Showing : Single-Cell • reset
3
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1.2k
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BiocParallel errors from muscat
BiocParallel muscat single-cell
2.1 years ago tangming2005 ▴ 190
0
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0
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716
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Job: PhD student position: Vertebrate brain origins and evolution
PhD single-cell ComparativeGenomics evolution
2.5 years ago henrik.kaessmann • 0
0
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0
replies
709
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Job: Bioinformatics postdoc in comparative genomics
single-cell evolution Genomics Postdoc
2.5 years ago henrik.kaessmann • 0
0
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0
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798
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Job: Job: Moderna Statistical genomics co-op 2022, single-cell applications in immunology, masters or PhDs
co-op immunology single-cell omics
2.6 years ago joyce.hsiao1 • 0
0
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0
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921
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Job: Computational Biologist, Blood Research Institute, Versiti, Wauwatosa, Wisconsin, USA
RNA-seq Job Single-Cell
2.9 years ago rbrns • 0
7
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3
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1.4k
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Effect of feature number on adjusted p-values
edgeR DESeq2 single-cell scRNAseq zinbwave
updated 2.9 years ago by ★ 28k • written 2.9 years ago by ▴ 20
1
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2
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887
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question for "Chapter 24 Zeisel mouse brain (STRT-Seq) in single-cell"
STRT-Seq single-cell tutorial
updated 3.8 years ago by ★ 28k • written 3.8 years ago by • 0
3
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3
replies
1.7k
views
Issue with scp transfer of DESeq2 objects
deseq2 scp Unix Single-Cell
updated 4.3 years ago by 25k • written 4.3 years ago by ▴ 20
5
votes
6
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3.3k
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How to build and map to a "pre-mRNA" reference transcriptome for single nucleus RNA-seq data?
tximeta ensembldb single-cell snRNA-seq tximport
updated 4.5 years ago by ★ 3.2k • written 4.5 years ago by ▴ 80
0
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1
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1.1k
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Scran: Performing DE after cell-typle identifaction on the corrected and integrated datasets
Scran MNN_correct Differential expression single-cell
5.1 years ago baldissera152 • 0
7
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12
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7.0k
views
How to identify real cells in 10X RNA-seq ?
single-cell 10X Cell calling DropletUtils cellranger
updated 5.1 years ago by ★ 28k • written 5.1 years ago by ▴ 20
0
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0
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862
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Job: Biostatistics Analyst II - high throughput single-cell assays
biostatistics single-cell high throughput Job
5.2 years ago careers • 0
3
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0
replies
1.1k
views
Job: Postdoctoral Scientist position at intersection of Single-Cell Cancer Genomics, Data Science and Bioconductor Software Development
job single-cell data science cancer genomics Job
5.3 years ago Stephanie Hicks ▴ 80
2
votes
2
replies
1.8k
views
[MnnCorrect] Remove batch effects but keep condition effects
single-cell scran mnncorrect rnaseq
updated 5.4 years ago by ★ 28k • written 5.4 years ago by ▴ 10
1
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0
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906
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Job: applied methods development for single-cell sequencing
single-cell job computational biology Job
5.4 years ago Simon Anders ★ 3.7k
3
votes
2
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1.6k
views
Seurat to SingleCellExperiment Converting error in MAC
singlecellexperiment single-cell rnaseq
updated 5.4 years ago by ★ 13k • written 5.4 years ago by ▴ 50
0
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0
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1.0k
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Job: PhD opportunity in Heidelberg for computational people
PhD position job single-cell Job
5.5 years ago Simon Anders ★ 3.7k
1
vote
5
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2.5k
views
newSCESet and SingleCellExperiment basic differences and TMM Normalization
singlecellexperiment single-cell rnaseq seurat scater
5.5 years ago hamza_karakurt ▴ 50
1
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1
reply
1.3k
views
Problem with finding mitochondrial genes in a human single cell RNA-Seq readCounts file
single-cell rnaseq mitochondria
updated 5.6 years ago by ★ 28k • written 5.6 years ago by • 0
0
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3
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963
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Error of makeTechTrend() of Scran
scran single-cell seq.default
updated 5.7 years ago by ★ 28k • written 5.7 years ago by • 0
1
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1
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1.4k
views
Adjust number of clusters with scran/buildSNNGraph
scran buildsnngraph cluster_walktrap single-cell
updated 5.7 years ago by ★ 28k • written 5.7 years ago by • 0
3
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3
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7.0k
views
rowSums() rowMeans() don't work on sparse matrix "dgCMatrix"
scater scran single-cell
updated 5.8 years ago by 25k • written 6.0 years ago by ▴ 10
2
votes
1
reply
2.3k
views
MAST: testing differential expression with a nested factorial design
MAST single-cell rna-seq
updated 6.0 years ago by ▴ 270 • written 6.0 years ago by ▴ 20
0
votes
28
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3.1k
views
Job: Postdoc on integrating and analyzing new transcriptome types in the Bgee database
rnaseq data integration single-cell pacbio across species Job
6.1 years ago bgee • 0
1
vote
3
replies
1.4k
views
Differential expressiong with two groups in BASiCS
BASiCS single-cell bayesian differential expression
updated 6.2 years ago by ▴ 10 • written 6.2 years ago by ▴ 10
4
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3
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1.9k
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single-cells RNA-seq analysis by MAST with unbalanced group size
mast single-cell rna-seq differential analysis
updated 6.3 years ago by ▴ 270 • written 6.3 years ago by ▴ 100
4
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5
replies
1.8k
views
SC3 gene clusters
SC3 single cell single-cell Tutorial
updated 6.5 years ago by 25k • written 6.5 years ago by ▴ 20
3
votes
3
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2.4k
views
How do you test a contrast in MAST?
MAST single-cell differential gene expression
updated 6.6 years ago by ▴ 270 • written 6.6 years ago by ▴ 40
5
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6
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2.7k
views
Error when merging SCESet objects
scater single-cell
updated 6.6 years ago by ★ 28k • written 6.6 years ago by ▴ 20
2
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3
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1.3k
views
Scran functions not found
single-cell scran
updated 6.6 years ago by ★ 28k • written 6.6 years ago by • 0
1
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1
reply
1.5k
views
Does SC3 correct counts for gene length?
sc3 scater single-cell rna-seq biclustering
updated 6.6 years ago by ▴ 150 • written 6.7 years ago by ▴ 20
2
votes
9
replies
2.5k
views
Zero inflation in RUV normalization and DE for single cell data
ruv ruvseq ruvnormalize single-cell zero-inflated
updated 6.7 years ago by ▴ 950 • written 6.7 years ago by ▴ 80
1
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0
replies
3.1k
views
Tutorial: BoF Bioc2017: Infrastructure for efficient storage and processing of large-scale single-cell genomics data
single-cell objectstorage Tutorial
6.7 years ago shepherl 3.8k
0
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5
replies
2.2k
views
[MnnCorrect] In case of known subpopulations
scran single-cell mnncorrect rnaseq
6.7 years ago Jens Preussner ▴ 30
4
votes
2
replies
1.4k
views
sc3_plot_expression, colour labels
sc3 single-cell
updated 6.9 years ago by ▴ 150 • written 6.9 years ago by ▴ 20
3
votes
3
replies
1.3k
views
Sharing SC3_interactive results
SC3 single-cell shiny
updated 6.9 years ago by ▴ 150 • written 6.9 years ago by ▴ 20
0
votes
4
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4.8k
views
Change point size and remove outline in scater's plotPCA
scater rnaseq single-cell
updated 6.0 years ago by • 0 • written 7.0 years ago by ▴ 70
0
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0
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1.1k
views
Rstudio crashes when running monocole
monocole single-cell rstudio
7.0 years ago Assa Yeroslaviz ★ 1.5k
2
votes
5
replies
1.9k
views
sc3_prepare function error
sc3 scater single-cell single cell
updated 7.2 years ago by ▴ 150 • written 7.2 years ago by ★ 1.5k
3
votes
6
replies
3.6k
views
How to properly normalize a single-cell sparse matrix?
Dropseq single-cell normalization sparse
updated 7.6 years ago by ★ 28k • written 7.6 years ago by ▴ 20
0
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0
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1.9k
views
News: Workshop on Statistical Challenges in Single-Cell Biology, April 30 to May 5, 2017, at Villa Monte Verita, Ascona
workshop statistics single-cell News
7.6 years ago Wolfgang Huber ★ 13k
0
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0
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2.0k
views
Job: Two Postdoc Positions in Evolutionary Single-Cell Genomics (experimental and computational)
evolution single-cell development differentiation cool Job
7.8 years ago Wolfgang Huber ★ 13k
42 results • Page 1 of 1
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Comment: Which input file is used for DGEList in EgdeR? by i.atanasoai • 0
Understood, Thank you very much for the reply, very kind.
Comment: Which input file is used for DGEList in EgdeR? by Michael Love 41k
"gene_counts_length_scaled.tsv file generated by the nf-core be exactly that?" No that is the counts scaled by the length. Counts + offset…
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa by Michael Love 41k
These genes are fine. They are just the ones where, by chance, the sample variance is below the sample mean. It happens. DESeq2 brings thes…
Comment: DEG with low counts by Michael Love 41k
These counts are too low, only a few samples above a count of 10. So for typical RNA-seq data that is underpowered to call differences. It…
Comment: DESeq filtering specific to contrasts by Michael Love 41k
If the counts are too low it in one group then you can't make the comparison either way (whether they are filtered out or just under-powere…
Votes
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
Comment: DEXSeq DEXSeqDataSet count matrix duplication
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