Showing : SEURAT • reset
0
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3
replies
746
views
How to compare expression levels of genes between scRNAseq and bulkRNAseq?
Seurat RNASeq DESeq2 scRNAseq
updated 7 months ago by • 0 • written 7 months ago by ▴ 10
0
votes
2
replies
1.1k
views
How to add Ensembl ids after Pseudobulk analysis by DESeq2
Seurat DESeq2 single-cell scRNA Pseudobulk
updated 15 months ago by ★ 4.1k • written 15 months ago by • 0
0
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5
replies
2.2k
views
scRNA-seq as pseudobulk for DEseq2: does AggregateExpression() normalize counts?
pseudobulk seurat DESeq2
updated 20 months ago by ★ 4.0k • written 20 months ago by • 0
1
vote
2
replies
3.0k
views
trying to add SingleR label to Seurat Object fails
SingleR Seurat
updated 21 months ago by ★ 4.9k • written 21 months ago by ★ 1.5k
0
votes
4
replies
4.9k
views
error in (function (classes, fdef, mtable) unable to find an inherited method for function logNormCounts for signature Seurat
seurat singleR
updated 2.2 years ago by • 0 • written 5.8 years ago by • 0
3
votes
1
reply
1.2k
views
'Seurat' package
singlecell seurat
updated 2.3 years ago by ★ 4.9k • written 2.3 years ago by ▴ 10
0
votes
2
replies
1.5k
views
ModuleExprScore function/ hdWGNCA
ModuleExprScore DotPlot hdWGNCA Seurat
2.4 years ago Yuko • 0
0
votes
1
reply
4.7k
views
DESeq2 after Seurat analysis on integrated datasets
DESeq2 SingleCell GeneExpression Seurat
updated 2.5 years ago by ★ 4.9k • written 2.5 years ago by • 0
1
vote
2
replies
1.4k
views
Error with FindConservedMarkers()
seurat
2.6 years ago Chris ▴ 20
1
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0
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2.7k
views
Convert SpatialExperiment Object to Seurat Object
scuttle scater seurat SpatialExperiment
2.6 years ago cathalgking ▴ 10
2
votes
1
reply
2.4k
views
Convert AnnotatedDataFrame S4 object from GEO datasets to Seurat Object
biobase SingleCellData seurat SingleCell
updated 3.6 years ago by 68k • written 3.6 years ago by • 0
0
votes
3
replies
2.1k
views
NA values for mitochondrial gene percentage
Seurat scRNAseq
3.7 years ago zahra.mesri95 • 0
1
vote
1
reply
1.8k
views
Seurat: normalized data in the integrated assay
seurat
updated 4.2 years ago by ▴ 760 • written 4.2 years ago by • 0
5
votes
15
replies
18k
views
Can't able to install Seurat in Rstudio
Rstudio Seurat
updated 4.3 years ago by ★ 4.0k • written 4.3 years ago by • 0
0
votes
0
replies
935
views
Using csClassify on a SeuratObject
scRNAseq csClassify Seurat
updated 4.3 years ago by ★ 4.9k • written 4.3 years ago by ▴ 10
2
votes
2
replies
3.0k
views
Error when converting Seurat to SingleCellExperiment
Seurat SingleCellExperiment
4.7 years ago lirongrossmann ▴ 50
6
votes
3
replies
4.0k
views
Full length single-cell RNA-seq - tximport output for downstream analysis
tximport Seurat Smart-Seq Smart-Seq2
updated 5.1 years ago by 43k • written 5.1 years ago by ▴ 40
3
votes
6
replies
4.0k
views
Carry over variable features when converting FastMNN SCE object to Seurat object
mnn batchelor scrna-seq seurat
updated 5.3 years ago by ★ 29k • written 5.3 years ago by • 0
5
votes
1
reply
2.3k
views
Best practice for correlating scRNA seq to bulkRNA seq data
seurat edgeR spearman correlation scRNAseq
updated 5.4 years ago by ★ 29k • written 5.4 years ago by ▴ 20
0
votes
2
replies
2.2k
views
PCA outliers cleaning
scRNAseq Pipeline Seurat SingleCellExperiment
5.8 years ago albadrs.93 ▴ 10
0
votes
3
replies
2.5k
views
Error: no applicable method for `RunTSNE` applied to an object of class "try-error"
Seurat scRNA debugging exceptions unit-test
updated 5.8 years ago by 25k • written 5.8 years ago by ▴ 20
2
votes
2
replies
3.3k
views
DE analysis for 10X scRNA-seq data with multiple conditions and multiple replicates
scRNA-seq Seurat DE
updated 6.0 years ago by ★ 29k • written 6.0 years ago by • 0
2
votes
4
replies
4.4k
views
How to convert large gene counts data into matrix?
R Bioconductor singlecell bioinformatics seurat
updated 18 months ago by 52k • written 6.1 years ago by • 0
1
vote
3
replies
13k
views
Seurat 2.3.4 installation
seurat
updated 6.3 years ago by 52k • written 6.3 years ago by ▴ 10
1
vote
1
reply
1.7k
views
gene counts in Seurat after RunCCA() and AlignSubspace()
scRNA-seq seurat CCA
updated 6.7 years ago by ★ 29k • written 6.7 years ago by ▴ 670
0
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1
reply
3.3k
views
Deconvolution Method in Seurat and convert from SingleCellExperiment
scater seurat singlecellexperiment rnaseq
updated 6.7 years ago by 52k • written 6.7 years ago by ▴ 60
0
votes
4
replies
3.5k
views
scRNA-seq: a question about the names of the columns in a Seurat object
scRNA-seq SEURAT
updated 6.7 years ago by ★ 13k • written 6.7 years ago by ▴ 670
1
vote
5
replies
3.3k
views
newSCESet and SingleCellExperiment basic differences and TMM Normalization
singlecellexperiment single-cell rnaseq seurat scater
6.9 years ago hamza_karakurt ▴ 60
2
votes
2
replies
15k
views
Seurat/DESeq2 - single cell RNA-seq differential expression
seurat deseq2
updated 7.1 years ago by 43k • written 7.1 years ago by ▴ 10
0
votes
1
reply
5.9k
views
Conversion to SingleCellExperiment from Seurat objects
Seurat SingleCellExperiment
7.3 years ago Wolfgang Huber ★ 13k
6
votes
2
replies
6.6k
views
Cell type specific cell markers for Seurat based analysis.
single cell seurat clustering
updated 8.1 years ago by ▴ 40 • written 8.1 years ago by ▴ 20
31 results • Page 1 of 1
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Replies
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by snijesh ▴ 200
I would like to clarify whether the command `res <- results(dds, name = "phaseLP.conditionTreated")` is the correct approach to generate …
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by James W. MacDonald 68k
Not sure I understand. You ask how to do something and then show how one would do so.
Comment: DiffBind getting Fold values of near 0 by littlefishes20 ▴ 10
Same issues. All peaks return to a fold near 0, although they are significant when visualizing in IGV. Please find the MAplot and volcanoPl…
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by snijesh ▴ 200
I have checked DEGs between Solvent Control (SC) of FP and LP and there are noticebale differences in terms of DEGs. ``` # Checking SC in …
Answer: A0A287BB68 not recognized as UNPROT key in org.Ss.eg.db using AnnotationDbi::sel by James W. MacDonald 68k
Apparently it's been over-ridden by a different UniProtKB ID ``` > select(org.Ss.eg.db, "MYH11", "UNIPROT", "SYMBOL") 'select()' retu…
Votes
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Comment: Using DESeq2 on single cell RNA Seq data of same cell type but different conditi
Can NanoString data be analyzed using DESeq2?
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