Showing : SingleCell • reset
3
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371
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'Seurat' package
singlecell seurat
updated 4 months ago by ★ 3.4k • written 4 months ago by ▴ 10
0
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1
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299
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Choosing the right lower limit for emptyDrops
SingleCell emptyDrops 10X
updated 4 months ago by ▴ 650 • written 4 months ago by • 0
0
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2
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299
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Why my log2fcs are too high?
DESeq2 SingleCell log2FC
5 months ago paria.alipour • 0
0
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2
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318
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Scaling and normalization by deconvolution of SMART-Seq 2 data
scran Clustering SingleCell Normalization
6 months ago Assa Yeroslaviz ★ 1.5k
1
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4
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377
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Single-cell differential expression analysis with multiple samples
SingleCell
6 months ago iaradsouza1 • 0
0
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7
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630
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fail to annotate chromosome data to single cell object
error SingleCell annotate
6 months ago sandra.garces.19 • 0
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0
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290
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Job: Open position in the CBIO lab: single-cell proteomics
Proteomics SingleCell JobPosting MassSpectrometry
6 months ago Laurent Gatto 1.6k
0
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3
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588
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Knee and Inflection of DropletUtils
SingleCell
updated 6 months ago by ★ 3.4k • written 7 months ago by • 0
0
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1
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1.0k
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DESeq2 after Seurat analysis on integrated datasets
DESeq2 SingleCell GeneExpression Seurat
updated 7 months ago by ★ 3.4k • written 7 months ago by • 0
1
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1
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355
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Pseudobulk running all groups together vs subsetting first
DESeq2 edgeR SingleCell
updated 7 months ago by 13k • written 7 months ago by • 0
0
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1
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316
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Job: Reopened: 'Omics data analyst for HPCBio, University of Illinois
SingleCell Spatial RNA-seq
7 months ago Jenny Drnevich ★ 2.0k
0
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3
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533
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Tissue Level Differential Expression Analysis
DESeq2 DifferentialExpression differentialex Pseudobulk SingleCell
updated 9 months ago by 40k • written 9 months ago by • 0
0
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1
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386
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Job: 'Omics data analyst for HPCBio, University of Illinois
SingleCell rnaseq methylationArrayAnalysis Spatial
written 9 months ago by ★ 2.0k
0
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1
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492
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Single-Cell Data Simulation from Bulk RNA-seq
SingleCell RNASeq RNASeqData scRNAseq
updated 10 months ago by 48k • written 10 months ago by • 0
0
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1
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537
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allele count data bioc object
SingleCell SingleCellMultiModal allele
updated 11 months ago by 40k • written 11 months ago by • 0
0
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0
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528
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Job: Postdoctoral Fellow in Epigenomcis/Neurobiology (MGH/Harvard Medical School, Boston)
GenomicVariation SingleCell Autism Neurogenesis Epigenetics
11 months ago sudhir.thakurela • 0
0
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0
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340
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Gene Id duplicated
SingleCell SingleCellData
updated 12 months ago by ★ 3.4k • written 12 months ago by • 0
0
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1
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423
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Set up "mock" cell type as the reference?
DESeq2 SingleCell
updated 12 months ago by 40k • written 12 months ago by ▴ 10
0
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0
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275
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weighting sample group
monocle SingleCell DifferentialExpression
12 months ago Sogand • 0
2
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2
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476
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How to detect LacZ tagged cells from single cell
SingleCell SingleCellExperiment SingleCellWorkflow SingleCellData
12 months ago k1m ▴ 20
0
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2
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551
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how to plot a fitting line on the testPseudotime
Pseudotime testPseudotime TSCAN SingleCell OSCA
12 months ago Guandong Shang ▴ 40
2
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4
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616
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Summary of library size factor is all equal to one
SingleCell SingleCellData SingleCellWorkflow SingleCellExperiment
12 months ago Romina • 0
0
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1
reply
791
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Error in .testForValidKeys(x, keys, keytype, fks) :
SingleCell AnnotationDbi
updated 13 months ago by 63k • written 13 months ago by • 0
0
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1
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597
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Error in running: classifySingleR from SingleR package
SingleR SingleCell
updated 14 months ago by ★ 3.4k • written 14 months ago by • 0
1
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2
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842
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DESeq2 aggregated single cell data
pseudobulk SingleCell DESeq2
14 months ago fluentin44 • 0
0
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0
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428
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Differential expression with single cell data: any good two component (hurdle) models recently?
SingleCellWorkflow DifferentialExpression SingleCell SingleCellMultiModal MAST
15 months ago Nik Tuzov ▴ 80
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485
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Performing DGE analysis with MAST on a variable with more than 2 levels
MAST DEG SingleCell
16 months ago zroger499 • 0
2
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1
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505
views
() followed by [] within an argument in singlecell OSCA workflow
SingleCell R OSCA
updated 17 months ago by ▴ 90 • written 17 months ago by • 0
2
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1
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1.2k
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Convert AnnotatedDataFrame S4 object from GEO datasets to Seurat Object
biobase SingleCellData seurat SingleCell
updated 20 months ago by 63k • written 20 months ago by • 0
0
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0
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509
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Issues geting meaninfull results for single cell DGE using MAST
MAST SingleCell
20 months ago zroger499 • 0
0
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0
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676
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Job: Postdoc Opening in Bioinformatics or Computational Biology
SpatialData scRNAseq SingleCell Omixer
20 months ago Sebastian Lewandowski • 0
2
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2
replies
900
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velociraptor preparation
SingleCellExperiment singlecell velociraptor scvelo
updated 21 months ago by ★ 3.4k • written 21 months ago by ▴ 40
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529
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Job: Research Scientists/Postdoctoral Candidates/Computational Biologists and Programmers excited about computational challenges in modeling CRISPR genome…
CRISPR SingleCell Genomics
24 months ago lpinello • 0
1
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2
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774
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Using limma duplicateCorrelation to account for donor/dataset effects in scRNA-Seq pseudobulk counts from multiple sources
limma SingleCell
24 months ago Andrew Pattison • 0
0
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0
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520
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Spike-In Cells for Normalization?
SpikeIn SingleCell
2.1 years ago mb1996 • 0
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0
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503
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Job: Computational postdoctoral fellow for cancer disparities research (Boston University)
DNASeq RNASeq SingleCell
2.1 years ago camp • 0
0
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0
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642
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Job: Senior Bioinformatician - University of Alabama at Birmingham
JobPosting Transcriptomics SingleCell RNA-seq
2.2 years ago lianov • 0
0
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1
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677
views
Differentially expressed genes across three different conditions
MAST SingleCell diffGeneAnalysis
updated 2.2 years ago by 63k • written 2.2 years ago by • 0
3
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2
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1.6k
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Merging only those samples sequenced over multiple batches - scRNA-seq
SingleCell SingleCellExperiment scater
2.6 years ago camerond • 0
0
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0
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716
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Job: Computational Biologist at Denali Therapeutics
Transcriptomics SingleCell JobPosting
2.7 years ago Steve Lianoglou 13k
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2
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1.1k
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Removal of cell cycle effect using batchelor::regressBatches() and proper usage of corrected UMI matrix
scRNAseq batchelor SingleCell SingleCellExperiment scran
2.8 years ago jirkanov • 0
2
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1
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1.5k
views
DESeq2 DE gene expression of scRNA-seq pseudobulk
DESeq2 SingleCell
updated 2.8 years ago by 40k • written 2.8 years ago by • 0
0
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1
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637
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improving running time of runNMF
runNMF scater singlecell SingleCellExperiment
updated 2.9 years ago by ★ 28k • written 2.9 years ago by ▴ 40
0
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0
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563
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Creating a stable batch-corrected scRNA-Seq data with multiple datasets and multiple integrations
scater singlecell scran BatchEffect
2.9 years ago hamza_karakurt ▴ 50
2
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6
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1.7k
views
Discarding ambient RNA using estimateAmbience
emptyDrop ambient singlecell estimateAmbience
updated 3.0 years ago by ★ 28k • written 3.0 years ago by ▴ 40
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6
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1.9k
views
Discrepancy between cell type and cluster using SingleCellExperiment and SingleR
singlecell singlecellexperiment umap singleR
updated 3.1 years ago by ★ 28k • written 3.1 years ago by ▴ 80
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2
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1.1k
views
most correlated genes in SingleR
singlecell singleR
updated 3.1 years ago by ★ 28k • written 3.1 years ago by ▴ 40
0
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1
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1000
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predicting cell type of clusters using singleR
singleR singlecell
updated 3.1 years ago by ★ 28k • written 3.1 years ago by ▴ 40
0
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3
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1.6k
views
marker genes in singleR
singleR singlecell singlecellexperiment
updated 3.1 years ago by ★ 28k • written 3.1 years ago by ▴ 40
0
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1
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1.1k
views
Error in .updateHubDB(hub_bfc, .class, url, proxy, localHub) :
annotation singlecell rna-seq
updated 3.6 years ago by 3.5k • written 3.6 years ago by • 0
50 results • Page 1 of 1
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Replies
Comment: biomaRt code/getBM function no longer importing 'coding' sequence via seqType ar by James W. MacDonald 63k
I should also point out that you can find this out by yourself by going to [ensembl][1], clicking on the Biomart link, and then scrolling t…
Answer: biomaRt code/getBM function no longer importing 'coding' sequence via seqType ar by James W. MacDonald 63k
It's my understanding that the archived Biomart data are not complete, which is likely why you cannot get sequences. But you apparently jus…
Comment: ComBat_seq function in sva package does not return a matrix by Federico ▴ 10
Thanks for your help, problem solved :)
Answer: ComBat_seq function in sva package does not return a matrix by ATpoint ★ 3.4k
That happens if your `x` is a data.frame rather than a matrix. It is listed under the Q&A section in https://github.com/zhangyuqing/ComBat-…
Answer: error running exp2grn by Fabricio Almeida-Silva ▴ 40
Hi, Adriana. It seems like the gene IDs you specified in `Host13tfs$Protein.ID` do not match any gene IDs in the row names of your expr…
Votes
ComBat_seq function in sva package does not return a matrix
Answer: ComBat_seq function in sva package does not return a matrix
Answer: ComBat_seq function in sva package does not return a matrix
Answer: ComBat_seq function in sva package does not return a matrix
Answer: ComBat_seq function in sva package does not return a matrix
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