Showing : singlecell • reset
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Job: Postdoctoral fellowships in Spatial Omics and Single Cell Genomics at the University of Padova (IT)
SingleCell Transcriptomics SpatialDatasets SpatialData
18 days ago Silvio • 0
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0
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300
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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
3 months ago Peter Hickey ▴ 740
3
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1
reply
818
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'Seurat' package
singlecell seurat
updated 13 months ago by ★ 4.2k • written 13 months ago by ▴ 10
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1
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720
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Choosing the right lower limit for emptyDrops
SingleCell emptyDrops 10X
updated 13 months ago by ▴ 740 • written 13 months ago by • 0
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2
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663
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Why my log2fcs are too high?
DESeq2 SingleCell log2FC
13 months ago paria.alipour • 0
0
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2
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812
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Scaling and normalization by deconvolution of SMART-Seq 2 data
scran Clustering SingleCell Normalization
14 months ago Assa Yeroslaviz ★ 1.5k
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4
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751
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Single-cell differential expression analysis with multiple samples
SingleCell
15 months ago iaradsouza1 • 0
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8
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1.2k
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fail to annotate chromosome data to single cell object
error SingleCell annotate
updated 7 months ago by • 0 • written 15 months ago by • 0
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0
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693
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Job: Open position in the CBIO lab: single-cell proteomics
Proteomics SingleCell JobPosting MassSpectrometry
15 months ago Laurent Gatto 1.6k
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3
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1.3k
views
Knee and Inflection of DropletUtils
SingleCell
updated 15 months ago by ★ 4.2k • written 15 months ago by • 0
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1
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2.7k
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DESeq2 after Seurat analysis on integrated datasets
DESeq2 SingleCell GeneExpression Seurat
updated 16 months ago by ★ 4.2k • written 16 months ago by • 0
1
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1
reply
737
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Pseudobulk running all groups together vs subsetting first
DESeq2 edgeR SingleCell
updated 16 months ago by ★ 13k • written 16 months ago by ▴ 50
0
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1
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719
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Job: Reopened: 'Omics data analyst for HPCBio, University of Illinois
SingleCell Spatial RNA-seq
16 months ago Jenny Drnevich ★ 2.0k
0
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3
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895
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Tissue Level Differential Expression Analysis
DESeq2 DifferentialExpression differentialex Pseudobulk SingleCell
updated 17 months ago by 42k • written 17 months ago by • 0
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1
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704
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Job: 'Omics data analyst for HPCBio, University of Illinois
SingleCell rnaseq methylationArrayAnalysis Spatial
written 18 months ago by ★ 2.0k
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2
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1.0k
views
Single-Cell Data Simulation from Bulk RNA-seq
SingleCell RNASeq RNASeqData scRNAseq
updated 8 weeks ago by • 0 • written 19 months ago by • 0
0
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1
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787
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allele count data bioc object
SingleCell SingleCellMultiModal allele
updated 20 months ago by 42k • written 20 months ago by • 0
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0
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895
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Job: Postdoctoral Fellow in Epigenomcis/Neurobiology (MGH/Harvard Medical School, Boston)
GenomicVariation SingleCell Autism Neurogenesis Epigenetics
20 months ago sudhir.thakurela • 0
0
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0
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589
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Gene Id duplicated
SingleCell SingleCellData
updated 20 months ago by ★ 4.2k • written 20 months ago by • 0
0
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1
reply
800
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Set up "mock" cell type as the reference?
DESeq2 SingleCell
updated 21 months ago by 42k • written 21 months ago by ▴ 10
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481
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weighting sample group
monocle SingleCell DifferentialExpression
21 months ago Sogand • 0
2
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2
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824
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How to detect LacZ tagged cells from single cell
SingleCell SingleCellExperiment SingleCellWorkflow SingleCellData
21 months ago k1m ▴ 20
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2
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1.0k
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how to plot a fitting line on the testPseudotime
Pseudotime testPseudotime TSCAN SingleCell OSCA
21 months ago Guandong Shang ▴ 40
2
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4
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967
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Summary of library size factor is all equal to one
SingleCell SingleCellData SingleCellWorkflow SingleCellExperiment
21 months ago Romina • 0
0
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1
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1.2k
views
Error in .testForValidKeys(x, keys, keytype, fks) :
SingleCell AnnotationDbi
updated 21 months ago by 66k • written 21 months ago by • 0
0
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1
reply
1.2k
views
Error in running: classifySingleR from SingleR package
SingleR SingleCell
updated 22 months ago by ★ 4.2k • written 22 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
23 months ago fluentin44 • 0
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0
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721
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Differential expression with single cell data: any good two component (hurdle) models recently?
SingleCellWorkflow DifferentialExpression SingleCell SingleCellMultiModal MAST
24 months ago Nik Tuzov ▴ 80
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745
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Performing DGE analysis with MAST on a variable with more than 2 levels
MAST DEG SingleCell
2.1 years ago zroger499 • 0
2
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1
reply
767
views
() followed by [] within an argument in singlecell OSCA workflow
SingleCell R OSCA
updated 2.2 years ago by ▴ 90 • written 2.2 years ago by • 0
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 2.4 years ago by 66k • written 2.4 years ago by • 0
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778
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Issues geting meaninfull results for single cell DGE using MAST
MAST SingleCell
2.4 years ago zroger499 • 0
0
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0
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947
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Job: Postdoc Opening in Bioinformatics or Computational Biology
SpatialData scRNAseq SingleCell Omixer
2.4 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 2.5 years ago by ★ 4.2k • written 2.5 years ago by ▴ 40
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0
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745
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Job: Research Scientists/Postdoctoral Candidates/Computational Biologists and Programmers excited about computational challenges in modeling CRISPR genome…
CRISPR SingleCell Genomics
2.7 years ago lpinello • 0
1
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2
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1.1k
views
Using limma duplicateCorrelation to account for donor/dataset effects in scRNA-Seq pseudobulk counts from multiple sources
limma SingleCell
2.7 years ago Andrew Pattison • 0
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0
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734
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Spike-In Cells for Normalization?
SpikeIn SingleCell
2.8 years ago mb1996 • 0
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0
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709
views
Job: Computational postdoctoral fellow for cancer disparities research (Boston University)
DNASeq RNASeq SingleCell
2.9 years ago camp ▴ 10
0
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0
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946
views
Job: Senior Bioinformatician - University of Alabama at Birmingham
JobPosting Transcriptomics SingleCell RNA-seq
2.9 years ago lianov • 0
0
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1
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966
views
Differentially expressed genes across three different conditions
MAST SingleCell diffGeneAnalysis
updated 3.0 years ago by 66k • written 3.0 years ago by • 0
3
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2
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2.3k
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Merging only those samples sequenced over multiple batches - scRNA-seq
SingleCell SingleCellExperiment scater
3.4 years ago camerond • 0
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0
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968
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Job: Computational Biologist at Denali Therapeutics
Transcriptomics SingleCell JobPosting
3.5 years ago Steve Lianoglou ★ 13k
0
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2
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1.5k
views
Removal of cell cycle effect using batchelor::regressBatches() and proper usage of corrected UMI matrix
scRNAseq batchelor SingleCell SingleCellExperiment scran
3.5 years ago jirkanov • 0
3
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1
reply
1.9k
views
DESeq2 DE gene expression of scRNA-seq pseudobulk
DESeq2 SingleCell
updated 3.6 years ago by 42k • written 3.6 years ago by ▴ 10
0
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1
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858
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improving running time of runNMF
runNMF scater singlecell SingleCellExperiment
updated 3.6 years ago by ★ 28k • written 3.6 years ago by ▴ 50
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0
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799
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Creating a stable batch-corrected scRNA-Seq data with multiple datasets and multiple integrations
scater singlecell scran BatchEffect
3.6 years ago hamza_karakurt ▴ 60
2
votes
6
replies
2.2k
views
Discarding ambient RNA using estimateAmbience
emptyDrop ambient singlecell estimateAmbience
updated 3.7 years ago by ★ 28k • written 3.7 years ago by ▴ 50
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6
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2.7k
views
Discrepancy between cell type and cluster using SingleCellExperiment and SingleR
singlecell singlecellexperiment umap singleR
updated 3.8 years ago by ★ 28k • written 3.8 years ago by ▴ 80
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2
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1.5k
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most correlated genes in SingleR
singlecell singleR
updated 3.8 years ago by ★ 28k • written 3.8 years ago by ▴ 50
0
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1
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1.5k
views
predicting cell type of clusters using singleR
singleR singlecell
updated 3.8 years ago by ★ 28k • written 3.8 years ago by ▴ 50
50 results • Page 1 of 1
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Comment: Trouble reading samplesheet in with diffbind to create dba by Mallory • 0
Thank you for your reply! There mustve been something wierd going on with my peak formats as you pointed out. I recalled all the peaks and …
Answer: Trouble reading samplesheet in with diffbind to create dba by Anthony • 0
I was struggling with this today too. For me it happened because my peak files were not in the correct format. The "10 elements" refers to …
Comment: gds in GEOmetadb 2023-06-26 version is empty by Frederico Moraes Ferreira ▴ 100
Try axel -n 20 https://gbnci.cancer.gov/geo/GEOmetadb.sqlite.gz
Comment: Most enriched pathway is not expressed when modifying universe parameter by James W. MacDonald 66k
The default for `enrichGO` is to subset to those with a p-value<0.05. You don't adjust that default argument, so you shouldn't have any GO …
Answer: In a 3 group DEG analysis with three batches, can I use 1 group in all three bat by Michael Love 42k
You can compare A and C thanks to the sharing of samples from B across 1, 2 and 3.
Votes
Answer: How to do DESeq2 on Kallisto Data
Comment: Most enriched pathway is not expressed when modifying universe parameter
Time-course, comparison of two groups
Answer: Behaviour of featureCounts when quantifying multi-mapping reads
Answer: GESA with certain gene list returns no result with human genom, but many result
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