Showing : scRNAseq • reset
2
votes
13
replies
2.2k
views
Running the DESeq2 "DESeqDataSetFromMatrix" function returns a dimname error
DESeq2 Scrna scRNAseq
2.8 years ago RDoc ▴ 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
1
vote
11
replies
3.4k
views
Error: Bioconductor version cannot be validated; no internet connection?
scRNAseq
updated 5 months ago by • 0 • written 10 months 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
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 Kelen ▴ 10
4
votes
7
replies
4.5k
views
removing rows from SingleCellExperiment container
sce singlecellexperiment scRNAseq subsetting
updated 5.3 years ago by ★ 28k • written 5.3 years ago by • 0
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
0
votes
6
replies
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 4.7 years ago by ▴ 670
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
1
vote
5
replies
838
views
Recommendation for large.n in filterByExpr
scRNAseq edgeR SingleCellExperiment
8 months ago duez.tolga • 0
0
votes
5
replies
1.5k
views
analysis of multiple time points * 2 replicates of scRNA-seq
scRNAseq
updated 4.2 years ago by ★ 28k • written 4.3 years ago by ▴ 670
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
4
votes
5
replies
1.4k
views
Pseudo-bulk celltype comparison across conditions from multiple-sources
DESeq2 edgeR scRNAseq
updated 13 months ago by ▴ 740 • written 13 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
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
4
replies
1.2k
views
Quality control of scRNA-seq data using mitochondrial ratio (drosophila)
Drosophila_melanogaster scRNAseq
21 months ago Chise ▴ 10
2
votes
4
replies
3.9k
views
differential expression for Single-cell RNAseq data using edgeR
edgeR single scRNAseq
2.8 years ago • updated 2.6 years ago mbenegas • 0
0
votes
4
replies
2.0k
views
how to make the "reconstructed" value in intergated scRNA-seq UMAP plot more readable
scater batchelor scRNAseq fastMNN
updated 20 months ago by ★ 28k • written 21 months ago by ▴ 40
2
votes
4
replies
1.2k
views
edgeR output doubts
logFC edgeR DifferentialExpression scRNAseq
2.7 years ago mbenegas • 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
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
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
0
votes
3
replies
1.5k
views
NA values for mitochondrial gene percentage
Seurat scRNAseq
2.4 years ago zahra.mesri95 • 0
0
votes
3
replies
1.0k
views
scRNA-seq: RS4' object has no attribute 'T'" in fastMNN R function
scanpy scRNAseq fastmnn r
18 months ago Madiha • 0
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
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
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
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
0
votes
3
replies
1.5k
views
MAST invalid Hypothesis, class objectORconnection error
R MAST scRNASeq
3.7 years ago TriS ▴ 200
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
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
2
replies
1.6k
views
PCA outliers cleaning
scRNAseq Pipeline Seurat SingleCellExperiment
4.5 years ago albadrs.93 ▴ 10
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
1
vote
2
replies
1.8k
views
install celldex in r4. 04
scRNAseq
written 3.1 years ago by • 0
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 ★ 4.0k • written 3.0 years ago by ▴ 10
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
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
2
replies
492
views
scRNA analysis : DEG between low and high-expressing cells
scRNAseq
6 months ago Momo • 0
0
votes
2
replies
890
views
Single-Cell Data Simulation from Bulk RNA-seq
SingleCell RNASeq RNASeqData scRNAseq
updated 9 days ago by • 0 • written 17 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
914
views
scRNAseq analysis on multiple datasets
scRNAseq
updated 2.6 years ago by ★ 1.3k • written 2.6 years ago by • 0
0
votes
2
replies
1.8k
views
calculateQCMetrics defunct, how to calculate the quality metrics by perCellQCMetrics
scRNAseq
updated 21 months ago by ★ 4.0k • written 22 months ago by • 0
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
1
vote
2
replies
781
views
ScRNAseq analysis scran :: quickcluster Error
scRNAseq quickcluster scRNA scran
4 months ago ruba-mahmoud • 0
0
votes
2
replies
671
views
Could not find function "Standard Chromosomes"
scrna scRNAseq
updated 6 months ago by • 0 • written 13 months ago by • 0
1
vote
2
replies
948
views
Combine scRNAseq data for bulk analysis using DESeq2
DESeq2 scRNAseq Fluidigm
18 months ago evocanres • 0
0
votes
2
replies
198
views
Non-empty droplets versus good quality cells
CellRanger emptyDrops scRNAseq 10X
5 weeks ago rocanja ▴ 60
50 results • Page 1 of 1
Recent ...
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Comment: Math expression in shapeCustom legend in EnhancedVolcano by pl23 • 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions by Michael Love 41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona ▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative? by Michael Love 41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Answer: ATACseq merge peaks by ATpoint ★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Votes
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
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