Showing : singlecell • reset
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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
7 weeks ago Peter Hickey ▴ 740
3
votes
1
reply
733
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'Seurat' package
singlecell seurat
updated 11 months ago by ★ 4.0k • written 11 months ago by ▴ 10
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1
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657
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Choosing the right lower limit for emptyDrops
SingleCell emptyDrops 10X
updated 11 months ago by ▴ 740 • written 11 months ago by • 0
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2
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615
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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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700
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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
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4
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685
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Single-cell differential expression analysis with multiple samples
SingleCell
13 months ago iaradsouza1 • 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 13 months ago by • 0
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637
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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
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3
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1.2k
views
Knee and Inflection of DropletUtils
SingleCell
updated 14 months ago by ★ 4.0k • written 14 months ago by • 0
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1
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2.3k
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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
1
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1
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653
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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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1
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644
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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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3
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848
views
Tissue Level Differential Expression Analysis
DESeq2 DifferentialExpression differentialex Pseudobulk SingleCell
updated 16 months ago by 41k • written 16 months ago by • 0
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1
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654
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Job: 'Omics data analyst for HPCBio, University of Illinois
SingleCell rnaseq methylationArrayAnalysis Spatial
written 16 months ago by ★ 2.0k
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2
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890
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Single-Cell Data Simulation from Bulk RNA-seq
SingleCell RNASeq RNASeqData scRNAseq
updated 9 days ago by • 0 • written 17 months ago by • 0
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1
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753
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allele count data bioc object
SingleCell SingleCellMultiModal allele
updated 18 months ago by 41k • written 18 months ago by • 0
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0
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828
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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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0
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535
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Gene Id duplicated
SingleCell SingleCellData
updated 19 months ago by ★ 4.0k • written 19 months ago by • 0
0
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1
reply
753
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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0
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450
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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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778
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How to detect LacZ tagged cells from single cell
SingleCell SingleCellExperiment SingleCellWorkflow SingleCellData
19 months ago k1m ▴ 20
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2
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945
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how to plot a fitting line on the testPseudotime
Pseudotime testPseudotime TSCAN SingleCell OSCA
19 months ago Guandong Shang ▴ 40
2
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4
replies
904
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Summary of library size factor is all equal to one
SingleCell SingleCellData SingleCellWorkflow SingleCellExperiment
19 months ago Romina • 0
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1
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1.1k
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Error in .testForValidKeys(x, keys, keytype, fks) :
SingleCell AnnotationDbi
updated 20 months ago by 65k • written 20 months ago by • 0
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1
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1.0k
views
Error in running: classifySingleR from SingleR package
SingleR SingleCell
updated 21 months ago by ★ 4.0k • written 21 months ago by • 0
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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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670
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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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702
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Performing DGE analysis with MAST on a variable with more than 2 levels
MAST DEG SingleCell
23 months ago zroger499 • 0
2
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1
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734
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
reply
1.6k
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
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0
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730
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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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877
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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
replies
1.2k
views
velociraptor preparation
SingleCellExperiment singlecell velociraptor scvelo
updated 2.4 years ago by ★ 4.0k • written 2.4 years ago by ▴ 40
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0
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710
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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
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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
0
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0
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699
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Spike-In Cells for Normalization?
SpikeIn SingleCell
2.7 years ago mb1996 • 0
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0
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680
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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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902
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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
929
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
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Merging only those samples sequenced over multiple batches - scRNA-seq
SingleCell SingleCellExperiment scater
3.2 years ago camerond • 0
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0
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930
views
Job: Computational Biologist at Denali Therapeutics
Transcriptomics SingleCell JobPosting
3.3 years ago Steve Lianoglou ★ 13k
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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
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1
reply
1.8k
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
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828
views
improving running time of runNMF
runNMF scater singlecell SingleCellExperiment
updated 3.5 years ago by ★ 28k • written 3.5 years ago by ▴ 40
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0
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760
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
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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
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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
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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
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
50 results • Page 1 of 1
Recent ...
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Answer: Dominance Index for Shotgun Metagenomics Data by Leo Lahti ▴ 40
1. Note that Simpson's dominance index (\lambda) is a different index than inverse Simpson (1/\lambda) or reciprocal Simpson (1-\lambda). T…
Comment: Math expression in shapeCustom legend in EnhancedVolcano by pl23 • 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions by Michael Love 41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona ▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative? by Michael Love 41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Votes
Answer: Dominance Index for Shotgun Metagenomics Data
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
Awards • All
Popular Question to Leo Lahti ▴ 40
Scholar to James W. MacDonald 65k
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Scholar to Michael Love 41k
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