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
10 weeks ago Peter Hickey ▴ 740
3
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1
reply
773
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'Seurat' package
singlecell seurat
updated 12 months ago by ★ 4.1k • written 12 months ago by ▴ 10
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1
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691
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Choosing the right lower limit for emptyDrops
SingleCell emptyDrops 10X
updated 12 months ago by ▴ 740 • written 12 months ago by • 0
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2
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637
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Why my log2fcs are too high?
DESeq2 SingleCell log2FC
12 months ago paria.alipour • 0
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2
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748
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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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714
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Single-cell differential expression analysis with multiple samples
SingleCell
14 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 6 months ago by • 0 • written 14 months ago by • 0
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665
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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
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3
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1.3k
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Knee and Inflection of DropletUtils
SingleCell
updated 14 months ago by ★ 4.1k • written 14 months ago by • 0
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1
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2.5k
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DESeq2 after Seurat analysis on integrated datasets
DESeq2 SingleCell GeneExpression Seurat
updated 15 months ago by ★ 4.1k • written 15 months ago by • 0
1
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1
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680
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Pseudobulk running all groups together vs subsetting first
DESeq2 edgeR SingleCell
updated 15 months ago by ★ 13k • written 15 months ago by ▴ 30
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1
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683
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Job: Reopened: 'Omics data analyst for HPCBio, University of Illinois
SingleCell Spatial RNA-seq
15 months ago Jenny Drnevich ★ 2.0k
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3
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870
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Tissue Level Differential Expression Analysis
DESeq2 DifferentialExpression differentialex Pseudobulk SingleCell
updated 16 months ago by 42k • written 16 months ago by • 0
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1
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679
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Job: 'Omics data analyst for HPCBio, University of Illinois
SingleCell rnaseq methylationArrayAnalysis Spatial
written 17 months ago by ★ 2.0k
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2
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949
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Single-Cell Data Simulation from Bulk RNA-seq
SingleCell RNASeq RNASeqData scRNAseq
updated 29 days ago by • 0 • written 18 months ago by • 0
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1
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767
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allele count data bioc object
SingleCell SingleCellMultiModal allele
updated 19 months ago by 42k • written 19 months ago by • 0
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863
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Job: Postdoctoral Fellow in Epigenomcis/Neurobiology (MGH/Harvard Medical School, Boston)
GenomicVariation SingleCell Autism Neurogenesis Epigenetics
19 months ago sudhir.thakurela • 0
0
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0
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554
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Gene Id duplicated
SingleCell SingleCellData
updated 19 months ago by ★ 4.1k • written 19 months ago by • 0
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1
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777
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Set up "mock" cell type as the reference?
DESeq2 SingleCell
updated 20 months ago by 42k • written 20 months ago by ▴ 10
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466
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weighting sample group
monocle SingleCell DifferentialExpression
20 months ago Sogand • 0
2
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2
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796
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How to detect LacZ tagged cells from single cell
SingleCell SingleCellExperiment SingleCellWorkflow SingleCellData
20 months ago k1m ▴ 20
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2
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970
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how to plot a fitting line on the testPseudotime
Pseudotime testPseudotime TSCAN SingleCell OSCA
20 months ago Guandong Shang ▴ 40
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4
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932
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Summary of library size factor is all equal to one
SingleCell SingleCellData SingleCellWorkflow SingleCellExperiment
20 months ago Romina • 0
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1
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1.2k
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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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1.1k
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Error in running: classifySingleR from SingleR package
SingleR SingleCell
updated 21 months ago by ★ 4.1k • 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
22 months ago fluentin44 • 0
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0
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694
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Differential expression with single cell data: any good two component (hurdle) models recently?
SingleCellWorkflow DifferentialExpression SingleCell SingleCellMultiModal MAST
23 months ago Nik Tuzov ▴ 80
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718
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Performing DGE analysis with MAST on a variable with more than 2 levels
MAST DEG SingleCell
2.0 years ago zroger499 • 0
2
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1
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749
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() followed by [] within an argument in singlecell OSCA workflow
SingleCell R OSCA
updated 2.1 years ago by ▴ 90 • written 2.1 years ago by • 0
2
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1
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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
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750
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Issues geting meaninfull results for single cell DGE using MAST
MAST SingleCell
2.3 years ago zroger499 • 0
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0
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903
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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
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1.2k
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velociraptor preparation
SingleCellExperiment singlecell velociraptor scvelo
updated 2.4 years ago by ★ 4.1k • written 2.4 years ago by ▴ 40
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724
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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
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2
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1.0k
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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
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713
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Spike-In Cells for Normalization?
SpikeIn SingleCell
2.7 years ago mb1996 • 0
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694
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Job: Computational postdoctoral fellow for cancer disparities research (Boston University)
DNASeq RNASeq SingleCell
2.8 years ago camp ▴ 10
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924
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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
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945
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Differentially expressed genes across three different conditions
MAST SingleCell diffGeneAnalysis
updated 2.9 years ago by 65k • written 2.9 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
3.3 years ago camerond • 0
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0
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946
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Job: Computational Biologist at Denali Therapeutics
Transcriptomics SingleCell JobPosting
3.4 years ago Steve Lianoglou ★ 13k
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2
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1.5k
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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
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1.9k
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DESeq2 DE gene expression of scRNA-seq pseudobulk
DESeq2 SingleCell
updated 3.5 years ago by 42k • written 3.5 years ago by • 0
0
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1
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841
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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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780
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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
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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
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6
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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
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most correlated genes in SingleR
singlecell singleR
updated 3.7 years ago by ★ 28k • written 3.7 years ago by ▴ 40
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1
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1.4k
views
predicting cell type of clusters using singleR
singleR singlecell
updated 3.8 years ago by ★ 28k • written 3.8 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 3.8 years ago by ★ 28k • written 3.8 years ago by ▴ 40
50 results • Page 1 of 1
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Comment: Ensembl plants at annotationHub? by Daniele • 0
Dear Johannes, Would it be possible to create the EnsDb for Triticum aestivum (IWGSC)? Thank you very much, Daniele
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools by BioinfGuru ▴ 30
Figured it out with ?eigencorplot, thanks Michael. I was trying to pass 10 PCs when I only had 8, and I was including metadata columns that…
Answer: DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set by makala • 0
Thanks a lot!
Comment: DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set by Erik Wright ▴ 150
Thanks for notifying us of this broken link. It should be fixed on the Downloads page now. [1] [1]: http://www2.decipher.codes/Classificat…
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa by Matthew Thornton ▴ 360
So it turns out that if the count and the size are the same in 'GOstats", the odds ratio is 'inf'. These are causing the issue. Thank you!!
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Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
Comment: Can DESeq2 rlog normalized matrix reflects time course result directly?
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