Showing : scRNASeq • reset
7
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3
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3.1k
views
Estimating cell size factors for single cell RNA-seq data
scrnaseq rnaseq normalization DESeq2
updated 6.7 years ago by 42k • written 6.7 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
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
8
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2
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1.6k
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
2
votes
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
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
1
vote
5
replies
861
views
Recommendation for large.n in filterByExpr
scRNAseq edgeR SingleCellExperiment
9 months ago • updated 8 months ago duez.tolga • 0
0
votes
1
reply
1.0k
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
686
views
Could not find function "Standard Chromosomes"
scrna scRNAseq
updated 6 months ago by • 0 • written 14 months ago by • 0
0
votes
6
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1.8k
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 4.8 years ago by ▴ 670
0
votes
1
reply
389
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
420
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
1.6k
views
Minimum number of cells required for the MAST
MAST scRNAseq differential expression
4.7 years ago Andrew_McDavid ▴ 270
1
vote
2
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964
views
Combine scRNAseq data for bulk analysis using DESeq2
DESeq2 scRNAseq Fluidigm
19 months ago • updated 18 months ago evocanres • 0
0
votes
2
replies
1.6k
views
PCA outliers cleaning
scRNAseq Pipeline Seurat SingleCellExperiment
4.5 years ago albadrs.93 ▴ 10
4
votes
3
replies
1.0k
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
143
views
Can you find the correct transcript in scRNA seq data
scRNAseq RNAseq
updated 28 days ago by ★ 4.1k • written 4 weeks ago by • 0
0
votes
2
replies
219
views
Non-empty droplets versus good quality cells
CellRanger emptyDrops scRNAseq 10X
7 weeks ago rocanja ▴ 60
0
votes
5
replies
1.5k
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
1
reply
1.6k
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
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 3.5 years ago by 65k • written 3.5 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
1.4k
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
1.6k
views
DE Analysis on Scran-Normalized Counts
DifferentialExpression scRNAseq scran
updated 3.2 years ago by ★ 28k • written 3.2 years ago by • 0
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 ▴ 740
5
votes
4
replies
2.1k
views
Using DESeq2 with GlmGamPoi
DESeq2 glmGamPoi scRNAseq
3.2 years ago • updated 3.1 years ago tatyana.perlova • 0
1
vote
2
replies
1.9k
views
install celldex in r4. 04
scRNAseq
written 3.1 years ago by • 0
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 7.1 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
7.0 years ago Andrew_McDavid ▴ 270
0
votes
3
replies
1.4k
views
Modeling Dose-response data in MAST
MAST sc-rnaseq scrnaseq
updated 6.8 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
6.7 years ago sfpacman • 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 ▴ 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 • updated 2.0 years ago Ismail • 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 2.8 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
21 months ago Chise ▴ 10
0
votes
1
reply
570
views
library(topGO) query
topGO scRNAseq
updated 9 months ago by ▴ 780 • written 9 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
4
votes
1
reply
1.8k
views
NAs in continuous coefficient and fold change in `zlm`
scrnaseq MAST differential gene expression
6.7 years ago Andrew_McDavid ▴ 270
0
votes
2
replies
517
views
scRNA analysis : DEG between low and high-expressing cells
scRNAseq
7 months ago Momo • 0
0
votes
2
replies
926
views
Single-Cell Data Simulation from Bulk RNA-seq
SingleCell RNASeq RNASeqData scRNAseq
updated 21 days ago by • 0 • written 17 months 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
0
votes
1
reply
850
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
1
vote
11
replies
3.5k
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
2.2 years ago Hasan Alanya • 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
50 results • Page 1 of 1
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Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 42k
> Any suggestions for methylation data segmentation? I think the same segmentation can be used.
Comment: deseq2 results by swbarnes2 ★ 1.3k
Cross-posted https://www.biostars.org/p/9594331/#9594458
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it by Mike Smith ★ 6.5k
The other answers here are all good and demonstrate the issue with floating point comparisons nicely. I'd like to add that your particular…
Comment: More regions in union when increasing DBA$config$mergeOverlap by Ian D. ▴ 70
Nudging my question. I could do with confirmation before proceeding with my current projects. Thank you.
Comment: Extremely small p-values using Limma for proteomic data by Robert Castelo ★ 3.3k
From the point of view of visualization, I find handy the fact that raw p-values give more resolution than adjusted ones, which allows one …
Votes
A: Volcanoplot with limma - RAW P-values or Adj.P-Values
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Answer: minfi latest update for EPIC V2 chip
A: Error in DESeqDataSet : some values in assay are not integers
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