Showing : Seurat • reset
0
votes
3
replies
389
views
How to compare expression levels of genes between scRNAseq and bulkRNAseq?
Seurat RNASeq DESeq2 scRNAseq
updated 5 weeks ago by • 0 • written 6 weeks ago by ▴ 10
0
votes
2
replies
847
views
How to add Ensembl ids after Pseudobulk analysis by DESeq2
Seurat DESeq2 single-cell scRNA Pseudobulk
updated 9 months ago by ★ 4.1k • written 9 months ago by • 0
0
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5
replies
1.8k
views
scRNA-seq as pseudobulk for DEseq2: does AggregateExpression() normalize counts?
pseudobulk seurat DESeq2
updated 14 months ago by ★ 4.0k • written 14 months ago by • 0
1
vote
2
replies
2.2k
views
trying to add SingleR label to Seurat Object fails
SingleR Seurat
updated 16 months ago by ★ 4.7k • written 16 months ago by ★ 1.5k
0
votes
4
replies
4.5k
views
error in (function (classes, fdef, mtable) unable to find an inherited method for function logNormCounts for signature Seurat
seurat singleR
updated 20 months ago by • 0 • written 5.3 years ago by • 0
3
votes
1
reply
1.1k
views
'Seurat' package
singlecell seurat
updated 22 months ago by ★ 4.7k • written 22 months ago by ▴ 10
0
votes
2
replies
1.3k
views
ModuleExprScore function/ hdWGNCA
ModuleExprScore DotPlot hdWGNCA Seurat
23 months ago Yuko • 0
0
votes
1
reply
4.1k
views
DESeq2 after Seurat analysis on integrated datasets
DESeq2 SingleCell GeneExpression Seurat
updated 2.1 years ago by ★ 4.7k • written 2.1 years ago by • 0
1
vote
2
replies
1.3k
views
Error with FindConservedMarkers()
seurat
2.1 years ago Chris ▴ 20
1
vote
0
replies
2.2k
views
Convert SpatialExperiment Object to Seurat Object
scuttle scater seurat SpatialExperiment
2.1 years ago cathalgking ▴ 10
2
votes
1
reply
2.2k
views
Convert AnnotatedDataFrame S4 object from GEO datasets to Seurat Object
biobase SingleCellData seurat SingleCell
updated 3.1 years ago by 68k • written 3.1 years ago by • 0
0
votes
3
replies
1.9k
views
NA values for mitochondrial gene percentage
Seurat scRNAseq
3.3 years ago • updated 3.2 years ago zahra.mesri95 • 0
1
vote
1
reply
1.6k
views
Seurat: normalized data in the integrated assay
seurat
updated 3.7 years ago by ▴ 750 • written 3.7 years ago by • 0
5
votes
15
replies
16k
views
Can't able to install Seurat in Rstudio
Rstudio Seurat
updated 3.8 years ago by ★ 4.0k • written 3.8 years ago by • 0
0
votes
0
replies
849
views
Using csClassify on a SeuratObject
scRNAseq csClassify Seurat
updated 3.8 years ago by ★ 4.7k • written 3.8 years ago by ▴ 10
2
votes
2
replies
2.7k
views
Error when converting Seurat to SingleCellExperiment
Seurat SingleCellExperiment
4.3 years ago lirongrossmann ▴ 50
6
votes
3
replies
3.7k
views
Full length single-cell RNA-seq - tximport output for downstream analysis
tximport Seurat Smart-Seq Smart-Seq2
updated 4.7 years ago by 43k • written 4.7 years ago by ▴ 40
3
votes
6
replies
3.7k
views
Carry over variable features when converting FastMNN SCE object to Seurat object
mnn batchelor scrna-seq seurat
updated 4.8 years ago by ★ 28k • written 4.8 years ago by • 0
5
votes
1
reply
2.1k
views
Best practice for correlating scRNA seq to bulkRNA seq data
seurat edgeR spearman correlation scRNAseq
updated 4.9 years ago by ★ 28k • written 4.9 years ago by ▴ 20
0
votes
2
replies
2.0k
views
PCA outliers cleaning
scRNAseq Pipeline Seurat SingleCellExperiment
5.3 years ago albadrs.93 ▴ 10
0
votes
3
replies
2.2k
views
Error: no applicable method for `RunTSNE` applied to an object of class "try-error"
Seurat scRNA debugging exceptions unit-test
updated 5.3 years ago by 25k • written 5.3 years ago by ▴ 20
2
votes
2
replies
3.2k
views
DE analysis for 10X scRNA-seq data with multiple conditions and multiple replicates
scRNA-seq Seurat DE
updated 5.5 years ago by ★ 28k • written 5.5 years ago by • 0
2
votes
4
replies
4.2k
views
How to convert large gene counts data into matrix?
R Bioconductor singlecell bioinformatics seurat
updated 13 months ago by 52k • written 5.6 years ago by • 0
1
vote
3
replies
13k
views
Seurat 2.3.4 installation
seurat
updated 5.8 years ago by 52k • written 5.8 years ago by ▴ 10
1
vote
1
reply
1.5k
views
gene counts in Seurat after RunCCA() and AlignSubspace()
scRNA-seq seurat CCA
updated 6.2 years ago by ★ 28k • written 6.2 years ago by ▴ 670
0
votes
1
reply
3.0k
views
Deconvolution Method in Seurat and convert from SingleCellExperiment
scater seurat singlecellexperiment rnaseq
updated 6.2 years ago by 52k • written 6.2 years ago by ▴ 60
0
votes
4
replies
3.3k
views
scRNA-seq: a question about the names of the columns in a Seurat object
scRNA-seq SEURAT
updated 6.2 years ago by ★ 13k • written 6.2 years ago by ▴ 670
1
vote
5
replies
3.0k
views
newSCESet and SingleCellExperiment basic differences and TMM Normalization
singlecellexperiment single-cell rnaseq seurat scater
6.4 years ago hamza_karakurt ▴ 60
2
votes
2
replies
14k
views
Seurat/DESeq2 - single cell RNA-seq differential expression
seurat deseq2
updated 6.6 years ago by 43k • written 6.6 years ago by ▴ 10
0
votes
1
reply
5.4k
views
Conversion to SingleCellExperiment from Seurat objects
Seurat SingleCellExperiment
6.8 years ago Wolfgang Huber ★ 13k
6
votes
2
replies
6.1k
views
Cell type specific cell markers for Seurat based analysis.
single cell seurat clustering
updated 7.7 years ago by ▴ 40 • written 7.7 years ago by ▴ 20
31 results • Page 1 of 1
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Comment: sesameDataCache is not work properly on my system by Samreen • 0
Any luck with this? I have tried all of the above and it still doesn't work. This is my session info and I'm on a cluster computing environ…
Answer: Using tximport for kallisto aligned TOIL data by James W. MacDonald 68k
If you just have the transcript data, you probably don't need (and maybe cannot use) `tximport`. Instead you could just do the naive thing …
Answer: Reading gene expression data in GPR format and converting it to xlsx format by James W. MacDonald 68k
Setting aside the inadvisability of putting these data into Excel (and I should point out that these data are not single-cell, but instead …
Comment: concentration tables suitable as input for new packages? by wilkinson • 0
I am grateful for your response. Software such as "Spectra" may parse MS-data to generate tables of concentrations, for instance. But inste…
Comment: Removing UTR from GTF for gene quantification by ATpoint ★ 4.7k
Consider asking at biostars or bioinformatics reddit, since this is not directly related to a Bioconductor problem. Anyway, a couple of th…
Votes
Answer: Differential expression of proteins using somascan data
Answer: Surprising behavior for DEXseq dispersion estimate plot?
Answer: Handle zero effective gene length when tximport RSEM results
Handle zero effective gene length when tximport RSEM results
How to remove genes with 0 counts in tximport?
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