Showing : SingleCell • reset
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News: Course: Single-cell analysis with R/Bioconductor
SingleCellExperiment SingleCell SingleCellWorkflow SingleCellData
3 months ago Ludwig Geistlinger ▴ 70
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3
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Possible issue following the logNormCounts(filtered) with resulted fit
single-cell SingleCell SingleCellExperiment SingleCellWorkflow SingleCellData
6 months ago Konstantinos Yeles ▴ 90
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570
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News: Single-cell RNA-seq analysis with R/Bioconductor (online course)
SingleCellExperiment SingleCell
14 months ago info ▴ 10
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736
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Job: Postdoctoral Research Associate in Computational Epigenomics
Phd SingleCell DNAMethylation Shanghai JobPosting
15 months ago xiaolong • 0
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817
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Job: Postdoctoral fellowships in Spatial Omics and Single Cell Genomics at the University of Padova (IT)
SingleCell Transcriptomics SpatialDatasets SpatialData
18 months ago Silvio • 0
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1.1k
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Job: Bioinformatics Spatial Omics and Proteomics Postdoc (Research Officer / Senior Research Officer) at WEHI (Melbourne, Australia)
Proteomics JobPosting SingleCell Spatial SpatialExperiment
21 months ago Peter Hickey ▴ 760
3
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1
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1.4k
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'Seurat' package
singlecell seurat
updated 2.6 years ago by ★ 5.0k • written 2.6 years ago by ▴ 10
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1
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1.5k
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Choosing the right lower limit for emptyDrops
SingleCell emptyDrops 10X
updated 2.6 years ago by ▴ 760 • written 2.6 years ago by • 0
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2
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1.2k
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Why my log2fcs are too high?
DESeq2 SingleCell log2FC
2.6 years ago paria.alipour • 0
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2
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1.6k
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Scaling and normalization by deconvolution of SMART-Seq 2 data
scran Clustering SingleCell Normalization
2.7 years ago Assa Yeroslaviz ★ 1.5k
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1.5k
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Single-cell differential expression analysis with multiple samples
SingleCell
2.7 years ago iaradsouza1 • 0
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8
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2.0k
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fail to annotate chromosome data to single cell object
error SingleCell annotate
updated 2.1 years ago by • 0 • written 2.7 years ago by • 0
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1.3k
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Job: Open position in the CBIO lab: single-cell proteomics
Proteomics SingleCell JobPosting MassSpectrometry
2.8 years ago Laurent Gatto 1.6k
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3
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2.3k
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Knee and Inflection of DropletUtils
SingleCell
updated 2.8 years ago by ★ 5.0k • written 2.8 years ago by • 0
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4.8k
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DESeq2 after Seurat analysis on integrated datasets
DESeq2 SingleCell GeneExpression Seurat
updated 2.8 years ago by ★ 5.0k • written 2.8 years ago by • 0
1
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1
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1.4k
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Pseudobulk running all groups together vs subsetting first
DESeq2 edgeR SingleCell
updated 2.8 years ago by ★ 13k • written 2.8 years ago by ▴ 70
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1
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1.2k
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Job: Reopened: 'Omics data analyst for HPCBio, University of Illinois
SingleCell Spatial RNA-seq
2.8 years ago Jenny Drnevich ★ 2.0k
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3
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1.4k
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Tissue Level Differential Expression Analysis
DESeq2 DifferentialExpression differentialex Pseudobulk SingleCell
updated 2.9 years ago by 43k • written 2.9 years ago by • 0
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1.1k
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Job: 'Omics data analyst for HPCBio, University of Illinois
SingleCell rnaseq methylationArrayAnalysis Spatial
written 3.0 years ago by ★ 2.0k
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3
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2.3k
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Single-Cell Data Simulation from Bulk RNA-seq
SingleCell RNASeq RNASeqData scRNAseq
updated 17 months ago by • 0 • written 3.1 years ago by • 0
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1.2k
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allele count data bioc object
SingleCell SingleCellMultiModal allele
updated 3.1 years ago by 43k • written 3.2 years ago by • 0
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Job: Postdoctoral Fellow in Epigenomcis/Neurobiology (MGH/Harvard Medical School, Boston)
GenomicVariation SingleCell Autism Neurogenesis Epigenetics
3.1 years ago sudhir.thakurela • 0
0
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0
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957
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Gene Id duplicated
SingleCell SingleCellData
updated 3.2 years ago by ★ 5.0k • written 3.2 years ago by • 0
0
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1
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1.2k
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Set up "mock" cell type as the reference?
DESeq2 SingleCell
updated 3.2 years ago by 43k • written 3.2 years ago by ▴ 10
0
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899
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weighting sample group
monocle SingleCell DifferentialExpression
3.2 years ago Sogand • 0
2
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4
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2.1k
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How to detect LacZ tagged cells from single cell
SingleCell SingleCellExperiment SingleCellWorkflow SingleCellData
updated 4 months ago by • 0 • written 3.2 years ago by ▴ 20
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2
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1.8k
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how to plot a fitting line on the testPseudotime
Pseudotime testPseudotime TSCAN SingleCell OSCA
3.2 years ago Guandong Shang ▴ 40
2
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4
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1.7k
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Summary of library size factor is all equal to one
SingleCell SingleCellData SingleCellWorkflow SingleCellExperiment
3.2 years ago Romina • 0
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1
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1.9k
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Error in .testForValidKeys(x, keys, keytype, fks) :
SingleCell AnnotationDbi
updated 3.3 years ago by 68k • written 3.3 years ago by • 0
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1
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1.9k
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Error in running: classifySingleR from SingleR package
SingleR SingleCell
updated 3.4 years ago by ★ 5.0k • written 3.4 years ago by • 0
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2.2k
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DESeq2 aggregated single cell data
pseudobulk SingleCell DESeq2
3.4 years ago fluentin44 • 0
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1.2k
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Differential expression with single cell data: any good two component (hurdle) models recently?
SingleCellWorkflow DifferentialExpression SingleCell SingleCellMultiModal MAST
3.5 years ago Nik Tuzov ▴ 90
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1.3k
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Performing DGE analysis with MAST on a variable with more than 2 levels
MAST DEG SingleCell
3.6 years ago zroger499 • 0
2
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1
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1.3k
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() followed by [] within an argument in singlecell OSCA workflow
SingleCell R OSCA
updated 3.6 years ago by ▴ 100 • written 3.6 years ago by • 0
2
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1
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2.6k
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Convert AnnotatedDataFrame S4 object from GEO datasets to Seurat Object
biobase SingleCellData seurat SingleCell
updated 3.9 years ago by 68k • written 3.9 years ago by • 0
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1.2k
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Issues geting meaninfull results for single cell DGE using MAST
MAST SingleCell
3.9 years ago zroger499 • 0
0
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0
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1.4k
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Job: Postdoc Opening in Bioinformatics or Computational Biology
SpatialData scRNAseq SingleCell Omixer
3.9 years ago Sebastian Lewandowski • 0
2
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2
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1.8k
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velociraptor preparation
SingleCellExperiment singlecell velociraptor scvelo
updated 4.0 years ago by ★ 5.0k • written 4.0 years ago by ▴ 40
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Job: Research Scientists/Postdoctoral Candidates/Computational Biologists and Programmers excited about computational challenges in modeling CRISPR genome…
CRISPR SingleCell Genomics
4.2 years ago lpinello • 0
1
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2
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1.8k
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Using limma duplicateCorrelation to account for donor/dataset effects in scRNA-Seq pseudobulk counts from multiple sources
limma SingleCell
4.2 years ago Andrew Pattison • 0
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0
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1.1k
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Spike-In Cells for Normalization?
SpikeIn SingleCell
4.3 years ago mb1996 • 0
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1.1k
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Job: Computational postdoctoral fellow for cancer disparities research (Boston University)
DNASeq RNASeq SingleCell
4.3 years ago camp ▴ 10
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0
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1.4k
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Job: Senior Bioinformatician - University of Alabama at Birmingham
JobPosting Transcriptomics SingleCell RNA-seq
4.4 years ago lianov • 0
0
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1
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1.5k
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Differentially expressed genes across three different conditions
MAST SingleCell diffGeneAnalysis
updated 4.4 years ago by 68k • written 4.4 years ago by • 0
3
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2
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3.5k
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Merging only those samples sequenced over multiple batches - scRNA-seq
SingleCell SingleCellExperiment scater
4.8 years ago camerond • 0
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0
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1.5k
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Job: Computational Biologist at Denali Therapeutics
Transcriptomics SingleCell JobPosting
4.9 years ago Steve Lianoglou ★ 13k
0
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2
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2.1k
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Removal of cell cycle effect using batchelor::regressBatches() and proper usage of corrected UMI matrix
scRNAseq batchelor SingleCell SingleCellExperiment scran
5.0 years ago jirkanov • 0
3
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1
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2.5k
views
DESeq2 DE gene expression of scRNA-seq pseudobulk
DESeq2 SingleCell
updated 5.0 years ago by 43k • written 5.0 years ago by ▴ 10
0
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1
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1.3k
views
improving running time of runNMF
runNMF scater singlecell SingleCellExperiment
updated 5.1 years ago by ★ 29k • written 5.1 years ago by ▴ 50
0
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0
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1.3k
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Creating a stable batch-corrected scRNA-Seq data with multiple datasets and multiple integrations
scater singlecell scran BatchEffect
5.1 years ago hamza_karakurt ▴ 60
58 results • Page 1 of 2
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Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Answer: PTM analysis in LIMPA by Gordon Smyth 53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR by James W. MacDonald 68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Answer: Question about DESeq2 Design for Paired Treatment Study by ATpoint ★ 5.0k
It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Awards • All
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