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scRNA
•
reset
1
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2
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560
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ScRNAseq analysis scran :: quickcluster Error
scRNAseq
quickcluster
scRNA
scran
3 months ago
ruba-mahmoud
• 0
4
votes
3
replies
967
views
Custom design for scRNA DGE with pseudobulking
scRNAseq
scrna
paireddesign
edgeR
pseudobulking
updated 7 months ago by
Gordon Smyth
50k • written 7 months ago by
garcia
• 0
0
votes
1
reply
355
views
If highly-expressed genes are upregulated, what happens to genes with lower expression after normalization?
scRNA
scRNAseq
updated 7 months ago by
ATpoint
★ 3.9k • written 7 months ago by
Omer
• 0
0
votes
2
replies
609
views
Could not find function "Standard Chromosomes"
scrna
scRNAseq
updated 4 months ago by
Gabriella
• 0 • written 12 months ago by
sarah.jobbins
• 0
1
vote
0
replies
575
views
Use scran's normalization by deconvolution for each individual sample or over all samples
scran
Normalization
scRNA
BatchEffect
14 months ago
r_grau
▴ 10
4
votes
5
replies
2.1k
views
`emptyDrops()` calling 'too many' non-empty droplets
DropletUtils
emptyDrops
scRNA
scRNAseq
10x
19 months ago
Peter Hickey
▴ 670
2
votes
13
replies
2.2k
views
Running the DESeq2 "DESeqDataSetFromMatrix" function returns a dimname error
DESeq2
Scrna
scRNAseq
2.7 years ago
RDoc
▴ 10
1
vote
1
reply
937
views
Combining treatment and control batches for analysis
scRNAseq
scRNA
batchelor
BatchEffect
updated 3.3 years ago by
Aaron Lun
★ 28k • written 3.3 years ago by
Adrien
• 0
1
vote
4
replies
1.7k
views
How to work with duplicates calculating the differentially expressed genes in PseudoBulk-singleCell RNA experiment using zinbwave?
scRNA
zinbwave
batch
IntegratedData
updated 3.5 years ago by
davide risso
▴ 950 • written 3.5 years ago by
Assa Yeroslaviz
★ 1.5k
0
votes
3
replies
1.6k
views
Error: no applicable method for `RunTSNE` applied to an object of class "try-error"
Seurat
scRNA
debugging
exceptions
unit-test
updated 4.4 years ago by
Martin Morgan
25k • written 4.4 years ago by
moldach
▴ 20
0
votes
1
reply
4.5k
views
monocle error at orderCells
scRNA
monocle
packages
Tutorial
4.6 years ago
444579004
• 0
1
vote
3
replies
1.4k
views
Differential Expression analysis between distinct scRNA-seq datasets
scrna
scrnaseq
differential gene expression
updated 6.4 years ago by
davide risso
▴ 950 • written 6.4 years ago by
d.depledge
• 0
0
votes
1
reply
867
views
DeSeq2 , Differntial expression
SCRNA
updated 6.4 years ago by
Aaron Lun
★ 28k • written 6.4 years ago by
sumetha
• 0
2
votes
1
reply
4.1k
views
Intepretation of Z scores for gene set enrichment analysis in MAST
MAST
scRNA
GSEA
updated 6.6 years ago by
Andrew_McDavid
▴ 270 • written 6.6 years ago by
siajunren
• 0
1
vote
2
replies
1.4k
views
sc-RNA data analysis using scater
scater
scrna
updated 7.1 years ago by
Aaron Lun
★ 28k • written 7.1 years ago by
hrishi27n
▴ 20
15 results • Page
1 of 1
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Replies
Comment: DEG Filtering
by
Gordon Smyth
50k
RMA normalization is good but batch correction using NOISeq isn't right. Data shouldn't be batch corrected before the limma analysis and NO…
Answer: maftools: Error in validateMaf(maf = maf, isTCGA = isTCGA, rdup = removeDuplicat
by
snijesh
▴ 20
You can try: using `read.delim` or `fread`. ``` my_maf = data.table::fread("path/to/maf/sample.maf") my_maf = read.maf(maf = my_maf) …
Comment: DEG Filtering
by
Amit
• 0
Hi Gordon, Thank you for your response and advice. I want to analyze Dataset GSE18090 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi) whic…
Comment: edgeR, 3 x 2 design with a batch effect and contrasts
by
Gordon Smyth
50k
Yes, that is a quote from [A guide to creating design matrices for gene expression experiments](https://bioconductor.org/packages/release/w…
Comment: edgeR, 3 x 2 design with a batch effect and contrasts
by
JKim
• 0
Thank you. I think I found why the order matters. > Although an intercept-free design matrix has been coded using the 0+ notation, the in…
Votes
C: How to check that the reads in two fastq files are in the same order
Answer: edgeR, 3 x 2 design with a batch effect and contrasts
Answer: Need help with creating and plotting temporal clustering analysis of DEGs
Answer: Problem converting msigdb Human symbols to Zebrafish in gmt format
Answer: Problem converting msigdb Human symbols to Zebrafish in gmt format
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