Showing : scRNAseq • reset
2
votes
4
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169
views
edgeR output doubts
logFC edgeR DifferentialExpression scRNAseq
5 weeks ago • updated 4 weeks ago mbenegas • 0
0
votes
1
reply
96
views
Identify a scRNASeq cell-population using a bulk RNA Seq dataset of that population?
RNASeq rnaseq scRNAseq
updated 5 weeks ago by ★ 27k • written 5 weeks ago by • 0
0
votes
0
replies
73
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Correlation plot using the count data from seurat object
scRNAseq
7 weeks ago Sam • 0
2
votes
4
replies
276
views
differential expression for Single-cell RNAseq data using edgeR
edgeR single scRNAseq
8 weeks ago • updated 14 days ago mbenegas • 0
1
vote
13
replies
263
views
Running the DESeq2 "DESeqDataSetFromMatrix" function returns a dimname error
DESeq2 Scrna scRNAseq
8 weeks ago RDoc • 0
0
votes
1
reply
124
views
Tool for simulating bulk RNA-Seq from single cell data
scRNAseq
updated 11 weeks ago by 58k • written 11 weeks ago by • 0
0
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0
replies
80
views
Using csClassify on a SeuratObject
scRNAseq csClassify Seurat
updated 3 months ago by ▴ 830 • written 3 months ago by • 0
4
votes
3
replies
262
views
Effect of feature number on adjusted p-values
edgeR DESeq2 single-cell scRNAseq zinbwave
updated 4 months ago by ★ 27k • written 4 months ago by ▴ 20
6
votes
2
replies
236
views
how can I annotate my scRNAseq clusters from a Rat experiment?
scRNAseq Rattus_norvegicus_Data annotation
updated 4 months ago by ▴ 830 • written 4 months ago by • 0
1
vote
2
replies
363
views
install celldex in r4. 04
scRNAseq
written 6 months ago by • 0
5
votes
4
replies
318
views
Using DESeq2 with GlmGamPoi
DESeq2 glmGamPoi scRNAseq
6 months ago tatyana.perlova • 0
2
votes
4
replies
254
views
Does hashedDrops support 'imbalanced' combinations of HTOs?
DropletUtils scRNAseq
updated 6 months ago by ★ 27k • written 7 months ago by ▴ 470
3
votes
6
replies
381
views
DE Analysis on Scran-Normalized Counts
DifferentialExpression scRNAseq scran
updated 7 months ago by ★ 27k • written 7 months ago by • 0
0
votes
2
replies
203
views
How to filter cells for scRNA-seq analysis based on expression level of surface marker?
scRNAseq
8 months ago • updated 7 months ago Iris Wing To • 0
0
votes
2
replies
296
views
Removal of cell cycle effect using batchelor::regressBatches() and proper usage of corrected UMI matrix
scRNAseq batchelor SingleCell SingleCellExperiment scran
9 months ago jirkanov • 0
1
vote
1
reply
249
views
Combining treatment and control batches for analysis
scRNAseq scRNA batchelor BatchEffect
updated 10 months ago by ★ 27k • written 10 months ago by • 0
1
vote
1
reply
256
views
Question: Removal of mRNA contamination from scRNA-seq data using SoupX: How to proceed when "Extremely high contamination estimated"?
scRNAseq SoupX
updated 10 months ago by 58k • written 10 months ago by ▴ 10
0
votes
3
replies
566
views
MAST invalid Hypothesis, class objectORconnection error
R MAST scRNASeq
13 months ago TriS ▴ 200
4
votes
1
reply
252
views
Best practice for correlating scRNA seq to bulkRNA seq data
seurat edgeR spearman correlation scRNAseq
updated 17 months ago by ★ 27k • written 17 months ago by • 0
1
vote
0
replies
218
views
News: News: Bioinformatics Summer School - July 2020 - UCLouvain (Belgium)
rnaseq course proteomics transcriptomics scrnaseq News
19 months ago Laurent Gatto 1.5k
0
votes
5
replies
628
views
analysis of multiple time points * 2 replicates of scRNA-seq
scRNAseq
updated 19 months ago by ★ 27k • written 19 months ago by ▴ 620
0
votes
2
replies
342
views
PCA outliers cleaning
scRNAseq Pipeline Seurat SingleCellExperiment
22 months ago albadrs.93 ▴ 10
0
votes
1
reply
314
views
Minimum number of cells required for the MAST
MAST scRNAseq differential expression
2.0 years ago Andrew_McDavid ▴ 260
0
votes
6
replies
791
views
analysis of multiple batches and multiple treatment conditions in scRNA-seq
limma deseq2 edger scRNAseq combat
updated 2.1 years ago by ▴ 260 • written 2.1 years ago by ▴ 620
3
votes
7
replies
1.0k
views
removing rows from SingleCellExperiment container
sce singlecellexperiment scRNAseq subsetting
updated 2.7 years ago by ★ 27k • written 2.7 years ago by • 0
2
votes
6
replies
580
views
Change the number of clusters with scater
scater scran scrnaseq clustering
updated 2.8 years ago by ★ 27k • written 2.8 years ago by ▴ 10
0
votes
1
reply
472
views
RNAseq scater error in plotQC()
scater plotQC scRNAseq
updated 3.1 years ago by ★ 27k • written 3.1 years ago by ▴ 90
6
votes
12
replies
1.8k
views
Merging RNAseq Datasets of Different Depths
singlecellexperiment scran sequencing depth batch effect scrnaseq
updated 3.2 years ago by ★ 27k • written 3.2 years ago by • 0
1
vote
1
reply
515
views
Mean Expression Calculation scRNA-seq (All cells or only Expressed Cells)
scrnaseq monocle
updated 3.4 years ago by ▴ 870 • written 3.4 years ago by ▴ 10
0
votes
2
replies
543
views
BASiCS spike info for single cell RNA sequences or Bayesian statistics help
BASiCS bayesian single cell scrnaseq
updated 3.6 years ago by ▴ 10 • written 3.6 years ago by ▴ 10
4
votes
5
replies
666
views
RNA Seq analysis vs. Single cell RNA seq analysis
rnaseq scrnaseq edger
3.9 years ago fawazfebin ▴ 30
1
vote
3
replies
622
views
Differential Expression analysis between distinct scRNA-seq datasets
scrna scrnaseq differential gene expression
updated 3.9 years ago by ▴ 870 • written 3.9 years ago by • 0
4
votes
1
reply
921
views
NAs in continuous coefficient and fold change in `zlm`
scrnaseq MAST differential gene expression
4.1 years ago Andrew_McDavid ▴ 260
1
vote
5
replies
934
views
computeSumFactors: warning about cluster size
scrnaseq scrn sizefactors
4.1 years ago sfpacman • 0
7
votes
3
replies
1.9k
views
Estimating cell size factors for single cell RNA-seq data
scrnaseq rnaseq normalization DESeq2
updated 4.1 years ago by 34k • written 4.1 years ago by ▴ 10
0
votes
3
replies
654
views
Modeling Dose-response data in MAST
MAST sc-rnaseq scrnaseq
updated 4.1 years ago by ▴ 260 • written 4.2 years ago by • 0
0
votes
1
reply
681
views
Removal of batch effects before non-linear clustering for scRNAseq
scrnaseq MAST
4.4 years ago Andrew_McDavid ▴ 260
3
votes
9
replies
2.2k
views
Why does scran's computeSumFactors produce different size factors for cells with the exact same gene counts?
scran scater drop-seq scrnaseq
updated 4.4 years ago by ★ 27k • written 4.4 years ago by ▴ 10
4
votes
3
replies
1.2k
views
using SC3 and scater for bulk-RNAseq
sc3 scater scRNAseq
updated 4.5 years ago by ▴ 150 • written 4.5 years ago by ★ 1.5k
39 results • Page 1 of 1
Recent ...
Replies
Answer: Error in makeTxDbFromGFF(txomeInfo$gtf) by Michael Love 34k
I see that tximeta found a linked transcriptome. Can you show this part of your code as well? How did you create the `linkedTxome`?
Comment: EdgeR, tumor normal pair, no replicatie but multiple patients, to focus on indi by Gordon Smyth 43k
You need to start by doing an ordinary paired analysis.
Comment: Recalculated abundance data output table with DEseq2 by Michael Love 34k
Yes, DESeq() then results(). When you print the table it will say MLE. No we don’t have a function to do that.
Comment: Recalculated abundance data output table with DEseq2 by michael.morash • 0
Thanks for getting back to me so quickly. The final comparison we are looking to report are the effects of filtering out low count genes us…
Comment: EdgeR, tumor normal pair, no replicatie but multiple patients, to focus on indi by Field -Ye • 0
Hi Professor Smyth, Thank you for pointing me to your previous publication. I went through the verbal part and found you did pursue the DG…
Votes
Answer: Degust: what normalization method does it use
Answer: ylim and xlim in Enhanced Volcano
Answer: EdgeR, tumor normal pair, no replicatie but multiple patients, to focus on indi
Error in .rowNamesDF<-(x, value = value) :duplicate row.names are not allowed DESeq2
Comment: How to build a GRangesList where each GRanges element is a CDS coordinate of gen
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