Showing : singlecell • reset
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Single-Cell Data Simulation from Bulk RNA-seq
SingleCell RNASeq RNASeqData scRNAseq
updated 16 days ago by • 0 • written 17 months ago by • 0
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215
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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
8 weeks ago Peter Hickey ▴ 740
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4
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3.8k
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How to convert large gene counts data into matrix?
R Bioconductor singlecell bioinformatics seurat
updated 11 weeks ago by 50k • written 4.8 years ago by • 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 5 months ago by • 0 • written 14 months ago by • 0
3
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1
reply
745
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'Seurat' package
singlecell seurat
updated 11 months ago by ★ 4.1k • written 11 months ago by ▴ 10
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1
reply
676
views
Choosing the right lower limit for emptyDrops
SingleCell emptyDrops 10X
updated 12 months ago by ▴ 740 • written 12 months ago by • 0
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2
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629
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Why my log2fcs are too high?
DESeq2 SingleCell log2FC
12 months ago paria.alipour • 0
0
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2
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713
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Scaling and normalization by deconvolution of SMART-Seq 2 data
scran Clustering SingleCell Normalization
13 months ago Assa Yeroslaviz ★ 1.5k
1
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4
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698
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Single-cell differential expression analysis with multiple samples
SingleCell
14 months ago iaradsouza1 • 0
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0
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646
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Job: Open position in the CBIO lab: single-cell proteomics
Proteomics SingleCell JobPosting MassSpectrometry
14 months ago Laurent Gatto 1.6k
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3
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1.2k
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Knee and Inflection of DropletUtils
SingleCell
updated 14 months ago by ★ 4.1k • written 14 months ago by • 0
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1
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2.4k
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DESeq2 after Seurat analysis on integrated datasets
DESeq2 SingleCell GeneExpression Seurat
updated 14 months ago by ★ 4.1k • written 14 months ago by • 0
0
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1
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661
views
Job: Reopened: 'Omics data analyst for HPCBio, University of Illinois
SingleCell Spatial RNA-seq
14 months ago Jenny Drnevich ★ 2.0k
1
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1
reply
666
views
Pseudobulk running all groups together vs subsetting first
DESeq2 edgeR SingleCell
updated 14 months ago by ★ 13k • written 14 months ago by ▴ 30
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3
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857
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Tissue Level Differential Expression Analysis
DESeq2 DifferentialExpression differentialex Pseudobulk SingleCell
updated 16 months ago by 41k • written 16 months ago by • 0
0
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1
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662
views
Job: 'Omics data analyst for HPCBio, University of Illinois
SingleCell rnaseq methylationArrayAnalysis Spatial
written 17 months ago by ★ 2.0k
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0
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842
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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
759
views
allele count data bioc object
SingleCell SingleCellMultiModal allele
updated 18 months ago by 41k • written 19 months ago by • 0
0
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0
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539
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Gene Id duplicated
SingleCell SingleCellData
updated 19 months ago by ★ 4.1k • written 19 months ago by • 0
0
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1
reply
761
views
Set up "mock" cell type as the reference?
DESeq2 SingleCell
updated 19 months ago by 41k • written 19 months ago by ▴ 10
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458
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weighting sample group
monocle SingleCell DifferentialExpression
19 months ago Sogand • 0
2
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2
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790
views
How to detect LacZ tagged cells from single cell
SingleCell SingleCellExperiment SingleCellWorkflow SingleCellData
20 months ago • updated 19 months ago k1m ▴ 20
2
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4
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914
views
Summary of library size factor is all equal to one
SingleCell SingleCellData SingleCellWorkflow SingleCellExperiment
20 months ago • updated 19 months ago Romina • 0
0
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2
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956
views
how to plot a fitting line on the testPseudotime
Pseudotime testPseudotime TSCAN SingleCell OSCA
20 months ago • updated 19 months ago Guandong Shang ▴ 40
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1
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1.1k
views
Error in .testForValidKeys(x, keys, keytype, fks) :
SingleCell AnnotationDbi
updated 20 months ago by 65k • written 20 months ago by • 0
0
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1
reply
1.0k
views
Error in running: classifySingleR from SingleR package
SingleR SingleCell
updated 21 months ago by ★ 4.1k • written 21 months ago by • 0
1
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2
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1.4k
views
DESeq2 aggregated single cell data
pseudobulk SingleCell DESeq2
21 months ago fluentin44 • 0
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0
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680
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Differential expression with single cell data: any good two component (hurdle) models recently?
SingleCellWorkflow DifferentialExpression SingleCell SingleCellMultiModal MAST
22 months ago Nik Tuzov ▴ 80
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0
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706
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Performing DGE analysis with MAST on a variable with more than 2 levels
MAST DEG SingleCell
24 months ago zroger499 • 0
2
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1
reply
738
views
() followed by [] within an argument in singlecell OSCA workflow
SingleCell R OSCA
updated 2.0 years ago by ▴ 90 • written 2.0 years ago by • 0
2
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1
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1.7k
views
Convert AnnotatedDataFrame S4 object from GEO datasets to Seurat Object
biobase SingleCellData seurat SingleCell
updated 2.3 years ago by 65k • written 2.3 years ago by • 0
0
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0
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734
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Issues geting meaninfull results for single cell DGE using MAST
MAST SingleCell
2.3 years ago zroger499 • 0
0
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0
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888
views
Job: Postdoc Opening in Bioinformatics or Computational Biology
SpatialData scRNAseq SingleCell Omixer
2.3 years ago Sebastian Lewandowski • 0
2
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2
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1.2k
views
velociraptor preparation
SingleCellExperiment singlecell velociraptor scvelo
updated 2.4 years ago by ★ 4.1k • written 2.4 years ago by ▴ 40
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0
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716
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Job: Research Scientists/Postdoctoral Candidates/Computational Biologists and Programmers excited about computational challenges in modeling CRISPR genome…
CRISPR SingleCell Genomics
2.6 years ago lpinello • 0
1
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2
replies
1.0k
views
Using limma duplicateCorrelation to account for donor/dataset effects in scRNA-Seq pseudobulk counts from multiple sources
limma SingleCell
2.6 years ago Andrew Pattison • 0
0
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0
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703
views
Spike-In Cells for Normalization?
SpikeIn SingleCell
2.7 years ago mb1996 • 0
0
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0
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685
views
Job: Computational postdoctoral fellow for cancer disparities research (Boston University)
DNASeq RNASeq SingleCell
2.7 years ago camp ▴ 10
0
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0
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910
views
Job: Senior Bioinformatician - University of Alabama at Birmingham
JobPosting Transcriptomics SingleCell RNA-seq
2.8 years ago lianov • 0
0
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1
reply
933
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
3
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2
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2.2k
views
Merging only those samples sequenced over multiple batches - scRNA-seq
SingleCell SingleCellExperiment scater
3.2 years ago camerond • 0
0
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0
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935
views
Job: Computational Biologist at Denali Therapeutics
Transcriptomics SingleCell JobPosting
3.3 years ago Steve Lianoglou ★ 13k
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 jirkanov • 0
2
votes
1
reply
1.9k
views
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
reply
831
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improving running time of runNMF
runNMF scater singlecell SingleCellExperiment
updated 3.5 years ago by ★ 28k • written 3.5 years ago by ▴ 40
0
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0
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767
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
2
votes
6
replies
2.1k
views
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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6
replies
2.6k
views
Discrepancy between cell type and cluster using SingleCellExperiment and SingleR
singlecell singlecellexperiment umap singleR
updated 3.7 years ago by ★ 28k • written 3.7 years ago by ▴ 80
0
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2
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1.5k
views
most correlated genes in SingleR
singlecell singleR
updated 3.7 years ago by ★ 28k • written 3.7 years ago by ▴ 40
0
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1
reply
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
50 results • Page 1 of 1
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Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2 by Kim • 0
Thank you Tim, this is a great help in getting me started!
Votes
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
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