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 13 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 3.6 years ago by ★ 28k • written 3.6 years ago by ▴ 80
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5
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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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890
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Summary of library size factor is all equal to one
SingleCell SingleCellData SingleCellWorkflow SingleCellExperiment
19 months ago Romina • 0
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4
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673
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Single-cell differential expression analysis with multiple samples
SingleCell
13 months ago iaradsouza1 • 0
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4
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How to convert large gene counts data into matrix?
R Bioconductor singlecell bioinformatics seurat
updated 9 weeks ago by 50k • written 4.7 years ago by • 0
0
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3
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1.9k
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marker genes in singleR
singleR singlecell singlecellexperiment
updated 3.7 years ago by ★ 28k • written 3.7 years ago by ▴ 40
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3
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835
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Tissue Level Differential Expression Analysis
DESeq2 DifferentialExpression differentialex Pseudobulk SingleCell
updated 15 months ago by 41k • written 15 months ago by • 0
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3
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1.2k
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Knee and Inflection of DropletUtils
SingleCell
updated 13 months ago by ★ 4.0k • written 13 months ago by • 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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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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690
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Scaling and normalization by deconvolution of SMART-Seq 2 data
scran Clustering SingleCell Normalization
12 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
2
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2
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1.1k
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velociraptor preparation
SingleCellExperiment singlecell velociraptor scvelo
updated 2.3 years ago by ★ 4.0k • written 2.3 years ago by ▴ 40
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2
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873
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Single-Cell Data Simulation from Bulk RNA-seq
SingleCell RNASeq RNASeqData scRNAseq
updated 2 days ago by • 0 • written 17 months ago by • 0
2
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2
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766
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How to detect LacZ tagged cells from single cell
SingleCell SingleCellExperiment SingleCellWorkflow SingleCellData
19 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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608
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Why my log2fcs are too high?
DESeq2 SingleCell log2FC
11 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
3.2 years ago camerond • 0
0
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2
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927
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how to plot a fitting line on the testPseudotime
Pseudotime testPseudotime TSCAN SingleCell OSCA
19 months ago Guandong Shang ▴ 40
1
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1
reply
645
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Pseudobulk running all groups together vs subsetting first
DESeq2 edgeR SingleCell
updated 14 months ago by ★ 13k • written 14 months ago by ▴ 30
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1
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1.8k
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Error in .updateHubDB(hub_bfc, .class, url, proxy, localHub) :
annotation singlecell rna-seq
updated 4.2 years ago by 3.8k • written 4.2 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 3.7 years ago by ▴ 40
0
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1
reply
822
views
improving running time of runNMF
runNMF scater singlecell SingleCellExperiment
updated 3.4 years ago by ★ 28k • written 3.4 years ago by ▴ 40
2
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1
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1.8k
views
DESeq2 DE gene expression of scRNA-seq pseudobulk
DESeq2 SingleCell
updated 3.4 years ago by 41k • written 3.4 years ago by • 0
0
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1
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1.1k
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Error in .testForValidKeys(x, keys, keytype, fks) :
SingleCell AnnotationDbi
updated 19 months ago by 65k • written 19 months ago by • 0
2
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1
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725
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() followed by [] within an argument in singlecell OSCA workflow
SingleCell R OSCA
updated 2.0 years ago by ▴ 90 • written 2.0 years ago by • 0
3
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1
reply
719
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'Seurat' package
singlecell seurat
updated 11 months ago by ★ 4.0k • written 11 months ago by ▴ 10
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1
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2.2k
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DESeq2 after Seurat analysis on integrated datasets
DESeq2 SingleCell GeneExpression Seurat
updated 14 months ago by ★ 4.0k • written 14 months ago by • 0
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1
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650
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Job: 'Omics data analyst for HPCBio, University of Illinois
SingleCell rnaseq methylationArrayAnalysis Spatial
written 16 months ago by ★ 2.0k
0
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1
reply
743
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Set up "mock" cell type as the reference?
DESeq2 SingleCell
updated 19 months ago by 41k • written 19 months ago by ▴ 10
2
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1
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1.6k
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Convert AnnotatedDataFrame S4 object from GEO datasets to Seurat Object
biobase SingleCellData seurat SingleCell
updated 2.2 years ago by 65k • written 2.2 years ago by • 0
0
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1
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918
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Differentially expressed genes across three different conditions
MAST SingleCell diffGeneAnalysis
updated 2.8 years ago by 65k • written 2.8 years ago by • 0
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1
reply
995
views
Error in running: classifySingleR from SingleR package
SingleR SingleCell
updated 20 months ago by ★ 4.0k • written 20 months ago by • 0
0
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1
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648
views
Choosing the right lower limit for emptyDrops
SingleCell emptyDrops 10X
updated 11 months ago by ▴ 740 • written 11 months ago by • 0
0
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1
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634
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Job: Reopened: 'Omics data analyst for HPCBio, University of Illinois
SingleCell Spatial RNA-seq
14 months ago Jenny Drnevich ★ 2.0k
0
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1
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742
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allele count data bioc object
SingleCell SingleCellMultiModal allele
updated 18 months ago by 41k • written 18 months ago by • 0
0
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674
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Job: Computational postdoctoral fellow for cancer disparities research (Boston University)
DNASeq RNASeq SingleCell
2.7 years ago camp • 0
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0
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528
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Gene Id duplicated
SingleCell SingleCellData
updated 18 months ago by ★ 4.0k • written 18 months ago by • 0
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0
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920
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Job: Computational Biologist at Denali Therapeutics
Transcriptomics SingleCell JobPosting
3.3 years ago Steve Lianoglou ★ 13k
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0
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692
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Spike-In Cells for Normalization?
SpikeIn SingleCell
2.7 years ago mb1996 • 0
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693
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Performing DGE analysis with MAST on a variable with more than 2 levels
MAST DEG SingleCell
23 months ago zroger499 • 0
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0
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627
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Job: Open position in the CBIO lab: single-cell proteomics
Proteomics SingleCell JobPosting MassSpectrometry
13 months ago Laurent Gatto 1.6k
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0
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722
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Issues geting meaninfull results for single cell DGE using MAST
MAST SingleCell
2.2 years ago zroger499 • 0
0
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0
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755
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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
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0
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702
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Job: Research Scientists/Postdoctoral Candidates/Computational Biologists and Programmers excited about computational challenges in modeling CRISPR genome…
CRISPR SingleCell Genomics
2.5 years ago lpinello • 0
0
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0
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893
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Job: Senior Bioinformatician - University of Alabama at Birmingham
JobPosting Transcriptomics SingleCell RNA-seq
2.7 years ago lianov • 0
0
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0
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871
views
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
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820
views
Job: Postdoctoral Fellow in Epigenomcis/Neurobiology (MGH/Harvard Medical School, Boston)
GenomicVariation SingleCell Autism Neurogenesis Epigenetics
18 months ago sudhir.thakurela • 0
50 results • Page 1 of 1
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Comment: The difference when using Limma compare between 3 conditions vs 2 conditions by Robert Castelo ★ 3.2k
Hi, your `c2` object storing all the gene sets is probably a `list` object, where element names are the names of the pathways given by MSig…
Comment: Differential peaks that were not identified in diffbind were identified in diseq by lonn • 0
I tried the default normalization and got similar results as above. Perhaps I need to try identifying the difference peak without using dif…
Answer: Cannabis and KEGGgraph by deeenes ▴ 30
Hello, I'm a developer of the `OmnipathR` package, and I wrote [a function][1] to access certain KEGG data: library(OmnipathR) cs…
Answer: RNAseq:Technical replicates from different batches by Gordon Smyth 50k
I am not entirely clear what you mean by "technical" replicates in this case. Are they resequencing of the same RNA samples or are they fre…
Comment: DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, param by russ.bainer ▴ 10
Hi, I'm hitting this too. As far as I can tell my DataTrack is fine, but perhaps I am missing something. Notably the same code works on o…
Votes
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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