Showing : single-cell • reset
7
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12
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8.0k
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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
3
votes
3
replies
7.7k
views
rowSums() rowMeans() don't work on sparse matrix "dgCMatrix"
scater scran single-cell
updated 6.5 years ago by 25k • written 6.7 years ago by ▴ 10
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
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
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
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
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
5
votes
6
replies
3.0k
views
Error when merging SCESet objects
scater single-cell
updated 7.3 years ago by ★ 28k • written 7.3 years ago by ▴ 20
3
votes
3
replies
3.0k
views
How do you test a contrast in MAST?
MAST single-cell differential gene expression
updated 7.3 years ago by ▴ 270 • written 7.3 years ago by ▴ 40
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 7.4 years ago by ▴ 980 • written 7.4 years ago by ▴ 90
2
votes
1
reply
2.9k
views
MAST: testing differential expression with a nested factorial design
MAST single-cell rna-seq
updated 6.7 years ago by ▴ 270 • written 6.8 years ago by ▴ 20
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
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
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 7.0 years ago by ▴ 270 • written 7.0 years ago by ▴ 100
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
8.5 years ago Wolfgang Huber ★ 13k
4
votes
5
replies
2.2k
views
SC3 gene clusters
SC3 single cell single-cell Tutorial
updated 7.2 years ago by 25k • written 7.2 years ago by ▴ 20
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
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
2
votes
2
replies
2.1k
views
[MnnCorrect] Remove batch effects but keep condition effects
single-cell scran mnncorrect rnaseq
updated 6.1 years ago by ★ 28k • written 6.1 years ago by ▴ 10
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
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
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
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 6.9 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
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
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
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
2
replies
1.5k
views
BiocParallel errors from muscat
BiocParallel muscat single-cell
2.8 years ago tangming2005 ▴ 200
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
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
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
5.8 years ago baldissera152 • 0
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
0
replies
1.2k
views
Job: PhD opportunity in Heidelberg for computational people
PhD position job single-cell Job
6.2 years ago Simon Anders ★ 3.8k
0
votes
0
replies
1.1k
views
Job: Computational Biologist, Blood Research Institute, Versiti, Wauwatosa, Wisconsin, USA
RNA-seq Job Single-Cell
3.7 years ago rbrns • 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
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
1.1k
views
Job: applied methods development for single-cell sequencing
single-cell job computational biology Job
6.1 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
5.9 years ago careers • 0
0
votes
0
replies
988
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
916
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
906
views
Job: Bioinformatics postdoc in comparative genomics
single-cell evolution Genomics Postdoc
3.3 years ago henrik.kaessmann • 0
0
votes
2
replies
664
views
How to add Ensembl ids after Pseudobulk analysis by DESeq2
Seurat DESeq2 single-cell scRNA Pseudobulk
updated 7 months ago by ★ 4.1k • written 7 months ago by • 0
43 results • Page 1 of 1
Recent ...
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Answer: promoters_txdb <- promoters(txdb, upstream = 2000) is not 2000 by James W. MacDonald 67k
If you use `promoters` and do not provide an argument for something that has a default, you will get the default argument. Your last call t…
Comment: org.Hs.eg.db issue by k.panov • 0
installed R on another PC, works perfectly. ergo, problem outside of R probably..... :-(
Comment: MBDseq analysis using qsea package by Lukas ▴ 20
Hi, I checked in with Matthias and here is his response: You need to indicate "samples": "The indices of the samples for which individu…
Comment: DESeq2 analysis with transcript counts by sindhuri • 0
Thank you for the response. Currently I am using the R studio for analysis and Im running DESeq2 for analysis of the **transcript counts.ts…
Comment: iam not able to do retrive data using GEOquery R package by James W. MacDonald 67k
Another alternative is to use the `GEOmetadb` package ([vignette here)][1], which will allow you to make queries to identify GEO datasets t…
Votes
Answer: Is there any chance to solve "the model matrix is not full rank" in DESeq2?
Answer: Issue carrying out DiffBind Analysis at a predefined peak set
Answer: Differential variability modelling with vst() expression
Answer: Differential variability modelling with vst() expression
Comment: Different annotation packages (org.Mm.eg.db, EnsDb.Mmusculus.v79, BiomaRt) retu
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