
2.0k
views
Mean Expression Calculation scRNA-seq (All cells or only Expressed Cells)
scrnaseq monocle
updated 6.0 years ago by ▴ 950 • written 6.0 years ago by ▴ 10
50 results • Page 1 of 1
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Answer: recount3 problem downloading data from source sra by Leonardo Collado Torres ★ 1.0k
Hi, I wasn't able to reproduce the issue on both bioc 3.19 (current release version) and 3.18 (closer to your session info). My guess is…
Answer: Running ENmix with mouse methylation manifest: readidat error - Error in readman by minardsmitha ▴ 10
Well it turns out there is a typo in the manifest file name. This particular issue is resolved by correcting the typo. A new error now …
Answer: Documenting resources in an `ExperimentHub` package? by James W. MacDonald 66k
The easiest way to do that IMO is to use emacs/ESS (or I believe there is some newfangled thing called RStudio? Not personally familiar, bu…
Comment: ChAMP installation issue by shepherl 3.9k
We are still waiting for the goseq to respond to our requests but will take action next week if it is not resolved. ChAMP is currently una…
Comment: How to arrange multiple plots into one page in NOISeq? by baptiste.bidon • 0
After facing the same problem, I realise that you can direct your plot in the matrix with the *par()* option `par(..., mfg = c(1,2))`. If i…
Votes
how to control age and gender effect in expression data using DESeq2
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?
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