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 41k • written 6.7 years ago by ▴ 10
4
votes
3
replies
1.8k
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
votes
5
replies
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
votes
2
replies
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
854
views
Recommendation for large.n in filterByExpr
scRNAseq edgeR SingleCellExperiment
8 months ago duez.tolga • 0
0
votes
1
reply
1.0k
views
DESeq2 error after installing BiocManager
scRNAseq RStudio DESeq2
updated 8 months ago by ★ 4.1k • written 8 months ago by • 0
0
votes
2
replies
683
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
387
views
FALSE error when checking a pre made sample data
Rstudio scRNAseq DESeq2
updated 8 months ago by ★ 4.1k • written 8 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
replies
962
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
138
views
Can you find the correct transcript in scRNA seq data
scRNAseq RNAseq
updated 24 days ago by ★ 4.1k • written 26 days ago by • 0
0
votes
2
replies
212
views
Non-empty droplets versus good quality cells
CellRanger emptyDrops scRNAseq 10X
6 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
1.5k
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
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
3.1 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 7.0 years ago by ★ 28k • written 7.0 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 • updated 10 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
2.0 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 2.7 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
565
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
511
views
scRNA analysis : DEG between low and high-expressing cells
scRNAseq
7 months ago Momo • 0
0
votes
2
replies
915
views
Single-Cell Data Simulation from Bulk RNA-seq
SingleCell RNASeq RNASeqData scRNAseq
updated 17 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
849
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 6.2 years ago by ▴ 10 • written 6.2 years ago by ▴ 10
50 results • Page 1 of 1
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Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2 by Kim • 0
Thank you Tim, this is a great help in getting me started!
Votes
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
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