Showing : singlecell • reset
5
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5
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1.4k
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Association analysis between gene expression and Phenotype
rna singlecell limma
updated 5.1 years ago by ★ 28k • written 5.1 years ago by ▴ 20
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
3.3 years ago • updated 3.2 years ago camerond • 0
3
votes
1
reply
748
views
'Seurat' package
singlecell seurat
updated 12 months ago by ★ 4.1k • written 12 months ago by ▴ 10
2
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4
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917
views
Summary of library size factor is all equal to one
SingleCell SingleCellData SingleCellWorkflow SingleCellExperiment
20 months ago Romina • 0
2
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6
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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
2
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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
2
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1
reply
739
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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2
replies
791
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How to detect LacZ tagged cells from single cell
SingleCell SingleCellExperiment SingleCellWorkflow SingleCellData
20 months ago k1m ▴ 20
2
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2
replies
1.2k
views
velociraptor preparation
SingleCellExperiment singlecell velociraptor scvelo
updated 2.4 years ago by ★ 4.1k • written 2.4 years ago by ▴ 40
2
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1
reply
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
2
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4
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3.8k
views
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
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
1
vote
4
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703
views
Single-cell differential expression analysis with multiple samples
SingleCell
14 months ago iaradsouza1 • 0
1
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2
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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
1
vote
1
reply
667
views
Pseudobulk running all groups together vs subsetting first
DESeq2 edgeR SingleCell
updated 14 months ago by ★ 13k • written 15 months ago by ▴ 30
0
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0
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736
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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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8
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1.2k
views
fail to annotate chromosome data to single cell object
error SingleCell annotate
updated 5 months ago by • 0 • written 14 months ago by • 0
0
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1
reply
1.2k
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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0
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649
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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
0
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3
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2.0k
views
marker genes in singleR
singleR singlecell singlecellexperiment
updated 3.7 years ago by ★ 28k • written 3.7 years ago by ▴ 40
0
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2
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632
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Why my log2fcs are too high?
DESeq2 SingleCell log2FC
12 months ago paria.alipour • 0
0
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1
reply
2.4k
views
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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0
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704
views
Spike-In Cells for Normalization?
SpikeIn SingleCell
2.7 years ago mb1996 • 0
0
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1
reply
666
views
Job: 'Omics data analyst for HPCBio, University of Illinois
SingleCell rnaseq methylationArrayAnalysis Spatial
written 17 months ago by ★ 2.0k
0
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0
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224
views
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
0
votes
1
reply
1.9k
views
Error in .updateHubDB(hub_bfc, .class, url, proxy, localHub) :
annotation singlecell rna-seq
updated 4.2 years ago by 3.9k • written 4.2 years ago by • 0
0
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0
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891
views
Job: Postdoc Opening in Bioinformatics or Computational Biology
SpatialData scRNAseq SingleCell Omixer
2.3 years ago Sebastian Lewandowski • 0
0
votes
1
reply
677
views
Choosing the right lower limit for emptyDrops
SingleCell emptyDrops 10X
updated 12 months ago by ▴ 740 • written 12 months ago by • 0
0
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0
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718
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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
0
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3
replies
1.2k
views
Knee and Inflection of DropletUtils
SingleCell
updated 14 months ago by ★ 4.1k • written 14 months ago by • 0
0
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0
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911
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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2
replies
919
views
Single-Cell Data Simulation from Bulk RNA-seq
SingleCell RNASeq RNASeqData scRNAseq
updated 18 days ago by • 0 • written 17 months ago by • 0
0
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0
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844
views
Job: Postdoctoral Fellow in Epigenomcis/Neurobiology (MGH/Harvard Medical School, Boston)
GenomicVariation SingleCell Autism Neurogenesis Epigenetics
18 months ago sudhir.thakurela • 0
0
votes
1
reply
664
views
Job: Reopened: 'Omics data analyst for HPCBio, University of Illinois
SingleCell Spatial RNA-seq
15 months ago • updated 14 months ago Jenny Drnevich ★ 2.0k
0
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0
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682
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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0
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459
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weighting sample group
monocle SingleCell DifferentialExpression
19 months ago Sogand • 0
0
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0
replies
686
views
Job: Computational postdoctoral fellow for cancer disparities research (Boston University)
DNASeq RNASeq SingleCell
2.8 years ago camp ▴ 10
0
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0
replies
541
views
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
766
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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2
replies
717
views
Scaling and normalization by deconvolution of SMART-Seq 2 data
scran Clustering SingleCell Normalization
13 months ago Assa Yeroslaviz ★ 1.5k
0
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1
reply
761
views
allele count data bioc object
SingleCell SingleCellMultiModal allele
updated 18 months ago by 41k • written 19 months ago by • 0
0
votes
1
reply
936
views
Differentially expressed genes across three different conditions
MAST SingleCell diffGeneAnalysis
updated 2.9 years ago by 65k • written 2.9 years ago by • 0
0
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1
reply
1.1k
views
Error in running: classifySingleR from SingleR package
SingleR SingleCell
updated 21 months ago by ★ 4.1k • written 21 months ago by • 0
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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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
votes
0
replies
770
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
votes
1
reply
833
views
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
replies
708
views
Performing DGE analysis with MAST on a variable with more than 2 levels
MAST DEG SingleCell
24 months ago zroger499 • 0
0
votes
0
replies
936
views
Job: Computational Biologist at Denali Therapeutics
Transcriptomics SingleCell JobPosting
3.4 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
50 results • Page 1 of 1
Recent ...
Replies
Comment: Method to find pathways different between 2 groups by Chris • 0
Sorry for not clear. I just try to find papers use this method for learning purpose.
Comment: Improving the design matrices vignette in RNAseq123 by Lluís Revilla Sancho ▴ 730
Cool. Thanks for looking into it.
Comment: Couldn't connect to server while using "pathways" by ATpoint ★ 4.1k
Please understand that we neither can see your screen, nor read minds. You at least need to provide the line of code and the name of the pa…
Answer: Method to find pathways different between 2 groups by Gordon Smyth 50k
> When I search camera limma on pubmed, I found 2 papers I am unclear what point you are trying to make. limma's camera method has been fo…
Comment: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
limma is available. It installs in R 4.4.0 and Bioc 3.19 for all platforms without any issues. It has not had any period of unavailability.…
Votes
Answer: Method to find pathways different between 2 groups
Comment: Trying to use enrichGO
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Handling multiple differential expression comparisons
Answer: fgsea significant result
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