Showing : seurat • reset
1
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145
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Seurat: normalized data in the integrated assay
seurat
updated 3 months ago by ▴ 470 • written 3 months ago by • 0
5
votes
15
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1.1k
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Can't able to install Seurat in Rstudio
Rstudio Seurat
updated 3 months ago by 3.4k • written 3 months ago by • 0
0
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0
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80
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Using csClassify on a SeuratObject
scRNAseq csClassify Seurat
updated 3 months ago by ▴ 830 • written 3 months ago by • 0
1
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2
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266
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Error when converting Seurat to SingleCellExperiment
Seurat SingleCellExperiment
9 months ago lirongrossmann ▴ 30
5
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3
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810
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Full length single-cell RNA-seq - tximport output for downstream analysis
tximport Seurat Smart-Seq Smart-Seq2
updated 14 months ago by 34k • written 14 months ago by ▴ 40
3
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6
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550
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Carry over variable features when converting FastMNN SCE object to Seurat object
mnn batchelor scrna-seq seurat
updated 15 months ago by ★ 27k • written 15 months ago by • 0
4
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1
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252
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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
0
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3
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544
views
error in (function (classes, fdef, mtable) unable to find an inherited method for function logNormCounts for signature Seurat
seurat singleR
updated 21 months ago by 43k • written 22 months ago by • 0
0
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2
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342
views
PCA outliers cleaning
scRNAseq Pipeline Seurat SingleCellExperiment
22 months ago albadrs.93 ▴ 10
0
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3
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511
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Error: no applicable method for `RunTSNE` applied to an object of class "try-error"
Seurat scRNA debugging exceptions unit-test
updated 22 months ago by 25k • written 22 months ago by ▴ 20
2
votes
2
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1.0k
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DE analysis for 10X scRNA-seq data with multiple conditions and multiple replicates
scRNA-seq Seurat DE
updated 2.0 years ago by ★ 27k • written 2.0 years ago by • 0
2
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4
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2.1k
views
How to convert large gene counts data into matrix?
R singlecell bioinformatics seurat
updated 6 months ago by • 0 • written 2.1 years ago by • 0
1
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3
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3.7k
views
Seurat 2.3.4 installation
seurat
updated 2.3 years ago by 43k • written 2.3 years ago by ▴ 10
1
vote
1
reply
416
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gene counts in Seurat after RunCCA() and AlignSubspace()
scRNA-seq seurat CCA
updated 2.7 years ago by ★ 27k • written 2.7 years ago by ▴ 620
0
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1
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1.1k
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Deconvolution Method in Seurat and convert from SingleCellExperiment
scater seurat singlecellexperiment rnaseq
updated 2.7 years ago by 43k • written 2.8 years ago by ▴ 50
0
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4
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895
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scRNA-seq: a question about the names of the columns in a Seurat object
scRNA-seq SEURAT
updated 2.8 years ago by 13k • written 2.8 years ago by ▴ 620
1
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5
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1.2k
views
newSCESet and SingleCellExperiment basic differences and TMM Normalization
singlecellexperiment single-cell rnaseq seurat scater
2.9 years ago hamza_karakurt ▴ 50
0
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2
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4.7k
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Seurat/DESeq2 - single cell RNA-seq differential expression
seurat deseq2
updated 3.1 years ago by 34k • written 3.1 years ago by • 0
0
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1
reply
1.8k
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Conversion to SingleCellExperiment from Seurat objects
Seurat SingleCellExperiment
3.3 years ago Wolfgang Huber 13k
6
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2
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3.3k
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Cell type specific cell markers for Seurat based analysis.
single cell seurat clustering
updated 4.2 years ago by ▴ 40 • written 4.2 years ago by ▴ 20
20 results • Page 1 of 1
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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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