Bioconductor SEURAT

Showing : SEURAT • reset

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818

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Seurat RNASeq DESeq2 scRNAseq

updated 8 months ago by jodan • 0 • written 9 months ago by Quang NN ▴ 10

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1.2k

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Seurat DESeq2 single-cell scRNA Pseudobulk

updated 17 months ago by Guido Hooiveld ★ 4.1k • written 17 months ago by Sara • 0

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2.3k

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pseudobulk seurat DESeq2

updated 22 months ago by Kevin Blighe ★ 4.0k • written 22 months ago by daiane.hemerichbrennan • 0

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3.1k

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SingleR Seurat

updated 23 months ago by ATpoint ★ 5.0k • written 23 months ago by Assa Yeroslaviz ★ 1.5k

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5.0k

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seurat singleR

updated 2.3 years ago by Marco • 0 • written 5.9 years ago by mathai.c • 0

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1.3k

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singlecell seurat

updated 2.5 years ago by ATpoint ★ 5.0k • written 2.5 years ago by Sooni ▴ 10

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1.5k

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ModuleExprScore DotPlot hdWGNCA Seurat

2.6 years ago • updated 2.5 years ago Yuko • 0

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4.8k

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DESeq2 SingleCell GeneExpression Seurat

updated 2.7 years ago by ATpoint ★ 5.0k • written 2.7 years ago by bio.boi • 0

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1.5k

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seurat

2.7 years ago Chris ▴ 20

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2.7k

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scuttle scater seurat SpatialExperiment

2.7 years ago cathalgking ▴ 10

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2.5k

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biobase SingleCellData seurat SingleCell

updated 3.7 years ago by James W. MacDonald 68k • written 3.7 years ago by NGS_enthusiast • 0

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2.2k

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Seurat scRNAseq

3.9 years ago zahra.mesri95 • 0

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1.8k

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seurat

updated 4.4 years ago by Peter Hickey ▴ 760 • written 4.4 years ago by zli1 • 0

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18k

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Rstudio Seurat

updated 4.4 years ago by Kevin Blighe ★ 4.0k • written 4.4 years ago by KOUSTAV • 0

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960

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scRNAseq csClassify Seurat

updated 4.4 years ago by ATpoint ★ 5.0k • written 4.4 years ago by curiousmind007 ▴ 10

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3.0k

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Seurat SingleCellExperiment

4.9 years ago lirongrossmann ▴ 50

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4.0k

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tximport Seurat Smart-Seq Smart-Seq2

updated 5.3 years ago by Michael Love 43k • written 5.3 years ago by lshepard ▴ 40

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4.1k

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mnn batchelor scrna-seq seurat

updated 5.4 years ago by Aaron Lun ★ 29k • written 5.4 years ago by heir_of_isildur88 • 0

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2.4k

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seurat edgeR spearman correlation scRNAseq

updated 5.5 years ago by Aaron Lun ★ 29k • written 5.5 years ago by tobias-messmer ▴ 20

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2.2k

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scRNAseq Pipeline Seurat SingleCellExperiment

6.0 years ago albadrs.93 ▴ 10

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2.5k

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Seurat scRNA debugging exceptions unit-test

updated 6.0 years ago by Martin Morgan 25k • written 6.0 years ago by moldach ▴ 20

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3.4k

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scRNA-seq Seurat DE

updated 6.1 years ago by Aaron Lun ★ 29k • written 6.1 years ago by ilee8 • 0

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4.5k

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R Bioconductor singlecell bioinformatics seurat

updated 20 months ago by Gordon Smyth 53k • written 6.3 years ago by sambunga094 • 0

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13k

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seurat

updated 6.4 years ago by Gordon Smyth 53k • written 6.4 years ago by Mike ▴ 10

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1.7k

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scRNA-seq seurat CCA

updated 6.8 years ago by Aaron Lun ★ 29k • written 6.8 years ago by Bogdan ▴ 670

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3.4k

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scater seurat singlecellexperiment rnaseq

updated 6.9 years ago by Gordon Smyth 53k • written 6.9 years ago by hamza_karakurt ▴ 60

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3.6k

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scRNA-seq SEURAT

updated 6.9 years ago by Steve Lianoglou ★ 13k • written 6.9 years ago by Bogdan ▴ 670

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3.3k

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singlecellexperiment single-cell rnaseq seurat scater

7.0 years ago hamza_karakurt ▴ 60

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15k

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seurat deseq2

updated 7.2 years ago by Michael Love 43k • written 7.2 years ago by Clara ▴ 10

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6.0k

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Seurat SingleCellExperiment

7.4 years ago Wolfgang Huber ★ 13k

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6.7k

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single cell seurat clustering

updated 8.3 years ago by ankur.chakravarthy.10 ▴ 40 • written 8.3 years ago by Bioinformatician_R ▴ 20

31 results • Page 1 of 1

Recent ...

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Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by James W. MacDonald 68k

Aaron already answered your question. If you have an HDF5 file, it will be read in as a `TENxMatrix` object, which isn't actually read in -…

Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by dan.gatti • 0

Very strange. We have the same package versions. I tried adding the mtx.class, type, and delayed arguments, but it's still making the coun…

Comment: DESeq2 for candidate gene analysis by piffelpaff ▴ 20

thank you so much for answering Dr. Love!

Answer: DESeq2 for candidate gene analysis by Michael Love 43k

Your plan 1 is reasonable. Run DESeq2 on the whole dataset to obtain size factors and moderated dispersion estimates and then extract the u…

Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by James W. MacDonald 68k

Oh. ``` > z <- read10xCounts(c(tmpdir, tmpdir), mtx.class = "SVT_SparseMatrix", delayed = TRUE) > class(counts(z)) [1] "DelayedMatrix" att…

Votes

A: Multi-level experiments in Limma

Answer: Should voomWithQualityWeights still be used when the sample-specific weights var

Answer: DESeq2 for candidate gene analysis

DESeq2 for candidate gene analysis

Answer: DESeq2 for candidate gene analysis

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