Showing : scRNAseq • reset
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unbalanced cell count and unbalanced read count across samples in pseudobulk differential expression analysis using scRNA-seq data
scRNAseq DifferentialExpression DESeq2
25 days ago • updated 20 days ago Ismail • 0
1
vote
1
reply
96
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Can we use 'SCT normalization' to find anchors and 'LogNormalize' for the integration?
Normalization scRNAseq
updated 6 weeks ago by ▴ 550 • written 6 weeks ago by • 0
2
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2
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229
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scuttle:: librarySizeFactors returning non-finite values
normalizeCounts scran librarySizeFactors scuttle scRNAseq
11 weeks ago behr201 • 0
2
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2
replies
245
views
How to deal with Expression set assembly problem?
deconvolution r scRNAseq bioinformatics
3 months ago Hasan Alanya • 0
0
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1
reply
145
views
Aberrant number of cells
CellBarcode DropletUtils emptyDrops() Cellranger scRNAseq
updated 11 days ago by ▴ 20 • written 3 months ago by • 0
0
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0
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229
views
Job: Postdoc Opening in Bioinformatics or Computational Biology
SpatialData scRNAseq SingleCell Omixer
3 months ago Sebastian Lewandowski • 0
0
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3
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304
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NA values for mitochondrial gene percentage
Seurat scRNAseq
5 months ago zahra.mesri95 • 0
0
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0
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120
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scRNA technical replicates in separate runs
SingleCellExperiment scRNAseq
5 months ago Núria • 0
0
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2
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233
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scRNAseq analysis on multiple datasets
scRNAseq
updated 7 months ago by ★ 1.0k • written 7 months ago by • 0
2
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4
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375
views
edgeR output doubts
logFC edgeR DifferentialExpression scRNAseq
9 months ago mbenegas • 0
0
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1
reply
374
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Identify a scRNASeq cell-population using a bulk RNA Seq dataset of that population?
RNASeq rnaseq scRNAseq
updated 9 months ago by ★ 27k • written 9 months ago by • 0
0
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0
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167
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Correlation plot using the count data from seurat object
scRNAseq
9 months ago Sam • 0
2
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4
replies
778
views
differential expression for Single-cell RNAseq data using edgeR
edgeR single scRNAseq
9 months ago • updated 8 months ago mbenegas • 0
2
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13
replies
668
views
Running the DESeq2 "DESeqDataSetFromMatrix" function returns a dimname error
DESeq2 Scrna scRNAseq
9 months ago RDoc ▴ 10
0
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1
reply
277
views
Tool for simulating bulk RNA-Seq from single cell data
scRNAseq
updated 10 months ago by 59k • written 10 months ago by • 0
0
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0
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174
views
Using csClassify on a SeuratObject
scRNAseq csClassify Seurat
updated 11 months ago by ★ 1.2k • written 12 months ago by • 0
4
votes
3
replies
451
views
Effect of feature number on adjusted p-values
edgeR DESeq2 single-cell scRNAseq zinbwave
updated 12 months ago by ★ 27k • written 12 months ago by ▴ 20
6
votes
2
replies
451
views
how can I annotate my scRNAseq clusters from a Rat experiment?
scRNAseq Rattus_norvegicus_Data annotation
updated 12 months ago by ★ 1.2k • written 12 months ago by • 0
1
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2
replies
720
views
install celldex in r4. 04
scRNAseq
written 14 months ago by • 0
5
votes
4
replies
637
views
Using DESeq2 with GlmGamPoi
DESeq2 glmGamPoi scRNAseq
14 months ago tatyana.perlova • 0
2
votes
4
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428
views
Does hashedDrops support 'imbalanced' combinations of HTOs?
DropletUtils scRNAseq
updated 14 months ago by ★ 27k • written 15 months ago by ▴ 550
5
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6
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613
views
DE Analysis on Scran-Normalized Counts
DifferentialExpression scRNAseq scran
updated 15 months ago by ★ 27k • written 15 months ago by • 0
0
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2
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404
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How to filter cells for scRNA-seq analysis based on expression level of surface marker?
scRNAseq
16 months ago • updated 15 months ago Iris Wing To • 0
0
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2
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522
views
Removal of cell cycle effect using batchelor::regressBatches() and proper usage of corrected UMI matrix
scRNAseq batchelor SingleCell SingleCellExperiment scran
17 months ago jirkanov • 0
1
vote
1
reply
406
views
Combining treatment and control batches for analysis
scRNAseq scRNA batchelor BatchEffect
updated 18 months ago by ★ 27k • written 18 months ago by • 0
1
vote
1
reply
454
views
Question: Removal of mRNA contamination from scRNA-seq data using SoupX: How to proceed when "Extremely high contamination estimated"?
scRNAseq SoupX
updated 18 months ago by 59k • written 18 months ago by ▴ 10
0
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3
replies
766
views
MAST invalid Hypothesis, class objectORconnection error
R MAST scRNASeq
21 months ago TriS ▴ 200
4
votes
1
reply
475
views
Best practice for correlating scRNA seq to bulkRNA seq data
seurat edgeR spearman correlation scRNAseq
updated 2.1 years ago by ★ 27k • written 2.1 years ago by ▴ 10
1
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0
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419
views
News: News: Bioinformatics Summer School - July 2020 - UCLouvain (Belgium)
rnaseq course proteomics transcriptomics scrnaseq News
2.3 years ago Laurent Gatto 1.5k
0
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5
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843
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analysis of multiple time points * 2 replicates of scRNA-seq
scRNAseq
updated 2.3 years ago by ★ 27k • written 2.3 years ago by ▴ 640
0
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2
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522
views
PCA outliers cleaning
scRNAseq Pipeline Seurat SingleCellExperiment
2.5 years ago albadrs.93 ▴ 10
0
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1
reply
578
views
Minimum number of cells required for the MAST
MAST scRNAseq differential expression
2.7 years ago Andrew_McDavid ▴ 260
0
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6
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980
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analysis of multiple batches and multiple treatment conditions in scRNA-seq
limma deseq2 edger scRNAseq combat
updated 2.8 years ago by ▴ 260 • written 2.8 years ago by ▴ 640
4
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7
replies
1.7k
views
removing rows from SingleCellExperiment container
sce singlecellexperiment scRNAseq subsetting
updated 3.4 years ago by ★ 27k • written 3.4 years ago by • 0
2
votes
6
replies
779
views
Change the number of clusters with scater
scater scran scrnaseq clustering
updated 3.5 years ago by ★ 27k • written 3.5 years ago by ▴ 20
0
votes
1
reply
579
views
RNAseq scater error in plotQC()
scater plotQC scRNAseq
updated 3.8 years ago by ★ 27k • written 3.8 years ago by ▴ 90
6
votes
12
replies
2.2k
views
Merging RNAseq Datasets of Different Depths
singlecellexperiment scran sequencing depth batch effect scrnaseq
updated 3.9 years ago by ★ 27k • written 3.9 years ago by • 0
1
vote
1
reply
718
views
Mean Expression Calculation scRNA-seq (All cells or only Expressed Cells)
scrnaseq monocle
updated 4.0 years ago by ▴ 890 • written 4.0 years ago by ▴ 10
0
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2
replies
651
views
BASiCS spike info for single cell RNA sequences or Bayesian statistics help
BASiCS bayesian single cell scrnaseq
updated 4.3 years ago by ▴ 10 • written 4.3 years ago by ▴ 10
4
votes
5
replies
782
views
RNA Seq analysis vs. Single cell RNA seq analysis
rnaseq scrnaseq edger
4.6 years ago • updated 4.5 years ago fawazfebin ▴ 30
1
vote
3
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741
views
Differential Expression analysis between distinct scRNA-seq datasets
scrna scrnaseq differential gene expression
updated 4.5 years ago by ▴ 890 • written 4.5 years ago by • 0
4
votes
1
reply
1.1k
views
NAs in continuous coefficient and fold change in `zlm`
scrnaseq MAST differential gene expression
4.8 years ago Andrew_McDavid ▴ 260
1
vote
5
replies
1.1k
views
computeSumFactors: warning about cluster size
scrnaseq scrn sizefactors
4.8 years ago sfpacman • 0
7
votes
3
replies
2.2k
views
Estimating cell size factors for single cell RNA-seq data
scrnaseq rnaseq normalization DESeq2
updated 4.8 years ago by 36k • written 4.8 years ago by ▴ 10
0
votes
3
replies
794
views
Modeling Dose-response data in MAST
MAST sc-rnaseq scrnaseq
updated 4.8 years ago by ▴ 260 • written 4.8 years ago by • 0
0
votes
1
reply
770
views
Removal of batch effects before non-linear clustering for scRNAseq
scrnaseq MAST
5.0 years ago Andrew_McDavid ▴ 260
3
votes
9
replies
2.6k
views
Why does scran's computeSumFactors produce different size factors for cells with the exact same gene counts?
scran scater drop-seq scrnaseq
updated 5.1 years ago by ★ 27k • written 5.1 years ago by ▴ 10
4
votes
3
replies
1.3k
views
using SC3 and scater for bulk-RNAseq
sc3 scater scRNAseq
updated 5.2 years ago by ▴ 150 • written 5.2 years ago by ★ 1.5k
48 results • Page 1 of 1
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Comment: Ensembl plants at annotationHub? by karenserrano • 0
Hi Johannes, Could I request the same EnsDb creation for Medicago truncatula? Thank you very much, Karen
Answer: EnrichGO not working with db created from annotationhub by Guido Hooiveld ★ 3.2k
Did you notice the first message that was returned after you ran `enrichGO()`? Thus: `--> No gene can be mapped....` This basically means…
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Hello my friends, I have exactly the same issue. May I ask if you have already solve this problem? I have tried `library(BiocParallel) regi…
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Yes we are currently working on generating a small example for cellCounts.
Comment: Separate exogenous from endogenous transcripts using Salmon RNAseq DTU by ksong • 0
Hi Dr Sudbery, yes I found looking at the coverage in IGV helps a lot. I did find some differences between CDS and UTR and between samples.…
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Comment: Separate exogenous from endogenous transcripts using Salmon RNAseq DTU
C: Appropriate pre-processing pipeline for Human Transcriptome Array HTA 2.0 with o
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Answer: Handling NA values in limma's voom design matrix
Answer: Handling NA values in limma's voom design matrix
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