Showing : singlecell • reset
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News: Single-cell RNA-seq analysis with R/Bioconductor (online course)
SingleCellExperiment SingleCell
3 months ago info ▴ 10
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Job: Postdoctoral Research Associate in Computational Epigenomics
Phd SingleCell DNAMethylation Shanghai JobPosting
4 months ago xiaolong • 0
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414
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Job: Postdoctoral fellowships in Spatial Omics and Single Cell Genomics at the University of Padova (IT)
SingleCell Transcriptomics SpatialDatasets SpatialData
8 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
11 months ago Peter Hickey ▴ 750
3
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1
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1.0k
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'Seurat' package
singlecell seurat
updated 21 months ago by ★ 4.6k • written 21 months ago by ▴ 10
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1
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1.0k
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Choosing the right lower limit for emptyDrops
SingleCell emptyDrops 10X
updated 21 months ago by ▴ 750 • written 21 months ago by • 0
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2
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893
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Why my log2fcs are too high?
DESeq2 SingleCell log2FC
21 months ago paria.alipour • 0
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2
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1.2k
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Scaling and normalization by deconvolution of SMART-Seq 2 data
scran Clustering SingleCell Normalization
22 months ago Assa Yeroslaviz ★ 1.5k
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4
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1.1k
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Single-cell differential expression analysis with multiple samples
SingleCell
23 months ago iaradsouza1 • 0
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8
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1.6k
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fail to annotate chromosome data to single cell object
error SingleCell annotate
updated 14 months ago by • 0 • written 23 months ago by • 0
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987
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Job: Open position in the CBIO lab: single-cell proteomics
Proteomics SingleCell JobPosting MassSpectrometry
23 months ago Laurent Gatto 1.6k
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3
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1.8k
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Knee and Inflection of DropletUtils
SingleCell
updated 23 months ago by ★ 4.6k • written 23 months ago by • 0
0
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1
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3.9k
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DESeq2 after Seurat analysis on integrated datasets
DESeq2 SingleCell GeneExpression Seurat
updated 23 months ago by ★ 4.6k • written 23 months ago by • 0
1
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1
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1.1k
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Pseudobulk running all groups together vs subsetting first
DESeq2 edgeR SingleCell
updated 24 months ago by ★ 13k • written 24 months ago by ▴ 70
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1
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893
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Job: Reopened: 'Omics data analyst for HPCBio, University of Illinois
SingleCell Spatial RNA-seq
24 months ago Jenny Drnevich ★ 2.0k
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3
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1.1k
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Tissue Level Differential Expression Analysis
DESeq2 DifferentialExpression differentialex Pseudobulk SingleCell
updated 2.1 years ago by 43k • written 2.1 years ago by • 0
0
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1
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871
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Job: 'Omics data analyst for HPCBio, University of Illinois
SingleCell rnaseq methylationArrayAnalysis Spatial
written 2.2 years ago by ★ 2.0k
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3
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1.7k
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Single-Cell Data Simulation from Bulk RNA-seq
SingleCell RNASeq RNASeqData scRNAseq
updated 6 months ago by • 0 • written 2.2 years ago by • 0
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1
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918
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allele count data bioc object
SingleCell SingleCellMultiModal allele
updated 2.3 years ago by 43k • written 2.3 years ago by • 0
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1.1k
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Job: Postdoctoral Fellow in Epigenomcis/Neurobiology (MGH/Harvard Medical School, Boston)
GenomicVariation SingleCell Autism Neurogenesis Epigenetics
2.3 years ago sudhir.thakurela • 0
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718
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Gene Id duplicated
SingleCell SingleCellData
updated 2.3 years ago by ★ 4.6k • written 2.3 years ago by • 0
0
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1
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987
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Set up "mock" cell type as the reference?
DESeq2 SingleCell
updated 2.4 years ago by 43k • written 2.4 years ago by ▴ 10
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667
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weighting sample group
monocle SingleCell DifferentialExpression
2.4 years ago Sogand • 0
2
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2
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1.1k
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How to detect LacZ tagged cells from single cell
SingleCell SingleCellExperiment SingleCellWorkflow SingleCellData
2.4 years ago k1m ▴ 20
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2
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1.4k
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how to plot a fitting line on the testPseudotime
Pseudotime testPseudotime TSCAN SingleCell OSCA
2.4 years ago Guandong Shang ▴ 40
2
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4
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1.2k
views
Summary of library size factor is all equal to one
SingleCell SingleCellData SingleCellWorkflow SingleCellExperiment
2.4 years ago Romina • 0
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1
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1.5k
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Error in .testForValidKeys(x, keys, keytype, fks) :
SingleCell AnnotationDbi
updated 2.4 years ago by 67k • written 2.4 years ago by • 0
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1
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1.7k
views
Error in running: classifySingleR from SingleR package
SingleR SingleCell
updated 2.5 years ago by ★ 4.6k • written 2.5 years ago by • 0
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2
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1.8k
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DESeq2 aggregated single cell data
pseudobulk SingleCell DESeq2
2.5 years ago fluentin44 • 0
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0
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893
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Differential expression with single cell data: any good two component (hurdle) models recently?
SingleCellWorkflow DifferentialExpression SingleCell SingleCellMultiModal MAST
2.6 years ago Nik Tuzov ▴ 90
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1.0k
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Performing DGE analysis with MAST on a variable with more than 2 levels
MAST DEG SingleCell
2.7 years ago zroger499 • 0
2
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1
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952
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() followed by [] within an argument in singlecell OSCA workflow
SingleCell R OSCA
updated 2.8 years ago by ▴ 90 • written 2.8 years ago by • 0
2
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1
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2.1k
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Convert AnnotatedDataFrame S4 object from GEO datasets to Seurat Object
biobase SingleCellData seurat SingleCell
updated 3.0 years ago by 67k • written 3.0 years ago by • 0
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1.0k
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Issues geting meaninfull results for single cell DGE using MAST
MAST SingleCell
3.0 years ago zroger499 • 0
0
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0
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1.1k
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Job: Postdoc Opening in Bioinformatics or Computational Biology
SpatialData scRNAseq SingleCell Omixer
3.0 years ago Sebastian Lewandowski • 0
2
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2
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1.5k
views
velociraptor preparation
SingleCellExperiment singlecell velociraptor scvelo
updated 3.1 years ago by ★ 4.6k • written 3.1 years ago by ▴ 40
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892
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Job: Research Scientists/Postdoctoral Candidates/Computational Biologists and Programmers excited about computational challenges in modeling CRISPR genome…
CRISPR SingleCell Genomics
3.3 years ago lpinello • 0
1
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2
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1.3k
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Using limma duplicateCorrelation to account for donor/dataset effects in scRNA-Seq pseudobulk counts from multiple sources
limma SingleCell
3.4 years ago • updated 3.3 years ago Andrew Pattison • 0
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920
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Spike-In Cells for Normalization?
SpikeIn SingleCell
3.4 years ago mb1996 • 0
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922
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Job: Computational postdoctoral fellow for cancer disparities research (Boston University)
DNASeq RNASeq SingleCell
3.5 years ago camp ▴ 10
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1.1k
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Job: Senior Bioinformatician - University of Alabama at Birmingham
JobPosting Transcriptomics SingleCell RNA-seq
3.5 years ago lianov • 0
0
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1
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1.2k
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Differentially expressed genes across three different conditions
MAST SingleCell diffGeneAnalysis
updated 3.6 years ago by 67k • written 3.6 years ago by • 0
3
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2
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2.9k
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Merging only those samples sequenced over multiple batches - scRNA-seq
SingleCell SingleCellExperiment scater
4.0 years ago camerond • 0
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0
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1.2k
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Job: Computational Biologist at Denali Therapeutics
Transcriptomics SingleCell JobPosting
4.1 years ago Steve Lianoglou ★ 13k
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2
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1.7k
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Removal of cell cycle effect using batchelor::regressBatches() and proper usage of corrected UMI matrix
scRNAseq batchelor SingleCell SingleCellExperiment scran
4.2 years ago • updated 4.1 years ago jirkanov • 0
3
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1
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2.2k
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DESeq2 DE gene expression of scRNA-seq pseudobulk
DESeq2 SingleCell
updated 4.2 years ago by 43k • written 4.2 years ago by ▴ 10
0
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1
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1.1k
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improving running time of runNMF
runNMF scater singlecell SingleCellExperiment
updated 4.2 years ago by ★ 28k • written 4.2 years ago by ▴ 50
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0
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999
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Creating a stable batch-corrected scRNA-Seq data with multiple datasets and multiple integrations
scater singlecell scran BatchEffect
4.3 years ago hamza_karakurt ▴ 60
2
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6
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2.7k
views
Discarding ambient RNA using estimateAmbience
emptyDrop ambient singlecell estimateAmbience
updated 4.4 years ago by ★ 28k • written 4.4 years ago by ▴ 50
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6
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3.2k
views
Discrepancy between cell type and cluster using SingleCellExperiment and SingleR
singlecell singlecellexperiment umap singleR
updated 4.4 years ago by ★ 28k • written 4.4 years ago by ▴ 80
50 results • Page 1 of 1
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Answer: Using genomicRanges / plyranges to calculate score of peaks within intervals by Michael Love 43k
This should be possible with plyranges using `join_overlap` and `group_by` on the metadata from the tile. E.g. create `tile.id` as a variab…
Answer: Reducing and aggregating GRanges with gaps using plyranges by Michael Love 43k
I added `min.gapwidth` to `reduce_ranges()` in recent plyranges releases: https://github.com/tidyomics/plyranges/pull/105
Answer: Find exact GRanges match keeping metadata columns by Michael Love 43k
You could use `minoverlap` but that requires an integer, not a fraction: ``` gr1 |> join_overlap_left(gr2, minoverlap=6) ``` Plyranges do…
Comment: Unused arguments error without used arguments in GSVA? by 1sunmic2 • 0
It was due to the comma. Thank you!
Answer: Unused arguments error without used arguments in GSVA? by Axel Klenk ★ 1.1k
Hi, here is a good place to ask questions when encountering problems with GSVA. I cannot reproduce this behaviour with the current release…
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Answer: Unused arguments error without used arguments in GSVA?
Answer: Unused arguments error without used arguments in GSVA?
Answer: Unused arguments error without used arguments in GSVA?
Unused arguments error without used arguments in GSVA?
Answer: Is it always preferable to recount library sizes of DGEList object in edgeR afte
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