Showing : SingleCell • reset
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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 weeks ago Peter Hickey ▴ 740
3
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1
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783
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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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693
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Choosing the right lower limit for emptyDrops
SingleCell emptyDrops 10X
updated 12 months ago by ▴ 740 • written 12 months ago by • 0
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2
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640
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Why my log2fcs are too high?
DESeq2 SingleCell log2FC
13 months ago • updated 12 months ago paria.alipour • 0
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2
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757
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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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4
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718
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Single-cell differential expression analysis with multiple samples
SingleCell
14 months ago iaradsouza1 • 0
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1.2k
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fail to annotate chromosome data to single cell object
error SingleCell annotate
updated 6 months ago by • 0 • written 14 months ago by • 0
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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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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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2.5k
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DESeq2 after Seurat analysis on integrated datasets
DESeq2 SingleCell GeneExpression Seurat
updated 15 months ago by ★ 4.1k • written 15 months ago by • 0
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1
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685
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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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687
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Job: Reopened: 'Omics data analyst for HPCBio, University of Illinois
SingleCell Spatial RNA-seq
15 months ago Jenny Drnevich ★ 2.0k
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3
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871
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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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684
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Job: 'Omics data analyst for HPCBio, University of Illinois
SingleCell rnaseq methylationArrayAnalysis Spatial
written 17 months ago by ★ 2.0k
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2
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958
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Single-Cell Data Simulation from Bulk RNA-seq
SingleCell RNASeq RNASeqData scRNAseq
updated 4 weeks ago by • 0 • written 18 months ago by • 0
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772
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allele count data bioc object
SingleCell SingleCellMultiModal allele
updated 19 months ago by 42k • written 19 months ago by • 0
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871
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Job: Postdoctoral Fellow in Epigenomcis/Neurobiology (MGH/Harvard Medical School, Boston)
GenomicVariation SingleCell Autism Neurogenesis Epigenetics
19 months ago sudhir.thakurela • 0
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562
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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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1
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781
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Set up "mock" cell type as the reference?
DESeq2 SingleCell
updated 20 months ago by 42k • written 20 months ago by ▴ 10
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470
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weighting sample group
monocle SingleCell DifferentialExpression
20 months ago Sogand • 0
2
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2
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801
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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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977
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how to plot a fitting line on the testPseudotime
Pseudotime testPseudotime TSCAN SingleCell OSCA
20 months ago Guandong Shang ▴ 40
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4
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941
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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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1.2k
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Error in .testForValidKeys(x, keys, keytype, fks) :
SingleCell AnnotationDbi
updated 20 months ago by 66k • written 21 months ago by • 0
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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
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2
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1.4k
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DESeq2 aggregated single cell data
pseudobulk SingleCell DESeq2
22 months ago fluentin44 • 0
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699
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Differential expression with single cell data: any good two component (hurdle) models recently?
SingleCellWorkflow DifferentialExpression SingleCell SingleCellMultiModal MAST
23 months ago Nik Tuzov ▴ 80
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723
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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
2
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1
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751
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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
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 66k • written 2.3 years ago by • 0
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752
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Issues geting meaninfull results for single cell DGE using MAST
MAST SingleCell
2.3 years ago zroger499 • 0
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916
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Job: Postdoc Opening in Bioinformatics or Computational Biology
SpatialData scRNAseq SingleCell Omixer
2.3 years ago Sebastian Lewandowski • 0
2
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2
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1.2k
views
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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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
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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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717
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Spike-In Cells for Normalization?
SpikeIn SingleCell
2.7 years ago mb1996 • 0
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696
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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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931
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Job: Senior Bioinformatician - University of Alabama at Birmingham
JobPosting Transcriptomics SingleCell RNA-seq
2.8 years ago lianov • 0
0
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1
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947
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Differentially expressed genes across three different conditions
MAST SingleCell diffGeneAnalysis
updated 2.9 years ago by 66k • written 2.9 years ago by • 0
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Merging only those samples sequenced over multiple batches - scRNA-seq
SingleCell SingleCellExperiment scater
3.3 years ago camerond • 0
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952
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Job: Computational Biologist at Denali Therapeutics
Transcriptomics SingleCell JobPosting
3.4 years ago Steve Lianoglou ★ 13k
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2
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1.5k
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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
2
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1
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1.9k
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DESeq2 DE gene expression of scRNA-seq pseudobulk
DESeq2 SingleCell
updated 3.5 years ago by 42k • written 3.5 years ago by • 0
0
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1
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845
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improving running time of runNMF
runNMF scater singlecell SingleCellExperiment
updated 3.5 years ago by ★ 28k • written 3.5 years ago by ▴ 40
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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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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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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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1
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1.4k
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predicting cell type of clusters using singleR
singleR singlecell
updated 3.8 years ago by ★ 28k • written 3.8 years ago by ▴ 40
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3
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2.0k
views
marker genes in singleR
singleR singlecell singlecellexperiment
updated 3.8 years ago by ★ 28k • written 3.8 years ago by ▴ 40
50 results • Page 1 of 1
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Comment: Ensembl plants at annotationHub? by Johannes Rainer ★ 2.0k
You can get the `EnsDb` EnsDb.Taestivum.v112.sqlite (for Ensembl 112/ ensemblgenomes 59) [here](https://www.dropbox.com/sh/msic0luivbldmb7/…
Comment: Errors in chromosome annotation-biomaRt by blackwidowzzz • 0
I recommend using a different dataset specific to your rat genome assembly version 8. You can search for available datasets within Ensembl …
Answer: Errors in chromosome annotation-biomaRt by James W. MacDonald 66k
If you are just using HGNC symbols for the lookup, and you are trying to get NCBI IDs, then I wouldn't use `biomaRt` because it's based on …
Comment: Help with ENmix readidat by James W. MacDonald 66k
Please don't add to posts from two years ago. Instead make a new post. Also, please read the help page for `readidat`. The only reason to …
Comment: LRT, more than two conditions and pairwise comparisons by James W. MacDonald 66k
In that case, probably easiest to subset to the groups being compared.
Votes
how to control age and gender effect in expression data using DESeq2
Answer: Error retrieving ensembl gene id using biomaRt...
Comment: LRT, more than two conditions and pairwise comparisons
Answer: Control group between 2 batches have different expression in RNAseq data
Answer: How to remove batch effect to combine RNAseq data from 2 different experiments?
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