Showing : SingleCell • reset
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Job: Job:Computational Biologist position at the University of Alabama at Birmingham
hiring RNASeq JobPosting SingleCell SpatialData
5 weeks ago lianov • 0
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News: Course: Single-cell analysis with R/Bioconductor
SingleCellExperiment SingleCell SingleCellWorkflow SingleCellData
5 months ago Ludwig Geistlinger ▴ 80
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3
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Possible issue following the logNormCounts(filtered) with resulted fit
single-cell SingleCell SingleCellExperiment SingleCellWorkflow SingleCellData
8 months ago Konstantinos Yeles ▴ 90
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News: Single-cell RNA-seq analysis with R/Bioconductor (online course)
SingleCellExperiment SingleCell
16 months ago info ▴ 10
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807
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Job: Postdoctoral Research Associate in Computational Epigenomics
Phd SingleCell DNAMethylation Shanghai JobPosting
17 months ago xiaolong • 0
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Job: Postdoctoral fellowships in Spatial Omics and Single Cell Genomics at the University of Padova (IT)
SingleCell Transcriptomics SpatialDatasets SpatialData
20 months ago Silvio • 0
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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
23 months ago Peter Hickey ▴ 760
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1.4k
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'Seurat' package
singlecell seurat
updated 2.8 years ago by ★ 5.0k • written 2.8 years ago by ▴ 10
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1
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1.6k
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Choosing the right lower limit for emptyDrops
SingleCell emptyDrops 10X
updated 2.8 years ago by ▴ 760 • written 2.8 years ago by • 0
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1.3k
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Why my log2fcs are too high?
DESeq2 SingleCell log2FC
2.8 years ago paria.alipour • 0
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1.8k
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Scaling and normalization by deconvolution of SMART-Seq 2 data
scran Clustering SingleCell Normalization
2.9 years ago Assa Yeroslaviz ★ 1.5k
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1.6k
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Single-cell differential expression analysis with multiple samples
SingleCell
2.9 years ago iaradsouza1 • 0
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8
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2.2k
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fail to annotate chromosome data to single cell object
error SingleCell annotate
updated 2.2 years ago by • 0 • written 2.9 years ago by • 0
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Job: Open position in the CBIO lab: single-cell proteomics
Proteomics SingleCell JobPosting MassSpectrometry
2.9 years ago Laurent Gatto 1.6k
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2.6k
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Knee and Inflection of DropletUtils
SingleCell
updated 3.0 years ago by ★ 5.0k • written 3.0 years ago by • 0
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5.5k
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DESeq2 after Seurat analysis on integrated datasets
DESeq2 SingleCell GeneExpression Seurat
updated 3.0 years ago by ★ 5.0k • written 3.0 years ago by • 0
1
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1
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1.6k
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Pseudobulk running all groups together vs subsetting first
DESeq2 edgeR SingleCell
updated 3.0 years ago by ★ 13k • written 3.0 years ago by ▴ 70
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1.2k
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Job: Reopened: 'Omics data analyst for HPCBio, University of Illinois
SingleCell Spatial RNA-seq
3.0 years ago Jenny Drnevich ★ 2.0k
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1.5k
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Tissue Level Differential Expression Analysis
DESeq2 DifferentialExpression differentialex Pseudobulk SingleCell
updated 3.1 years ago by 43k • written 3.1 years ago by • 0
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Job: 'Omics data analyst for HPCBio, University of Illinois
SingleCell rnaseq methylationArrayAnalysis Spatial
written 3.2 years ago by ★ 2.0k
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Single-Cell Data Simulation from Bulk RNA-seq
SingleCell RNASeq RNASeqData scRNAseq
updated 19 months ago by • 0 • written 3.2 years ago by • 0
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1.3k
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allele count data bioc object
SingleCell SingleCellMultiModal allele
updated 3.3 years ago by 43k • written 3.4 years ago by • 0
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1.4k
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Job: Postdoctoral Fellow in Epigenomcis/Neurobiology (MGH/Harvard Medical School, Boston)
GenomicVariation SingleCell Autism Neurogenesis Epigenetics
3.3 years ago sudhir.thakurela • 0
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1.0k
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Gene Id duplicated
SingleCell SingleCellData
updated 3.4 years ago by ★ 5.0k • written 3.4 years ago by • 0
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1
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1.3k
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Set up "mock" cell type as the reference?
DESeq2 SingleCell
updated 3.4 years ago by 43k • written 3.4 years ago by ▴ 10
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952
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weighting sample group
monocle SingleCell DifferentialExpression
3.4 years ago Sogand • 0
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4
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2.2k
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How to detect LacZ tagged cells from single cell
SingleCell SingleCellExperiment SingleCellWorkflow SingleCellData
updated 6 months ago by • 0 • written 3.4 years ago by ▴ 20
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2
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1.9k
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how to plot a fitting line on the testPseudotime
Pseudotime testPseudotime TSCAN SingleCell OSCA
3.4 years ago Guandong Shang ▴ 40
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4
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1.8k
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Summary of library size factor is all equal to one
SingleCell SingleCellData SingleCellWorkflow SingleCellExperiment
3.4 years ago Romina • 0
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1.9k
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Error in .testForValidKeys(x, keys, keytype, fks) :
SingleCell AnnotationDbi
updated 3.5 years ago by 68k • written 3.5 years ago by • 0
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2.0k
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Error in running: classifySingleR from SingleR package
SingleR SingleCell
updated 3.5 years ago by ★ 5.0k • written 3.5 years ago by • 0
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DESeq2 aggregated single cell data
pseudobulk SingleCell DESeq2
3.6 years ago fluentin44 • 0
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Differential expression with single cell data: any good two component (hurdle) models recently?
SingleCellWorkflow DifferentialExpression SingleCell SingleCellMultiModal MAST
3.6 years ago Nik Tuzov ▴ 90
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Performing DGE analysis with MAST on a variable with more than 2 levels
MAST DEG SingleCell
3.8 years ago zroger499 • 0
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1
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1.3k
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() followed by [] within an argument in singlecell OSCA workflow
SingleCell R OSCA
updated 3.8 years ago by ▴ 100 • written 3.8 years ago by • 0
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1
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2.9k
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Convert AnnotatedDataFrame S4 object from GEO datasets to Seurat Object
biobase SingleCellData seurat SingleCell
updated 4.1 years ago by 68k • written 4.1 years ago by • 0
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Issues geting meaninfull results for single cell DGE using MAST
MAST SingleCell
4.1 years ago zroger499 • 0
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Job: Postdoc Opening in Bioinformatics or Computational Biology
SpatialData scRNAseq SingleCell Omixer
4.1 years ago Sebastian Lewandowski • 0
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2
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1.8k
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velociraptor preparation
SingleCellExperiment singlecell velociraptor scvelo
updated 4.2 years ago by ★ 5.0k • written 4.2 years ago by ▴ 40
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Job: Research Scientists/Postdoctoral Candidates/Computational Biologists and Programmers excited about computational challenges in modeling CRISPR genome…
CRISPR SingleCell Genomics
4.4 years ago lpinello • 0
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Using limma duplicateCorrelation to account for donor/dataset effects in scRNA-Seq pseudobulk counts from multiple sources
limma SingleCell
4.4 years ago Andrew Pattison • 0
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1.2k
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Spike-In Cells for Normalization?
SpikeIn SingleCell
4.5 years ago mb1996 • 0
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1.2k
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Job: Computational postdoctoral fellow for cancer disparities research (Boston University)
DNASeq RNASeq SingleCell
4.5 years ago camp ▴ 10
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1.4k
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Job: Senior Bioinformatician - University of Alabama at Birmingham
JobPosting Transcriptomics SingleCell RNA-seq
4.6 years ago lianov • 0
0
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1
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1.6k
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Differentially expressed genes across three different conditions
MAST SingleCell diffGeneAnalysis
updated 4.6 years ago by 68k • written 4.6 years ago by • 0
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Merging only those samples sequenced over multiple batches - scRNA-seq
SingleCell SingleCellExperiment scater
5.0 years ago camerond • 0
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1.6k
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Job: Computational Biologist at Denali Therapeutics
Transcriptomics SingleCell JobPosting
5.1 years ago Steve Lianoglou ★ 13k
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2.1k
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Removal of cell cycle effect using batchelor::regressBatches() and proper usage of corrected UMI matrix
scRNAseq batchelor SingleCell SingleCellExperiment scran
5.2 years ago jirkanov • 0
3
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1
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2.6k
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DESeq2 DE gene expression of scRNA-seq pseudobulk
DESeq2 SingleCell
updated 5.2 years ago by 43k • written 5.2 years ago by ▴ 10
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1
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1.4k
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improving running time of runNMF
runNMF scater singlecell SingleCellExperiment
updated 5.3 years ago by ★ 29k • written 5.3 years ago by ▴ 50
59 results • Page 1 of 2
Recent ...
Replies
Comment: Which preprocessing steps are needed before running limpa? by miro165sabo • 0
Hi @gordonsmyth, thank you a lot for very fast and valuable response. I edited the question to provide more details.
Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ? by Gordon Smyth 53k
I tend to use dpcCN(), because it more robust than dpc() to experiments with lots of samples and big differences between samples. You coul…
Answer: Which preprocessing steps are needed before running limpa? by Gordon Smyth 53k
Please see the example limpa analyses given at <http://github.com/smythlab/limpa>, especially the kidney cancer case study. limpa does not…
Comment: Why does IDTaxa trainingSet for SILVA contain "_2" suffixes in the taxonomy name by Korneel • 0
Thanks for the quick reply! If I understand correctly, I think if I keep track of the full lineage, I shouldn't have any risk of collapsin…
Comment: Pathway abundance data from Curatedmetagenomics by yesquokkan • 0
Hello, I was also wondering about the same issue. Did you figure it out?
Votes
Answer: Which preprocessing steps are needed before running limpa?
Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ?
Answer: Which preprocessing steps are needed before running limpa?
Answer: Which preprocessing steps are needed before running limpa?
Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ?
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