Showing : SingleCell • reset
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Differential expression with single cell data: any good two component (hurdle) models recently?
SingleCellWorkflow DifferentialExpression SingleCell SingleCellMultiModal MAST
3 days ago Nik Tuzov ▴ 70
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76
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Performing DGE analysis with MAST on a variable with more than 2 levels
MAST DEG SingleCell
6 weeks ago zroger499 • 0
2
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1
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111
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() followed by [] within an argument in singlecell OSCA workflow
SingleCell R OSCA
updated 9 weeks ago by ▴ 70 • written 9 weeks ago by • 0
2
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1
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339
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Convert AnnotatedDataFrame S4 object from GEO datasets to Seurat Object
biobase SingleCellData seurat SingleCell
updated 5 months ago by 60k • written 5 months ago by • 0
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143
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Issues geting meaninfull results for single cell DGE using MAST
MAST SingleCell
5 months ago zroger499 • 0
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276
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Job: Postdoc Opening in Bioinformatics or Computational Biology
SpatialData scRNAseq SingleCell Omixer
5 months ago Sebastian Lewandowski • 0
1
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2
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359
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velociraptor preparation
SingleCellExperiment singlecell velociraptor scvelo
updated 6 months ago by ★ 1.3k • written 6 months ago by ▴ 30
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217
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Job: Research Scientists/Postdoctoral Candidates/Computational Biologists and Programmers excited about computational challenges in modeling CRISPR genome…
CRISPR SingleCell Genomics
8 months ago lpinello • 0
1
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2
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357
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Using limma duplicateCorrelation to account for donor/dataset effects in scRNA-Seq pseudobulk counts from multiple sources
limma SingleCell
9 months ago Andrew Pattison • 0
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186
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Spike-In Cells for Normalization?
SpikeIn SingleCell
10 months ago mb1996 • 0
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242
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Job: Computational postdoctoral fellow for cancer disparities research (Boston University)
DNASeq RNASeq SingleCell
10 months ago camp • 0
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270
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Job: Senior Bioinformatician - University of Alabama at Birmingham
JobPosting Transcriptomics SingleCell RNA-seq
11 months ago lianov • 0
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1
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260
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Differentially expressed genes across three different conditions
MAST SingleCell diffGeneAnalysis
updated 12 months ago by 60k • written 12 months ago by • 0
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2
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486
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Merging only those samples sequenced over multiple batches - scRNA-seq
SingleCell SingleCellExperiment scater
17 months ago • updated 16 months ago camerond • 0
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411
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Job: Computational Biologist at Denali Therapeutics
Transcriptomics SingleCell JobPosting
18 months ago Steve Lianoglou 13k
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2
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553
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Removal of cell cycle effect using batchelor::regressBatches() and proper usage of corrected UMI matrix
scRNAseq batchelor SingleCell SingleCellExperiment scran
18 months ago jirkanov • 0
2
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1
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802
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DESeq2 DE gene expression of scRNA-seq pseudobulk
DESeq2 SingleCell
updated 19 months ago by 37k • written 19 months ago by • 0
0
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1
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313
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improving running time of runNMF
runNMF scater singlecell SingleCellExperiment
updated 19 months ago by ★ 27k • written 19 months ago by ▴ 40
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266
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Creating a stable batch-corrected scRNA-Seq data with multiple datasets and multiple integrations
scater singlecell scran BatchEffect
20 months ago hamza_karakurt ▴ 50
2
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865
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Discarding ambient RNA using estimateAmbience
emptyDrop ambient singlecell estimateAmbience
updated 21 months ago by ★ 27k • written 21 months ago by ▴ 40
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6
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884
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Discrepancy between cell type and cluster using SingleCellExperiment and SingleR
singlecell singlecellexperiment umap singleR
updated 22 months ago by ★ 27k • written 22 months ago by ▴ 60
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2
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542
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most correlated genes in SingleR
singlecell singleR
updated 22 months ago by ★ 27k • written 22 months ago by ▴ 40
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1
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423
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predicting cell type of clusters using singleR
singleR singlecell
updated 22 months ago by ★ 27k • written 22 months ago by ▴ 40
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969
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marker genes in singleR
singleR singlecell singlecellexperiment
updated 23 months ago by ★ 27k • written 23 months ago by ▴ 40
0
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1
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330
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Error in .updateHubDB(hub_bfc, .class, url, proxy, localHub) :
annotation singlecell rna-seq
updated 2.4 years ago by 3.1k • written 2.4 years ago by • 0
2
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4
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2.7k
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How to convert large gene counts data into matrix?
R singlecell bioinformatics seurat
updated 16 months ago by • 0 • written 2.9 years ago by • 0
5
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5
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639
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Association analysis between gene expression and Phenotype
rna singlecell limma
updated 3.2 years ago by ★ 27k • written 3.3 years ago by ▴ 20
27 results • Page 1 of 1
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Replies
Comment: How to combine VCF-class and data.frame with annotations by didanax972 • 0
If you have more than one VCF file and want to merge all VCF files then you create one VCF file without any data loss by using VCF Merge & …
Comment: VariantAnnotation R Package - Merging Two VCF files by didanax972 • 0
In case you like to merge the numerous VCF files into a single file then you should opt for the VCF Merger tool. This tool is a dedicated a…
Comment: merging VCF files by didanax972 • 0
Use Merge VCF a quick and instant solution to combine multiple VCF files into a new VCF file. The tool effortlessly merges multiple VCF fil…
Comment: Error: DESeq(dds , useT = TRUE, minmu = 1e-06, test = "LRT", : likelih by ATpoint ★ 1.3k
Would you mind reading the vignette towards how the LRT works: http://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2…
Comment: cellCounts() function floating point error by Yang Liao ▴ 340
Thanks for the report but the error cannot be reproduced. We tested `Rsubread` 2.10.3 in `R` 4.2.0 and `Bioconductor` 3.15, and `cellCounts…
Votes
C: DESeq2 lfcShrink() usage of coef vs. usage of contrast
C: DESeq2 lfcShrink() usage of coef vs. usage of contrast
Comment: Using Age or other numerical variable to model expression in deseq2
Comment: Using Age or other numerical variable to model expression in deseq2
Answer: Using Age or other numerical variable to model expression in deseq2
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