Showing : scRNASeq • reset
2
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2
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1.9k
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How to deal with Expression set assembly problem?
deconvolution r scRNAseq bioinformatics
3.7 years ago Hasan Alanya • 0
0
votes
1
reply
1.6k
views
Aberrant number of cells
CellBarcode DropletUtils emptyDrops() Cellranger scRNAseq
updated 3.4 years ago by ▴ 20 • written 3.7 years ago by • 0
0
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0
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1.3k
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Job: Postdoc Opening in Bioinformatics or Computational Biology
SpatialData scRNAseq SingleCell Omixer
3.7 years ago Sebastian Lewandowski • 0
0
votes
3
replies
2.1k
views
NA values for mitochondrial gene percentage
Seurat scRNAseq
3.8 years ago zahra.mesri95 • 0
0
votes
0
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972
views
scRNA technical replicates in separate runs
SingleCellExperiment scRNAseq
3.9 years ago • updated 3.8 years ago Núria • 0
0
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2
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1.5k
views
scRNAseq analysis on multiple datasets
scRNAseq
updated 4.0 years ago by ★ 1.4k • written 4.0 years ago by • 0
2
votes
4
replies
1.9k
views
edgeR output doubts
logFC edgeR DifferentialExpression scRNAseq
4.2 years ago mbenegas ▴ 10
0
votes
1
reply
1.7k
views
Identify a scRNASeq cell-population using a bulk RNA Seq dataset of that population?
RNASeq rnaseq scRNAseq
updated 4.2 years ago by ★ 29k • written 4.2 years ago by ▴ 10
0
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0
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1.1k
views
Correlation plot using the count data from seurat object
scRNAseq
4.2 years ago Sam • 0
3
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4
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5.7k
views
differential expression for Single-cell RNAseq data using edgeR
edgeR single scRNAseq
4.2 years ago • updated 4.1 years ago mbenegas ▴ 10
2
votes
13
replies
3.5k
views
Running the DESeq2 "DESeqDataSetFromMatrix" function returns a dimname error
DESeq2 Scrna scRNAseq
4.2 years ago RDoc ▴ 10
0
votes
1
reply
1.3k
views
Tool for simulating bulk RNA-Seq from single cell data
scRNAseq
updated 4.3 years ago by 68k • written 4.3 years ago by • 0
0
votes
0
replies
953
views
Using csClassify on a SeuratObject
scRNAseq csClassify Seurat
updated 4.4 years ago by ★ 4.9k • written 4.4 years ago by ▴ 10
7
votes
3
replies
2.1k
views
Effect of feature number on adjusted p-values
edgeR DESeq2 single-cell scRNAseq zinbwave
updated 4.4 years ago by ★ 29k • written 4.4 years ago by ▴ 20
8
votes
2
replies
2.5k
views
how can I annotate my scRNAseq clusters from a Rat experiment?
scRNAseq Rattus_norvegicus_Data annotation
updated 4.4 years ago by ★ 4.9k • written 4.4 years ago by ▴ 10
1
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2
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2.7k
views
install celldex in r4. 04
scRNAseq
written 4.6 years ago by • 0
5
votes
4
replies
3.2k
views
Using DESeq2 with GlmGamPoi
DESeq2 glmGamPoi scRNAseq
4.6 years ago tatyana.perlova • 0
2
votes
4
replies
1.8k
views
Does hashedDrops support 'imbalanced' combinations of HTOs?
DropletUtils scRNAseq
updated 4.6 years ago by ★ 29k • written 4.6 years ago by ▴ 760
5
votes
6
replies
2.6k
views
DE Analysis on Scran-Normalized Counts
DifferentialExpression scRNAseq scran
updated 4.6 years ago by ★ 29k • written 4.6 years ago by • 0
0
votes
2
replies
3.0k
views
How to filter cells for scRNA-seq analysis based on expression level of surface marker?
scRNAseq
4.7 years ago Iris Wing To • 0
0
votes
2
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2.0k
views
Removal of cell cycle effect using batchelor::regressBatches() and proper usage of corrected UMI matrix
scRNAseq batchelor SingleCell SingleCellExperiment scran
4.8 years ago jirkanov • 0
1
vote
1
reply
1.5k
views
Combining treatment and control batches for analysis
scRNAseq scRNA batchelor BatchEffect
updated 4.9 years ago by ★ 29k • written 4.9 years ago by • 0
1
vote
1
reply
2.0k
views
Question: Removal of mRNA contamination from scRNA-seq data using SoupX: How to proceed when "Extremely high contamination estimated"?
scRNAseq SoupX
updated 4.9 years ago by 68k • written 4.9 years ago by ▴ 10
0
votes
3
replies
2.0k
views
MAST invalid Hypothesis, class objectORconnection error
R MAST scRNASeq
5.1 years ago TriS ▴ 200
5
votes
1
reply
2.3k
views
Best practice for correlating scRNA seq to bulkRNA seq data
seurat edgeR spearman correlation scRNAseq
updated 5.5 years ago by ★ 29k • written 5.5 years ago by ▴ 20
1
vote
0
replies
1.4k
views
News: News: Bioinformatics Summer School - July 2020 - UCLouvain (Belgium)
rnaseq course proteomics transcriptomics scrnaseq News
5.7 years ago Laurent Gatto 1.6k
0
votes
5
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2.0k
views
analysis of multiple time points * 2 replicates of scRNA-seq
scRNAseq
updated 5.7 years ago by ★ 29k • written 5.7 years ago by ▴ 670
0
votes
2
replies
2.2k
views
PCA outliers cleaning
scRNAseq Pipeline Seurat SingleCellExperiment
5.9 years ago albadrs.93 ▴ 10
0
votes
1
reply
2.6k
views
Minimum number of cells required for the MAST
MAST scRNAseq differential expression
6.1 years ago Andrew_McDavid ▴ 280
0
votes
6
replies
2.3k
views
analysis of multiple batches and multiple treatment conditions in scRNA-seq
limma deseq2 edger scRNAseq combat
updated 6.2 years ago by ▴ 280 • written 6.2 years ago by ▴ 670
4
votes
7
replies
6.1k
views
removing rows from SingleCellExperiment container
sce singlecellexperiment scRNAseq subsetting
updated 6.8 years ago by ★ 29k • written 6.8 years ago by • 0
2
votes
6
replies
2.4k
views
Change the number of clusters with scater
scater scran scrnaseq clustering
updated 6.9 years ago by ★ 29k • written 6.9 years ago by ▴ 20
0
votes
1
reply
1.2k
views
RNAseq scater error in plotQC()
scater plotQC scRNAseq
updated 7.2 years ago by ★ 29k • written 7.2 years ago by ▴ 90
6
votes
12
replies
5.2k
views
Merging RNAseq Datasets of Different Depths
singlecellexperiment scran sequencing depth batch effect scrnaseq
updated 7.3 years ago by ★ 29k • written 7.3 years ago by • 0
1
vote
1
reply
3.3k
views
Mean Expression Calculation scRNA-seq (All cells or only Expressed Cells)
scrnaseq monocle
updated 7.4 years ago by ▴ 980 • written 7.4 years ago by ▴ 10
0
votes
2
replies
1.8k
views
BASiCS spike info for single cell RNA sequences or Bayesian statistics help
BASiCS bayesian single cell scrnaseq
updated 7.7 years ago by ▴ 10 • written 7.7 years ago by ▴ 10
4
votes
5
replies
2.1k
views
RNA Seq analysis vs. Single cell RNA seq analysis
rnaseq scrnaseq edger
8.0 years ago • updated 7.9 years ago fawazfebin ▴ 60
1
vote
3
replies
2.2k
views
Differential Expression analysis between distinct scRNA-seq datasets
scrna scrnaseq differential gene expression
updated 7.9 years ago by ▴ 980 • written 7.9 years ago by • 0
4
votes
1
reply
2.4k
views
NAs in continuous coefficient and fold change in `zlm`
scrnaseq MAST differential gene expression
8.1 years ago Andrew_McDavid ▴ 280
1
vote
5
replies
2.1k
views
computeSumFactors: warning about cluster size
scrnaseq scrn sizefactors
8.2 years ago sfpacman • 0
7
votes
3
replies
3.9k
views
Estimating cell size factors for single cell RNA-seq data
scrnaseq rnaseq normalization DESeq2
updated 8.2 years ago by 43k • written 8.2 years ago by ▴ 10
0
votes
3
replies
2.0k
views
Modeling Dose-response data in MAST
MAST sc-rnaseq scrnaseq
updated 8.2 years ago by ▴ 280 • written 8.2 years ago by • 0
0
votes
1
reply
1.7k
views
Removal of batch effects before non-linear clustering for scRNAseq
scrnaseq MAST
8.4 years ago Andrew_McDavid ▴ 280
3
votes
9
replies
5.4k
views
Why does scran's computeSumFactors produce different size factors for cells with the exact same gene counts?
scran scater drop-seq scrnaseq
updated 8.5 years ago by ★ 29k • written 8.5 years ago by ▴ 10
4
votes
3
replies
2.4k
views
using SC3 and scater for bulk-RNAseq
sc3 scater scRNAseq
updated 8.6 years ago by ▴ 150 • written 8.6 years ago by ★ 1.5k
95 results • Page 2 of 2
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Comment: Streamlining the computing time for MiloDE p-value correction in large dataset? by ATpoint ★ 4.9k
Is a method that is so computationally expensive really beneficial and necessary? You seem to have biological replication, don't you, so ps…
Answer: NA values for DESeq2 p-values and adjusted p-values using large sample sizes by ATpoint ★ 4.9k
Outliers without replacement, independent filtering or all-zero counts for that gene. That's the three options that trigger NAs https://bio…
Comment: R course in Boston December 19-20 by eja.gaasa2e.r.m • 0
The upcoming XLSolutions R course in Boston on December 19 20 is a great opportunity to enhance your data skills. Whether you re a beginner…
Answer: Gatins Set error by James W. MacDonald 68k
`GatingSet` isn't a function in `flowCore`. It is however in `flowWorkspace`, which you would need to load first.
Answer: How to model DE for RNA-seq in concordant monozygotic twins? by Gordon Smyth 53k
Your question is more about science than it is about software syntax, and I can't give advice about how to conduct a scientific analysis, n…
Votes
Comment: incomplete imputation of missing values with LEA impute() function
Answer: Expected memory usage for analyzing large single-cell seq datasets (> 450,000 ce
Answer: ordinary t from limma [was: How would I normally compare swirl?]
Comment: readDNAStringSet with non DNA characters
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
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