Showing : singlecell • reset
5
votes
5
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1.4k
views
Association analysis between gene expression and Phenotype
rna singlecell limma
updated 5.1 years ago by ★ 28k • written 5.1 years ago by ▴ 20
3
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2
replies
2.2k
views
Merging only those samples sequenced over multiple batches - scRNA-seq
SingleCell SingleCellExperiment scater
3.2 years ago camerond • 0
3
votes
1
reply
732
views
'Seurat' package
singlecell seurat
updated 11 months ago by ★ 4.0k • written 11 months ago by ▴ 10
2
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4
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903
views
Summary of library size factor is all equal to one
SingleCell SingleCellData SingleCellWorkflow SingleCellExperiment
19 months ago Romina • 0
2
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6
replies
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
2
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1
reply
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
2
votes
1
reply
733
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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2
replies
778
views
How to detect LacZ tagged cells from single cell
SingleCell SingleCellExperiment SingleCellWorkflow SingleCellData
19 months ago k1m ▴ 20
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 ★ 4.0k • written 2.4 years ago by ▴ 40
2
votes
1
reply
1.6k
views
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
2
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4
replies
3.8k
views
How to convert large gene counts data into matrix?
R Bioconductor singlecell bioinformatics seurat
updated 10 weeks ago by 50k • written 4.8 years ago by • 0
1
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2
replies
1.4k
views
DESeq2 aggregated single cell data
pseudobulk SingleCell DESeq2
21 months ago fluentin44 • 0
1
vote
4
replies
685
views
Single-cell differential expression analysis with multiple samples
SingleCell
13 months ago iaradsouza1 • 0
1
vote
2
replies
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
1
vote
1
reply
653
views
Pseudobulk running all groups together vs subsetting first
DESeq2 edgeR SingleCell
updated 14 months ago by ★ 13k • written 14 months ago by ▴ 30
0
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0
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729
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Issues geting meaninfull results for single cell DGE using MAST
MAST SingleCell
2.3 years ago zroger499 • 0
0
votes
8
replies
1.1k
views
fail to annotate chromosome data to single cell object
error SingleCell annotate
updated 5 months ago by • 0 • written 13 months ago by • 0
0
votes
1
reply
1.1k
views
Error in .testForValidKeys(x, keys, keytype, fks) :
SingleCell AnnotationDbi
updated 20 months ago by 65k • written 20 months ago by • 0
0
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0
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636
views
Job: Open position in the CBIO lab: single-cell proteomics
Proteomics SingleCell JobPosting MassSpectrometry
13 months ago Laurent Gatto 1.6k
0
votes
3
replies
2.0k
views
marker genes in singleR
singleR singlecell singlecellexperiment
updated 3.7 years ago by ★ 28k • written 3.7 years ago by ▴ 40
0
votes
2
replies
615
views
Why my log2fcs are too high?
DESeq2 SingleCell log2FC
12 months ago paria.alipour • 0
0
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1
reply
2.3k
views
DESeq2 after Seurat analysis on integrated datasets
DESeq2 SingleCell GeneExpression Seurat
updated 14 months ago by ★ 4.0k • written 14 months ago by • 0
0
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0
replies
698
views
Spike-In Cells for Normalization?
SpikeIn SingleCell
2.7 years ago mb1996 • 0
0
votes
1
reply
654
views
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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0
replies
197
views
Job: Bioinformatics Spatial Omics and Proteomics Postdoc (Research Officer / Senior Research Officer) at WEHI (Melbourne, Australia)
Proteomics JobPosting SingleCell Spatial SpatialExperiment
7 weeks ago Peter Hickey ▴ 740
0
votes
1
reply
1.8k
views
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
votes
0
replies
876
views
Job: Postdoc Opening in Bioinformatics or Computational Biology
SpatialData scRNAseq SingleCell Omixer
2.3 years ago Sebastian Lewandowski • 0
0
votes
1
reply
657
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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0
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709
views
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
votes
3
replies
1.2k
views
Knee and Inflection of DropletUtils
SingleCell
updated 13 months ago by ★ 4.0k • written 14 months ago by • 0
0
votes
0
replies
900
views
Job: Senior Bioinformatician - University of Alabama at Birmingham
JobPosting Transcriptomics SingleCell RNA-seq
2.7 years ago lianov • 0
0
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2
replies
889
views
Single-Cell Data Simulation from Bulk RNA-seq
SingleCell RNASeq RNASeqData scRNAseq
updated 8 days ago by • 0 • written 17 months ago by • 0
0
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0
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827
views
Job: Postdoctoral Fellow in Epigenomcis/Neurobiology (MGH/Harvard Medical School, Boston)
GenomicVariation SingleCell Autism Neurogenesis Epigenetics
18 months ago sudhir.thakurela • 0
0
votes
1
reply
641
views
Job: Reopened: 'Omics data analyst for HPCBio, University of Illinois
SingleCell Spatial RNA-seq
14 months ago Jenny Drnevich ★ 2.0k
0
votes
0
replies
669
views
Differential expression with single cell data: any good two component (hurdle) models recently?
SingleCellWorkflow DifferentialExpression SingleCell SingleCellMultiModal MAST
22 months ago Nik Tuzov ▴ 80
0
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0
replies
450
views
weighting sample group
monocle SingleCell DifferentialExpression
19 months ago Sogand • 0
0
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0
replies
679
views
Job: Computational postdoctoral fellow for cancer disparities research (Boston University)
DNASeq RNASeq SingleCell
2.7 years ago camp ▴ 10
0
votes
0
replies
535
views
Gene Id duplicated
SingleCell SingleCellData
updated 19 months ago by ★ 4.0k • written 19 months ago by • 0
0
votes
1
reply
752
views
Set up "mock" cell type as the reference?
DESeq2 SingleCell
updated 19 months ago by 41k • written 19 months ago by ▴ 10
0
votes
2
replies
700
views
Scaling and normalization by deconvolution of SMART-Seq 2 data
scran Clustering SingleCell Normalization
13 months ago Assa Yeroslaviz ★ 1.5k
0
votes
1
reply
751
views
allele count data bioc object
SingleCell SingleCellMultiModal allele
updated 18 months ago by 41k • written 18 months ago by • 0
0
votes
1
reply
927
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
0
votes
1
reply
1.0k
views
Error in running: classifySingleR from SingleR package
SingleR SingleCell
updated 21 months ago by ★ 4.0k • written 21 months ago by • 0
0
votes
2
replies
1.5k
views
most correlated genes in SingleR
singlecell singleR
updated 3.7 years ago by ★ 28k • written 3.7 years ago by ▴ 40
0
votes
6
replies
2.6k
views
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
0
votes
0
replies
759
views
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
votes
1
reply
826
views
improving running time of runNMF
runNMF scater singlecell SingleCellExperiment
updated 3.5 years ago by ★ 28k • written 3.5 years ago by ▴ 40
0
votes
0
replies
700
views
Performing DGE analysis with MAST on a variable with more than 2 levels
MAST DEG SingleCell
23 months ago zroger499 • 0
0
votes
0
replies
929
views
Job: Computational Biologist at Denali Therapeutics
Transcriptomics SingleCell JobPosting
3.3 years ago Steve Lianoglou ★ 13k
0
votes
2
replies
1.4k
views
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
50 results • Page 1 of 1
Recent ...
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Answer: Deseq2. decontXcounts not integers. Useful alternative? by Michael Love 41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Answer: ATACseq merge peaks by ATpoint ★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Comment: Deseq2. decontXcounts not integers. Useful alternative? by camp ▴ 10
Yes, @atpoint is correct. decontX decontaminated counts are not integers due to the way the variation inference algorithm works, but you ca…
Comment: Deseq2. decontXcounts not integers. Useful alternative? by ATpoint ★ 4.0k
I do not know this decontamination tool you use but generally: If these counts are basically "corrected" raw counts in the sense that they'…
Answer: Improving the design matrices vignette in RNAseq123 by Gordon Smyth 50k
Thanks to Shian Su, we have confirmed that the problem in the design matrices vignette html is caused by a bug in knitr 1.44 (to do with sp…
Votes
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
Answer: Cross-species analysis - how to compute the mid parent value?
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