Showing : SingleCell • reset
2
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4
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How to convert large gene counts data into matrix?
R Bioconductor singlecell bioinformatics seurat
updated 9 weeks ago by 50k • written 4.7 years ago by • 0
0
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6
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2.6k
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Discrepancy between cell type and cluster using SingleCellExperiment and SingleR
singlecell singlecellexperiment umap singleR
updated 3.6 years ago by ★ 28k • written 3.6 years ago by ▴ 80
0
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1
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2.2k
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DESeq2 after Seurat analysis on integrated datasets
DESeq2 SingleCell GeneExpression Seurat
updated 14 months ago by ★ 4.0k • written 14 months ago by • 0
3
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2
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2.2k
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Merging only those samples sequenced over multiple batches - scRNA-seq
SingleCell SingleCellExperiment scater
3.2 years ago camerond • 0
2
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6
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2.1k
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Discarding ambient RNA using estimateAmbience
emptyDrop ambient singlecell estimateAmbience
updated 3.6 years ago by ★ 28k • written 3.6 years ago by ▴ 40
0
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3
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1.9k
views
marker genes in singleR
singleR singlecell singlecellexperiment
updated 3.7 years ago by ★ 28k • written 3.7 years ago by ▴ 40
2
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1
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1.8k
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DESeq2 DE gene expression of scRNA-seq pseudobulk
DESeq2 SingleCell
updated 3.4 years ago by 41k • written 3.4 years ago by • 0
0
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1
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1.8k
views
Error in .updateHubDB(hub_bfc, .class, url, proxy, localHub) :
annotation singlecell rna-seq
updated 4.2 years ago by 3.8k • written 4.2 years ago by • 0
2
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1
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1.6k
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Convert AnnotatedDataFrame S4 object from GEO datasets to Seurat Object
biobase SingleCellData seurat SingleCell
updated 2.2 years ago by 65k • written 2.2 years ago by • 0
0
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2
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1.5k
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most correlated genes in SingleR
singlecell singleR
updated 3.6 years ago by ★ 28k • written 3.6 years ago by ▴ 40
0
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2
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1.4k
views
Removal of cell cycle effect using batchelor::regressBatches() and proper usage of corrected UMI matrix
scRNAseq batchelor SingleCell SingleCellExperiment scran
3.4 years ago • updated 3.3 years ago jirkanov • 0
5
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5
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1.4k
views
Association analysis between gene expression and Phenotype
rna singlecell limma
updated 5.1 years ago by ★ 28k • written 5.1 years ago by ▴ 20
0
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1
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1.4k
views
predicting cell type of clusters using singleR
singleR singlecell
updated 3.7 years ago by ★ 28k • written 3.7 years ago by ▴ 40
1
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2
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1.3k
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DESeq2 aggregated single cell data
pseudobulk SingleCell DESeq2
21 months ago fluentin44 • 0
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3
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1.2k
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Knee and Inflection of DropletUtils
SingleCell
updated 13 months ago by ★ 4.0k • written 13 months ago by • 0
2
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2
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1.1k
views
velociraptor preparation
SingleCellExperiment singlecell velociraptor scvelo
updated 2.3 years ago by ★ 4.0k • written 2.3 years ago by ▴ 40
0
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1
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1.1k
views
Error in .testForValidKeys(x, keys, keytype, fks) :
SingleCell AnnotationDbi
updated 19 months ago by 65k • written 19 months ago by • 0
0
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8
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1.1k
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fail to annotate chromosome data to single cell object
error SingleCell annotate
updated 4 months ago by • 0 • written 13 months ago by • 0
1
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2
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1.0k
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Using limma duplicateCorrelation to account for donor/dataset effects in scRNA-Seq pseudobulk counts from multiple sources
limma SingleCell
2.5 years ago Andrew Pattison • 0
0
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1
reply
977
views
Error in running: classifySingleR from SingleR package
SingleR SingleCell
updated 20 months ago by ★ 4.0k • written 20 months ago by • 0
0
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2
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920
views
how to plot a fitting line on the testPseudotime
Pseudotime testPseudotime TSCAN SingleCell OSCA
19 months ago Guandong Shang ▴ 40
0
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0
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914
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Job: Computational Biologist at Denali Therapeutics
Transcriptomics SingleCell JobPosting
3.3 years ago Steve Lianoglou ★ 13k
0
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1
reply
912
views
Differentially expressed genes across three different conditions
MAST SingleCell diffGeneAnalysis
updated 2.8 years ago by 65k • written 2.8 years ago by • 0
0
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0
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886
views
Job: Senior Bioinformatician - University of Alabama at Birmingham
JobPosting Transcriptomics SingleCell RNA-seq
2.7 years ago lianov • 0
2
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4
replies
884
views
Summary of library size factor is all equal to one
SingleCell SingleCellData SingleCellWorkflow SingleCellExperiment
19 months ago Romina • 0
0
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0
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865
views
Job: Postdoc Opening in Bioinformatics or Computational Biology
SpatialData scRNAseq SingleCell Omixer
2.2 years ago Sebastian Lewandowski • 0
0
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1
reply
829
views
Single-Cell Data Simulation from Bulk RNA-seq
SingleCell RNASeq RNASeqData scRNAseq
updated 17 months ago by 50k • written 17 months ago by • 0
0
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3
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829
views
Tissue Level Differential Expression Analysis
DESeq2 DifferentialExpression differentialex Pseudobulk SingleCell
updated 15 months ago by 41k • written 15 months ago by • 0
0
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0
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815
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Job: Postdoctoral Fellow in Epigenomcis/Neurobiology (MGH/Harvard Medical School, Boston)
GenomicVariation SingleCell Autism Neurogenesis Epigenetics
18 months ago sudhir.thakurela • 0
0
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1
reply
814
views
improving running time of runNMF
runNMF scater singlecell SingleCellExperiment
updated 3.4 years ago by ★ 28k • written 3.4 years ago by ▴ 40
2
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2
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756
views
How to detect LacZ tagged cells from single cell
SingleCell SingleCellExperiment SingleCellWorkflow SingleCellData
19 months ago k1m ▴ 20
0
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0
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752
views
Creating a stable batch-corrected scRNA-Seq data with multiple datasets and multiple integrations
scater singlecell scran BatchEffect
3.5 years ago hamza_karakurt ▴ 50
0
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1
reply
737
views
Set up "mock" cell type as the reference?
DESeq2 SingleCell
updated 19 months ago by 41k • written 19 months ago by ▴ 10
0
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1
reply
734
views
allele count data bioc object
SingleCell SingleCellMultiModal allele
updated 18 months ago by 41k • written 18 months ago by • 0
2
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1
reply
721
views
() followed by [] within an argument in singlecell OSCA workflow
SingleCell R OSCA
updated 24 months ago by ▴ 90 • written 24 months ago by • 0
3
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1
reply
716
views
'Seurat' package
singlecell seurat
updated 11 months ago by ★ 4.0k • written 11 months ago by ▴ 10
0
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0
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716
views
Issues geting meaninfull results for single cell DGE using MAST
MAST SingleCell
2.2 years ago zroger499 • 0
0
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0
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700
views
Job: Research Scientists/Postdoctoral Candidates/Computational Biologists and Programmers excited about computational challenges in modeling CRISPR genome…
CRISPR SingleCell Genomics
2.5 years ago lpinello • 0
0
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0
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689
views
Performing DGE analysis with MAST on a variable with more than 2 levels
MAST DEG SingleCell
23 months ago zroger499 • 0
0
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0
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687
views
Spike-In Cells for Normalization?
SpikeIn SingleCell
2.6 years ago mb1996 • 0
0
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2
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679
views
Scaling and normalization by deconvolution of SMART-Seq 2 data
scran Clustering SingleCell Normalization
12 months ago Assa Yeroslaviz ★ 1.5k
0
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0
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671
views
Job: Computational postdoctoral fellow for cancer disparities research (Boston University)
DNASeq RNASeq SingleCell
2.7 years ago camp • 0
1
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4
replies
668
views
Single-cell differential expression analysis with multiple samples
SingleCell
13 months ago iaradsouza1 • 0
0
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0
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655
views
Differential expression with single cell data: any good two component (hurdle) models recently?
SingleCellWorkflow DifferentialExpression SingleCell SingleCellMultiModal MAST
22 months ago Nik Tuzov ▴ 80
0
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1
reply
643
views
Job: 'Omics data analyst for HPCBio, University of Illinois
SingleCell rnaseq methylationArrayAnalysis Spatial
written 16 months ago by ★ 2.0k
0
votes
1
reply
642
views
Choosing the right lower limit for emptyDrops
SingleCell emptyDrops 10X
updated 11 months ago by ▴ 690 • written 11 months ago by • 0
1
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1
reply
636
views
Pseudobulk running all groups together vs subsetting first
DESeq2 edgeR SingleCell
updated 14 months ago by ★ 13k • written 14 months ago by ▴ 30
0
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1
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625
views
Job: Reopened: 'Omics data analyst for HPCBio, University of Illinois
SingleCell Spatial RNA-seq
14 months ago Jenny Drnevich ★ 2.0k
0
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0
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619
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Job: Open position in the CBIO lab: single-cell proteomics
Proteomics SingleCell JobPosting MassSpectrometry
13 months ago Laurent Gatto 1.6k
0
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2
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599
views
Why my log2fcs are too high?
DESeq2 SingleCell log2FC
11 months ago paria.alipour • 0
50 results • Page 1 of 1
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Replies
Comment: A ComBat-seq issue: the covariates are confounded by schlumbohm • 0
Dear ATpoint, thank you for the comment. I did correct the question. For the group, I did accidentally share the input for all three batch…
Comment: Memory errors using read.bismark? by Peter Hickey ▴ 690
If you process serially (i.e. with `BPPARAM = SerialParam()`) then you might be okay. The final object will be on the order of 250 GB in-me…
Answer: blockwiseModule crashes in the end and doesn't generate modules by xaweh28128 • 0
Test your word skills and see if you can crack the code in today's Wordle puzzle. [Nytimes wordle](https://wordlenytimes.net/quordle-game/)…
Comment: Memory errors using read.bismark? by Juan Higareda • 0
Thanks for the answer. Actually, processing one file and keeping it in memory wasn't the problem, is more processing all the 15 files to bu…
Answer: Differentially expressed genes in monocle pseudotime by Gordon Smyth 50k
You might try the methods in this paper: Cheng J, Smyth GK*, Chen Y* (2023). Unraveling the timeline of gene expression: A pseudotempora…
Votes
Comment: Not fully paired differential gene expression analysis
Comment: [DiffBind] Obtaining normalization factors
Answer: ComplexHeatmap: add pch to rowAnnotation when the input is a data frame with var
Comment: Not fully paired differential gene expression analysis
Answer: GSVA error
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