Showing : single-cell • reset
7
votes
3
replies
1.8k
views
Effect of feature number on adjusted p-values
edgeR DESeq2 single-cell scRNAseq zinbwave
updated 3.7 years ago by ★ 28k • written 3.7 years ago by ▴ 20
7
votes
12
replies
8.0k
views
How to identify real cells in 10X RNA-seq ?
single-cell 10X Cell calling DropletUtils cellranger
updated 5.9 years ago by ★ 28k • written 5.9 years ago by ▴ 20
5
votes
6
replies
3.0k
views
Error when merging SCESet objects
scater single-cell
updated 7.4 years ago by ★ 28k • written 7.4 years ago by ▴ 20
5
votes
6
replies
4.2k
views
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 5.3 years ago by ★ 3.4k • written 5.3 years ago by ▴ 80
4
votes
5
replies
2.2k
views
SC3 gene clusters
SC3 single cell single-cell Tutorial
updated 7.3 years ago by 25k • written 7.3 years ago by ▴ 20
4
votes
3
replies
2.4k
views
single-cells RNA-seq analysis by MAST with unbalanced group size
mast single-cell rna-seq differential analysis
updated 7.1 years ago by ▴ 270 • written 7.1 years ago by ▴ 100
4
votes
2
replies
1.9k
views
Seurat to SingleCellExperiment Converting error in MAC
singlecellexperiment single-cell rnaseq
updated 6.2 years ago by ★ 13k • written 6.2 years ago by ▴ 60
4
votes
2
replies
1.6k
views
sc3_plot_expression, colour labels
sc3 single-cell
updated 7.6 years ago by ▴ 150 • written 7.6 years ago by ▴ 20
3
votes
0
replies
1.3k
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
6.0 years ago Stephanie Hicks ▴ 80
3
votes
3
replies
1.9k
views
Issue with scp transfer of DESeq2 objects
deseq2 scp Unix Single-Cell
updated 5.1 years ago by 25k • written 5.1 years ago by ▴ 20
3
votes
3
replies
1.6k
views
Sharing SC3_interactive results
SC3 single-cell shiny
updated 7.7 years ago by ▴ 150 • written 7.7 years ago by ▴ 20
3
votes
6
replies
4.2k
views
How to properly normalize a single-cell sparse matrix?
Dropseq single-cell normalization sparse
updated 8.4 years ago by ★ 28k • written 8.4 years ago by ▴ 20
3
votes
2
replies
1.5k
views
BiocParallel errors from muscat
BiocParallel muscat single-cell
2.8 years ago tangming2005 ▴ 200
3
votes
3
replies
7.8k
views
rowSums() rowMeans() don't work on sparse matrix "dgCMatrix"
scater scran single-cell
updated 6.6 years ago by 25k • written 6.7 years ago by ▴ 10
3
votes
3
replies
3.0k
views
How do you test a contrast in MAST?
MAST single-cell differential gene expression
updated 7.4 years ago by ▴ 270 • written 7.4 years ago by ▴ 40
2
votes
2
replies
2.1k
views
[MnnCorrect] Remove batch effects but keep condition effects
single-cell scran mnncorrect rnaseq
updated 6.2 years ago by ★ 28k • written 6.2 years ago by ▴ 10
2
votes
9
replies
3.0k
views
Zero inflation in RUV normalization and DE for single cell data
ruv ruvseq ruvnormalize single-cell zero-inflated
updated 7.5 years ago by ▴ 980 • written 7.5 years ago by ▴ 90
2
votes
3
replies
1.5k
views
Scran functions not found
single-cell scran
updated 7.4 years ago by ★ 28k • written 7.4 years ago by • 0
2
votes
5
replies
2.1k
views
sc3_prepare function error
sc3 scater single-cell single cell
updated 7.9 years ago by ▴ 150 • written 7.9 years ago by ★ 1.5k
2
votes
1
reply
3.0k
views
MAST: testing differential expression with a nested factorial design
MAST single-cell rna-seq
updated 6.8 years ago by ▴ 270 • written 6.8 years ago by ▴ 20
1
vote
3
replies
1.7k
views
Differential expressiong with two groups in BASiCS
BASiCS single-cell bayesian differential expression
updated 6.9 years ago by ▴ 10 • written 7.0 years ago by ▴ 10
1
vote
1
reply
1.7k
views
Adjust number of clusters with scran/buildSNNGraph
scran buildsnngraph cluster_walktrap single-cell
updated 6.5 years ago by ★ 28k • written 6.5 years ago by • 0
1
vote
1
reply
1.7k
views
Does SC3 correct counts for gene length?
sc3 scater single-cell rna-seq biclustering
updated 7.4 years ago by ▴ 150 • written 7.4 years ago by ▴ 20
1
vote
1
reply
1.6k
views
Problem with finding mitochondrial genes in a human single cell RNA-Seq readCounts file
single-cell rnaseq mitochondria
updated 6.4 years ago by ★ 28k • written 6.4 years ago by • 0
1
vote
5
replies
2.9k
views
newSCESet and SingleCellExperiment basic differences and TMM Normalization
singlecellexperiment single-cell rnaseq seurat scater
6.3 years ago hamza_karakurt ▴ 60
1
vote
2
replies
1.1k
views
question for "Chapter 24 Zeisel mouse brain (STRT-Seq) in single-cell"
STRT-Seq single-cell tutorial
updated 4.6 years ago by ★ 28k • written 4.6 years ago by • 0
1
vote
0
replies
3.4k
views
Tutorial: BoF Bioc2017: Infrastructure for efficient storage and processing of large-scale single-cell genomics data
single-cell objectstorage Tutorial
7.5 years ago shepherl 4.1k
1
vote
0
replies
1.1k
views
Job: applied methods development for single-cell sequencing
single-cell job computational biology Job
6.2 years ago Simon Anders ★ 3.8k
0
votes
2
replies
696
views
How to add Ensembl ids after Pseudobulk analysis by DESeq2
Seurat DESeq2 single-cell scRNA Pseudobulk
updated 8 months ago by ★ 4.1k • written 8 months ago by • 0
0
votes
0
replies
2.1k
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
8.4 years ago Wolfgang Huber ★ 13k
0
votes
0
replies
1.2k
views
Rstudio crashes when running monocole
monocole single-cell rstudio
7.7 years ago Assa Yeroslaviz ★ 1.5k
0
votes
4
replies
5.4k
views
Change point size and remove outline in scater's plotPCA
scater rnaseq single-cell
updated 6.8 years ago by • 0 • written 7.7 years ago by ▴ 70
0
votes
5
replies
2.5k
views
[MnnCorrect] In case of known subpopulations
scran single-cell mnncorrect rnaseq
7.5 years ago Jens Preussner ▴ 30
0
votes
28
replies
3.8k
views
Job: Postdoc on integrating and analyzing new transcriptome types in the Bgee database
rnaseq data integration single-cell pacbio across species Job
6.8 years ago bgee • 0
0
votes
3
replies
1.1k
views
Error of makeTechTrend() of Scran
scran single-cell seq.default
updated 6.4 years ago by ★ 28k • written 6.4 years ago by • 0
0
votes
0
replies
1.2k
views
Job: PhD opportunity in Heidelberg for computational people
PhD position job single-cell Job
6.3 years ago Simon Anders ★ 3.8k
0
votes
0
replies
1.0k
views
Job: Biostatistics Analyst II - high throughput single-cell assays
biostatistics single-cell high throughput Job
6.0 years ago careers • 0
0
votes
1
reply
1.3k
views
Scran: Performing DE after cell-typle identifaction on the corrected and integrated datasets
Scran MNN_correct Differential expression single-cell
5.9 years ago baldissera152 • 0
0
votes
0
replies
914
views
Job: Bioinformatics postdoc in comparative genomics
single-cell evolution Genomics Postdoc
3.3 years ago henrik.kaessmann • 0
0
votes
0
replies
1.2k
views
Job: Computational Biologist, Blood Research Institute, Versiti, Wauwatosa, Wisconsin, USA
RNA-seq Job Single-Cell
3.7 years ago rbrns • 0
0
votes
0
replies
996
views
Job: Job: Moderna Statistical genomics co-op 2022, single-cell applications in immunology, masters or PhDs
co-op immunology single-cell omics
3.3 years ago joyce.hsiao1 • 0
0
votes
0
replies
923
views
Job: PhD student position: Vertebrate brain origins and evolution
PhD single-cell ComparativeGenomics evolution
3.3 years ago henrik.kaessmann • 0
0
votes
0
replies
2.2k
views
Job: Two Postdoc Positions in Evolutionary Single-Cell Genomics (experimental and computational)
evolution single-cell development differentiation cool Job
8.6 years ago Wolfgang Huber ★ 13k
43 results • Page 1 of 1
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Comment: Rain error: invalid annotation of time points by Dominik • 0
Hi, I kept running into the same issue until I double checked their help and understood, that columns and rows have to be designed in anoth…
Answer: How to generate circular cnetplot and color nodes and edges in the same plot ? by Guido Hooiveld ★ 4.1k
Since the release of `enrichplot` of October 2024, the code of the function `cnetplot` has been completely rewritten by Guangchuang in orde…
Comment: CUT&Tag differential peak analysis using Diffbind, with pre-calculated normaliza by mec25 • 0
I am unable to find the math behind the dba.normalize(), for instance when the E-coli fraction is used is the signal mutliplied by the fact…
Comment: How to sort negative log2FC or FC in RNAseq for GSEA? by Quang NN ▴ 10
Thank you so much for taking time to provide this clarification!
Comment: How can I generate a heatmap and clustering of differentially expressed genes in by Renuka • 0
Thanks Kelvin i had same doubt .Do i need to do log2 (FPKMcounts) for this
Votes
Answer: DESeq2- merging technical vs biological replicates
Answer: SingleCellExperiment convenience function for metadata+expression?
How to correct for tumor purity using DESeq2 to analyze TCGA tumor sample expression.
Answer: EdgeR Biological CVs
Answer: Error in download.file for TCGAutils::symbolsToRanges
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Popular Question to shepherl 4.1k
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