Showing : SingleCell • reset
5
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Association analysis between gene expression and Phenotype
rna singlecell limma
updated 3.2 years ago by ★ 27k • written 3.2 years ago by ▴ 20
2
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6
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822
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Discarding ambient RNA using estimateAmbience
emptyDrop ambient singlecell estimateAmbience
updated 20 months ago by ★ 27k • written 20 months ago by ▴ 40
0
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1
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304
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improving running time of runNMF
runNMF scater singlecell SingleCellExperiment
updated 18 months ago by ★ 27k • written 18 months ago by ▴ 40
2
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1
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749
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DESeq2 DE gene expression of scRNA-seq pseudobulk
DESeq2 SingleCell
updated 18 months ago by 37k • written 18 months ago by • 0
0
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2
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531
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Removal of cell cycle effect using batchelor::regressBatches() and proper usage of corrected UMI matrix
scRNAseq batchelor SingleCell SingleCellExperiment scran
17 months ago jirkanov • 0
3
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2
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Merging only those samples sequenced over multiple batches - scRNA-seq
SingleCell SingleCellExperiment scater
15 months ago camerond • 0
2
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1
reply
90
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() followed by [] within an argument in singlecell OSCA workflow
SingleCell R OSCA
updated 5 weeks ago by ▴ 30 • written 5 weeks ago by • 0
1
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3
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327
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velociraptor preparation
SingleCellExperiment singlecell velociraptor scvelo
updated 5 months ago by ★ 1.2k • written 5 months ago by ▴ 30
2
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1
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283
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Convert AnnotatedDataFrame S4 object from GEO datasets to Seurat Object
biobase SingleCellData seurat SingleCell
updated 3 months ago by 59k • written 4 months ago by • 0
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1
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244
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Differentially expressed genes across three different conditions
MAST SingleCell diffGeneAnalysis
updated 10 months ago by 59k • written 11 months ago by • 0
1
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2
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334
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Using limma duplicateCorrelation to account for donor/dataset effects in scRNA-Seq pseudobulk counts from multiple sources
limma SingleCell
7 months ago Andrew Pattison • 0
0
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1
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314
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Error in .updateHubDB(hub_bfc, .class, url, proxy, localHub) :
annotation singlecell rna-seq
updated 2.3 years ago by 3.1k • written 2.3 years ago by • 0
0
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3
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935
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marker genes in singleR
singleR singlecell singlecellexperiment
updated 21 months ago by ★ 27k • written 21 months ago by ▴ 40
0
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1
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412
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predicting cell type of clusters using singleR
singleR singlecell
updated 21 months ago by ★ 27k • written 21 months ago by ▴ 40
0
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2
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513
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most correlated genes in SingleR
singlecell singleR
updated 21 months ago by ★ 27k • written 21 months ago by ▴ 40
0
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6
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849
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Discrepancy between cell type and cluster using SingleCellExperiment and SingleR
singlecell singlecellexperiment umap singleR
updated 21 months ago by ★ 27k • written 21 months ago by ▴ 60
2
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4
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2.7k
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How to convert large gene counts data into matrix?
R singlecell bioinformatics seurat
updated 15 months ago by • 0 • written 2.8 years ago by • 0
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Job: Senior Bioinformatician - University of Alabama at Birmingham
JobPosting Transcriptomics SingleCell RNA-seq
10 months ago lianov • 0
0
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0
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397
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Job: Computational Biologist at Denali Therapeutics
Transcriptomics SingleCell JobPosting
17 months ago Steve Lianoglou 13k
0
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51
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Performing DGE analysis with MAST on a variable with more than 2 levels
MAST DEG SingleCell
13 days ago zroger499 • 0
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0
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122
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Issues geting meaninfull results for single cell DGE using MAST
MAST SingleCell
4 months ago zroger499 • 0
0
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0
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226
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Job: Computational postdoctoral fellow for cancer disparities research (Boston University)
DNASeq RNASeq SingleCell
9 months ago camp • 0
0
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0
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172
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Spike-In Cells for Normalization?
SpikeIn SingleCell
9 months ago mb1996 • 0
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0
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256
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Creating a stable batch-corrected scRNA-Seq data with multiple datasets and multiple integrations
scater singlecell scran BatchEffect
18 months ago hamza_karakurt ▴ 50
0
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0
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251
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Job: Postdoc Opening in Bioinformatics or Computational Biology
SpatialData scRNAseq SingleCell Omixer
4 months ago Sebastian Lewandowski • 0
0
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0
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204
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Job: Research Scientists/Postdoctoral Candidates/Computational Biologists and Programmers excited about computational challenges in modeling CRISPR genome…
CRISPR SingleCell Genomics
7 months ago lpinello • 0
26 results • Page 1 of 1
Recent ...
Replies
Answer: Feature request: syntax for dropping unused seqlevels in GRanges objects by story.benjamin ▴ 10
## Drop all unused seqlevels: seqlevels(gr) <- seqlevelsInUse(gr)
Comment: CPM after RUVseq by Jess • 0
Thank you, it was!
Answer: unable to install RBGL by James W. MacDonald 59k
That might have been transitory. If you try again, does it work, or is it consistent?
Comment: error with: .make_splicings <- function(exons, cds, stop_codons=NULL) by James W. MacDonald 59k
It's not clear from this what the problem is. Rather than running under `snakemake` you might run the R code directly. I mean it's obvious …
Comment: CPM after RUVseq by James W. MacDonald 59k
I am unfamiliar with a `counts` function (your `counts(set)`), so it's not clear what exactly you are putting into that `DGEList`. But if i…
Votes
Comment: CPM after RUVseq
A: Using the plotting functions of clusterProfiler / enrichplot with enrichment res
Answer: CPM after RUVseq
Comment: Merging two plated in R
Answer: Merging two plated in R
Awards • All
Popular Question to svlachavas ▴ 780
Scholar to Guido Hooiveld ★ 3.2k
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Teacher to Aaron Lun ★ 27k
Scholar to James W. MacDonald 59k
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