Showing : singlecell • reset
3
votes
1
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478
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'Seurat' package
singlecell seurat
updated 6 months ago by ★ 3.6k • written 6 months ago by ▴ 10
0
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1
reply
414
views
Choosing the right lower limit for emptyDrops
SingleCell emptyDrops 10X
updated 6 months ago by ▴ 650 • written 6 months ago by • 0
0
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2
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394
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Why my log2fcs are too high?
DESeq2 SingleCell log2FC
7 months ago paria.alipour • 0
0
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2
replies
425
views
Scaling and normalization by deconvolution of SMART-Seq 2 data
scran Clustering SingleCell Normalization
8 months ago Assa Yeroslaviz ★ 1.5k
1
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4
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476
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Single-cell differential expression analysis with multiple samples
SingleCell
8 months ago iaradsouza1 • 0
0
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8
replies
807
views
fail to annotate chromosome data to single cell object
error SingleCell annotate
updated 9 days ago by • 0 • written 8 months ago by • 0
0
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0
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392
views
Job: Open position in the CBIO lab: single-cell proteomics
Proteomics SingleCell JobPosting MassSpectrometry
8 months ago Laurent Gatto 1.6k
0
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3
replies
778
views
Knee and Inflection of DropletUtils
SingleCell
updated 8 months ago by ★ 3.6k • written 9 months ago by • 0
0
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1
reply
1.3k
views
DESeq2 after Seurat analysis on integrated datasets
DESeq2 SingleCell GeneExpression Seurat
updated 9 months ago by ★ 3.6k • written 9 months ago by • 0
1
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1
reply
446
views
Pseudobulk running all groups together vs subsetting first
DESeq2 edgeR SingleCell
updated 9 months ago by 13k • written 9 months ago by • 0
0
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1
reply
429
views
Job: Reopened: 'Omics data analyst for HPCBio, University of Illinois
SingleCell Spatial RNA-seq
9 months ago Jenny Drnevich ★ 2.0k
0
votes
3
replies
643
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Tissue Level Differential Expression Analysis
DESeq2 DifferentialExpression differentialex Pseudobulk SingleCell
updated 11 months ago by 41k • written 11 months ago by • 0
0
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1
reply
473
views
Job: 'Omics data analyst for HPCBio, University of Illinois
SingleCell rnaseq methylationArrayAnalysis Spatial
written 11 months ago by ★ 2.0k
0
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1
reply
610
views
Single-Cell Data Simulation from Bulk RNA-seq
SingleCell RNASeq RNASeqData scRNAseq
updated 12 months ago by 48k • written 12 months ago by • 0
0
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1
reply
614
views
allele count data bioc object
SingleCell SingleCellMultiModal allele
updated 13 months ago by 41k • written 13 months ago by • 0
0
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0
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624
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Job: Postdoctoral Fellow in Epigenomcis/Neurobiology (MGH/Harvard Medical School, Boston)
GenomicVariation SingleCell Autism Neurogenesis Epigenetics
13 months ago sudhir.thakurela • 0
0
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0
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410
views
Gene Id duplicated
SingleCell SingleCellData
updated 14 months ago by ★ 3.6k • written 14 months ago by • 0
0
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1
reply
531
views
Set up "mock" cell type as the reference?
DESeq2 SingleCell
updated 14 months ago by 41k • written 14 months ago by ▴ 10
0
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0
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341
views
weighting sample group
monocle SingleCell DifferentialExpression
14 months ago Sogand • 0
2
votes
2
replies
574
views
How to detect LacZ tagged cells from single cell
SingleCell SingleCellExperiment SingleCellWorkflow SingleCellData
14 months ago k1m ▴ 20
0
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2
replies
685
views
how to plot a fitting line on the testPseudotime
Pseudotime testPseudotime TSCAN SingleCell OSCA
14 months ago Guandong Shang ▴ 40
2
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4
replies
715
views
Summary of library size factor is all equal to one
SingleCell SingleCellData SingleCellWorkflow SingleCellExperiment
14 months ago Romina • 0
0
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1
reply
916
views
Error in .testForValidKeys(x, keys, keytype, fks) :
SingleCell AnnotationDbi
updated 15 months ago by 64k • written 15 months ago by • 0
0
votes
1
reply
704
views
Error in running: classifySingleR from SingleR package
SingleR SingleCell
updated 16 months ago by ★ 3.6k • written 16 months ago by • 0
1
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2
replies
1.0k
views
DESeq2 aggregated single cell data
pseudobulk SingleCell DESeq2
16 months ago fluentin44 • 0
0
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0
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509
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Differential expression with single cell data: any good two component (hurdle) models recently?
SingleCellWorkflow DifferentialExpression SingleCell SingleCellMultiModal MAST
17 months ago Nik Tuzov ▴ 80
0
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0
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563
views
Performing DGE analysis with MAST on a variable with more than 2 levels
MAST DEG SingleCell
18 months ago zroger499 • 0
2
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1
reply
590
views
() followed by [] within an argument in singlecell OSCA workflow
SingleCell R OSCA
updated 19 months ago by ▴ 90 • written 19 months ago by • 0
2
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1
reply
1.3k
views
Convert AnnotatedDataFrame S4 object from GEO datasets to Seurat Object
biobase SingleCellData seurat SingleCell
updated 22 months ago by 64k • written 22 months ago by • 0
0
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0
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578
views
Issues geting meaninfull results for single cell DGE using MAST
MAST SingleCell
22 months ago zroger499 • 0
0
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0
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747
views
Job: Postdoc Opening in Bioinformatics or Computational Biology
SpatialData scRNAseq SingleCell Omixer
22 months ago Sebastian Lewandowski • 0
2
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2
replies
984
views
velociraptor preparation
SingleCellExperiment singlecell velociraptor scvelo
updated 23 months ago by ★ 3.6k • written 23 months ago by ▴ 40
0
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0
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596
views
Job: Research Scientists/Postdoctoral Candidates/Computational Biologists and Programmers excited about computational challenges in modeling CRISPR genome…
CRISPR SingleCell Genomics
2.1 years ago lpinello • 0
1
vote
2
replies
865
views
Using limma duplicateCorrelation to account for donor/dataset effects in scRNA-Seq pseudobulk counts from multiple sources
limma SingleCell
2.2 years ago Andrew Pattison • 0
0
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0
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590
views
Spike-In Cells for Normalization?
SpikeIn SingleCell
2.3 years ago mb1996 • 0
0
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0
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565
views
Job: Computational postdoctoral fellow for cancer disparities research (Boston University)
DNASeq RNASeq SingleCell
2.3 years ago camp • 0
0
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0
replies
714
views
Job: Senior Bioinformatician - University of Alabama at Birmingham
JobPosting Transcriptomics SingleCell RNA-seq
2.3 years ago lianov • 0
0
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1
reply
762
views
Differentially expressed genes across three different conditions
MAST SingleCell diffGeneAnalysis
updated 2.4 years ago by 64k • written 2.4 years ago by • 0
3
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2
replies
1.7k
views
Merging only those samples sequenced over multiple batches - scRNA-seq
SingleCell SingleCellExperiment scater
2.8 years ago camerond • 0
0
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0
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777
views
Job: Computational Biologist at Denali Therapeutics
Transcriptomics SingleCell JobPosting
2.9 years ago Steve Lianoglou 13k
0
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2
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1.2k
views
Removal of cell cycle effect using batchelor::regressBatches() and proper usage of corrected UMI matrix
scRNAseq batchelor SingleCell SingleCellExperiment scran
3.0 years ago jirkanov • 0
2
votes
1
reply
1.6k
views
DESeq2 DE gene expression of scRNA-seq pseudobulk
DESeq2 SingleCell
updated 3.0 years ago by 41k • written 3.0 years ago by • 0
0
votes
1
reply
706
views
improving running time of runNMF
runNMF scater singlecell SingleCellExperiment
updated 3.0 years ago by ★ 28k • written 3.0 years ago by ▴ 40
0
votes
0
replies
630
views
Creating a stable batch-corrected scRNA-Seq data with multiple datasets and multiple integrations
scater singlecell scran BatchEffect
3.1 years ago hamza_karakurt ▴ 50
2
votes
6
replies
1.8k
views
Discarding ambient RNA using estimateAmbience
emptyDrop ambient singlecell estimateAmbience
updated 3.2 years ago by ★ 28k • written 3.2 years ago by ▴ 40
0
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6
replies
2.1k
views
Discrepancy between cell type and cluster using SingleCellExperiment and SingleR
singlecell singlecellexperiment umap singleR
updated 3.2 years ago by ★ 28k • written 3.2 years ago by ▴ 80
0
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2
replies
1.2k
views
most correlated genes in SingleR
singlecell singleR
updated 3.3 years ago by ★ 28k • written 3.3 years ago by ▴ 40
0
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1
reply
1.1k
views
predicting cell type of clusters using singleR
singleR singlecell
updated 3.3 years ago by ★ 28k • written 3.3 years ago by ▴ 40
0
votes
3
replies
1.7k
views
marker genes in singleR
singleR singlecell singlecellexperiment
updated 3.3 years ago by ★ 28k • written 3.3 years ago by ▴ 40
0
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1
reply
1.4k
views
Error in .updateHubDB(hub_bfc, .class, url, proxy, localHub) :
annotation singlecell rna-seq
updated 3.8 years ago by 3.6k • written 3.8 years ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Result from GSEA for non-model organism not as expected by James W. MacDonald 64k
I asked you in a previous thread to **not add comments to old threads** and instead start a new one. Please follow that advice. It's fine i…
Comment: Problem making orgdb package for bacteria (Pseudomonas) using annotation hub and by James W. MacDonald 64k
This is something you should be able to work out on your own. When you get an error, you have to read it and try to figure out what it mean…
Comment: Subtracting INPUT reads from ChIP read counts. by ann-sophie.gironne • 0
Hi Rory! I'm trying to scale my bigwig files so the visualization on IGV matches what the DiffBind analysis results, being that the sample…
Comment: Ensembl down??? by James W. MacDonald 64k
Yup, they seem to be down. What exactly are you trying to do? There may be other options.
Answer: Result from GSEA for non-model organism not as expected by Aastha Kapoor • 0
I have a similar issue, I have transcriptome data of an inhouse sequenced bacterial genome. I made the database for that bacteria using mak…
Votes
Comment: Ensembl down???
Answer: Limma/DESeq2 for unbalanced nested design (paired samples)
Result from GSEA for non-model organism not as expected
Comment: DESeq2 estimateSizeFactors iterate takes too long
Answer: DESeq2 estimateSizeFactors iterate takes too long
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