Showing : SingleCell • reset
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fail to annotate chromosome data to single cell object
error SingleCell annotate
updated 5 months ago by • 0 • written 14 months ago by • 0
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6
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2.1k
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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
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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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5
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1.4k
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Association analysis between gene expression and Phenotype
rna singlecell limma
updated 5.1 years ago by ★ 28k • written 5.1 years ago by ▴ 20
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4
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921
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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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4
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708
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Single-cell differential expression analysis with multiple samples
SingleCell
14 months ago iaradsouza1 • 0
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4
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3.8k
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How to convert large gene counts data into matrix?
R Bioconductor singlecell bioinformatics seurat
updated 12 weeks ago by 50k • written 4.8 years ago by • 0
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3
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2.0k
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marker genes in singleR
singleR singlecell singlecellexperiment
updated 3.8 years ago by ★ 28k • written 3.8 years ago by ▴ 40
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3
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865
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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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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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1.0k
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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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2
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1.4k
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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
0
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2
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727
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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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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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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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2
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930
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Single-Cell Data Simulation from Bulk RNA-seq
SingleCell RNASeq RNASeqData scRNAseq
updated 23 days ago by • 0 • written 18 months ago by • 0
2
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2
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794
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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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1.4k
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DESeq2 aggregated single cell data
pseudobulk SingleCell DESeq2
21 months ago fluentin44 • 0
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2
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635
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Why my log2fcs are too high?
DESeq2 SingleCell log2FC
12 months ago paria.alipour • 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
3.3 years ago • updated 3.2 years ago camerond • 0
0
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2
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964
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how to plot a fitting line on the testPseudotime
Pseudotime testPseudotime TSCAN SingleCell OSCA
20 months ago Guandong Shang ▴ 40
1
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1
reply
672
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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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1.9k
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Error in .updateHubDB(hub_bfc, .class, url, proxy, localHub) :
annotation singlecell rna-seq
updated 4.3 years ago by 3.9k • written 4.3 years ago by • 0
0
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1
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1.4k
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predicting cell type of clusters using singleR
singleR singlecell
updated 3.7 years ago by ★ 28k • written 3.8 years ago by ▴ 40
0
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1
reply
836
views
improving running time of runNMF
runNMF scater singlecell SingleCellExperiment
updated 3.5 years ago by ★ 28k • written 3.5 years ago by ▴ 40
2
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1
reply
1.9k
views
DESeq2 DE gene expression of scRNA-seq pseudobulk
DESeq2 SingleCell
updated 3.4 years ago by 42k • written 3.5 years ago by • 0
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
2
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1
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744
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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
3
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1
reply
764
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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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2.4k
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DESeq2 after Seurat analysis on integrated datasets
DESeq2 SingleCell GeneExpression Seurat
updated 14 months ago by ★ 4.1k • written 15 months ago by • 0
0
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1
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671
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Job: 'Omics data analyst for HPCBio, University of Illinois
SingleCell rnaseq methylationArrayAnalysis Spatial
written 17 months ago by ★ 2.0k
0
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1
reply
773
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Set up "mock" cell type as the reference?
DESeq2 SingleCell
updated 19 months ago by 42k • written 20 months ago by ▴ 10
2
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1
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1.7k
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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
0
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1
reply
940
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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
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
0
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1
reply
682
views
Choosing the right lower limit for emptyDrops
SingleCell emptyDrops 10X
updated 12 months ago by ▴ 740 • written 12 months ago by • 0
0
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1
reply
673
views
Job: Reopened: 'Omics data analyst for HPCBio, University of Illinois
SingleCell Spatial RNA-seq
15 months ago Jenny Drnevich ★ 2.0k
0
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1
reply
764
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allele count data bioc object
SingleCell SingleCellMultiModal allele
updated 19 months ago by 42k • written 19 months ago by • 0
0
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0
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689
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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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0
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547
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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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0
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939
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Job: Computational Biologist at Denali Therapeutics
Transcriptomics SingleCell JobPosting
3.4 years ago Steve Lianoglou ★ 13k
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0
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706
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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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716
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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
0
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0
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656
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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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0
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739
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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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773
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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
0
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0
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722
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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
0
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0
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915
views
Job: Senior Bioinformatician - University of Alabama at Birmingham
JobPosting Transcriptomics SingleCell RNA-seq
2.8 years ago lianov • 0
0
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0
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897
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Job: Postdoc Opening in Bioinformatics or Computational Biology
SpatialData scRNAseq SingleCell Omixer
2.3 years ago Sebastian Lewandowski • 0
0
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0
replies
851
views
Job: Postdoctoral Fellow in Epigenomcis/Neurobiology (MGH/Harvard Medical School, Boston)
GenomicVariation SingleCell Autism Neurogenesis Epigenetics
19 months ago • updated 18 months ago sudhir.thakurela • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: deseq2 results by swbarnes2 ★ 1.4k
Ask the people who made the libraires if there was anything unusual in the QC of the outlier sample. Try to figure out what biologically …
Comment: Can't post a question containing code? by NATASHA • 0
did you find a solution? I´m having the same problem
Comment: error by NATASHA • 0
Please ignore, i didnt copy all the scrip
Comment: Extremely small p-values using Limma for proteomic data by James W. MacDonald 65k
If you ever find yourself using the `@` function, you should reconsider what you are doing. There are vanishingly small instances when an e…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 42k
Here is some example code <https://gist.github.com/mikelove/cbbc84634b6854c865cb5eb08ad9b245>
Votes
A: AIC-like measure for DESeq2
Comment: Extremely small p-values using Limma for proteomic data
Comment: Log-cpm values from limma
Comment: Log-cpm values from limma
Comment: deseq2 results
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