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
8 weeks ago Peter Hickey ▴ 740
3
votes
1
reply
739
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'Seurat' package
singlecell seurat
updated 11 months ago by ★ 4.1k • written 11 months ago by ▴ 10
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1
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664
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Choosing the right lower limit for emptyDrops
SingleCell emptyDrops 10X
updated 11 months ago by ▴ 740 • written 12 months ago by • 0
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2
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620
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Why my log2fcs are too high?
DESeq2 SingleCell log2FC
12 months ago paria.alipour • 0
0
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2
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706
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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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690
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Single-cell differential expression analysis with multiple samples
SingleCell
13 months ago iaradsouza1 • 0
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8
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1.1k
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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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639
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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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3
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1.2k
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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
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2.3k
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DESeq2 after Seurat analysis on integrated datasets
DESeq2 SingleCell GeneExpression Seurat
updated 14 months ago by ★ 4.1k • written 14 months ago by • 0
1
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1
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661
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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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648
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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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3
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852
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Tissue Level Differential Expression Analysis
DESeq2 DifferentialExpression differentialex Pseudobulk SingleCell
updated 16 months ago by 41k • written 16 months ago by • 0
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1
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655
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Job: 'Omics data analyst for HPCBio, University of Illinois
SingleCell rnaseq methylationArrayAnalysis Spatial
written 16 months ago by ★ 2.0k
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2
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899
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Single-Cell Data Simulation from Bulk RNA-seq
SingleCell RNASeq RNASeqData scRNAseq
updated 13 days ago by • 0 • written 17 months ago by • 0
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1
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758
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allele count data bioc object
SingleCell SingleCellMultiModal allele
updated 18 months ago by 41k • written 18 months ago by • 0
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831
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Job: Postdoctoral Fellow in Epigenomcis/Neurobiology (MGH/Harvard Medical School, Boston)
GenomicVariation SingleCell Autism Neurogenesis Epigenetics
18 months ago sudhir.thakurela • 0
0
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0
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536
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Gene Id duplicated
SingleCell SingleCellData
updated 19 months ago by ★ 4.1k • written 19 months ago by • 0
0
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1
reply
759
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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
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455
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weighting sample group
monocle SingleCell DifferentialExpression
19 months ago Sogand • 0
2
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2
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785
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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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949
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how to plot a fitting line on the testPseudotime
Pseudotime testPseudotime TSCAN SingleCell OSCA
20 months ago • updated 19 months ago Guandong Shang ▴ 40
2
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4
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909
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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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1
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1.1k
views
Error in .testForValidKeys(x, keys, keytype, fks) :
SingleCell AnnotationDbi
updated 20 months ago by 65k • written 20 months ago by • 0
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1
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1.0k
views
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
views
DESeq2 aggregated single cell data
pseudobulk SingleCell DESeq2
21 months ago fluentin44 • 0
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0
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673
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Differential expression with single cell data: any good two component (hurdle) models recently?
SingleCellWorkflow DifferentialExpression SingleCell SingleCellMultiModal MAST
22 months ago Nik Tuzov ▴ 80
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0
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703
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Performing DGE analysis with MAST on a variable with more than 2 levels
MAST DEG SingleCell
24 months ago zroger499 • 0
2
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1
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735
views
() 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
2
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1
reply
1.6k
views
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
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732
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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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881
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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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711
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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
1
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2
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1.0k
views
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
0
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0
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700
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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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681
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Job: Computational postdoctoral fellow for cancer disparities research (Boston University)
DNASeq RNASeq SingleCell
2.7 years ago camp ▴ 10
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0
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906
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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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930
views
Differentially expressed genes across three different conditions
MAST SingleCell diffGeneAnalysis
updated 2.8 years ago by 65k • written 2.8 years ago by • 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
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0
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931
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Job: Computational Biologist at Denali Therapeutics
Transcriptomics SingleCell JobPosting
3.3 years ago Steve Lianoglou ★ 13k
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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
2
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1
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1.9k
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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829
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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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0
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762
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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
views
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
views
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
views
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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3
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2.0k
views
marker genes in singleR
singleR singlecell singlecellexperiment
updated 3.7 years ago by ★ 28k • written 3.7 years ago by ▴ 40
50 results • Page 1 of 1
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Comment: Help with error using camera() in limma by James W. MacDonald 65k
Again, this is where you need to read the help page and try to diagnose. It says ``` index: an index vector or a list of index vectors. …
Comment: Help with error using camera() in limma by Chris • 0
Thanks James! That is a great tip. cameraRes <- camera(numeric_matrix, geneSets, inter.gene.cor=0.01, design) Error in Stat[iset]…
Answer: Help with error using camera() in limma by James W. MacDonald 65k
The first step should be to read the help page, which says ``` Usage: ## Default S3 method: camera(y, index, design, cont…
Comment: Assist me in determining whether the analysis process using the limma package ha by James W. MacDonald 65k
The description of the analysis says there are 120 genes at a 1.5 fold change and a p<0.05. They don't mention any multiplicity correction.…
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions by Chris • 0
When using `arrayWeights()`, you mean the variability within the same group, is that correct? I alway run `arrayWeights()` because I naive …
Votes
Answer: Help with error using camera() in limma
Answer: Help with error using camera() in limma
Comment: Why p value inconsistent when using different number of pathway score?
Nominations for Bioconductor Awards 2024!
Answer: Improving the design matrices vignette in RNAseq123
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Scholar to James W. MacDonald 65k
Popular Question to jeffrey.maurer • 0
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Commentator to Leonard Goldstein ▴ 200
Popular Question to Matthew Ritchie ▴ 1000
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