Showing : Single-Cell • reset
5
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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
votes
4
replies
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 6.9 years ago by ▴ 70
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
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
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
3
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2
replies
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
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
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
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
0
votes
5
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2.2k
views
[MnnCorrect] In case of known subpopulations
scran single-cell mnncorrect rnaseq
6.7 years ago Jens Preussner ▴ 30
0
votes
28
replies
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
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
3
votes
3
replies
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
1
vote
1
reply
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
0
votes
3
replies
961
views
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
vote
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
1
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5
replies
2.5k
views
newSCESet and SingleCellExperiment basic differences and TMM Normalization
singlecellexperiment single-cell rnaseq seurat scater
5.5 years ago hamza_karakurt ▴ 50
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
7
votes
12
replies
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
3
votes
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
1
vote
2
replies
886
views
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
7
votes
3
replies
1.4k
views
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
3
votes
2
replies
1.2k
views
BiocParallel errors from muscat
BiocParallel muscat single-cell
2.1 years ago tangming2005 ▴ 190
1
vote
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
3
replies
1.3k
views
Scran functions not found
single-cell scran
updated 6.6 years ago by ★ 28k • written 6.6 years ago by • 0
5
votes
6
replies
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
3
votes
3
replies
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
4
votes
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
4
votes
3
replies
1.9k
views
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
1
vote
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
votes
0
replies
918
views
Job: Computational Biologist, Blood Research Institute, Versiti, Wauwatosa, Wisconsin, USA
RNA-seq Job Single-Cell
2.9 years ago rbrns • 0
0
votes
0
replies
797
views
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
votes
0
replies
1.0k
views
Job: PhD opportunity in Heidelberg for computational people
PhD position job single-cell Job
5.5 years ago Simon Anders ★ 3.7k
0
votes
0
replies
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
1
vote
0
replies
906
views
Job: applied methods development for single-cell sequencing
single-cell job computational biology Job
5.4 years ago Simon Anders ★ 3.7k
0
votes
0
replies
708
views
Job: Bioinformatics postdoc in comparative genomics
single-cell evolution Genomics Postdoc
2.5 years ago henrik.kaessmann • 0
0
votes
0
replies
1.1k
views
Rstudio crashes when running monocole
monocole single-cell rstudio
7.0 years ago Assa Yeroslaviz ★ 1.5k
3
votes
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
0
votes
0
replies
861
views
Job: Biostatistics Analyst II - high throughput single-cell assays
biostatistics single-cell high throughput Job
5.2 years ago careers • 0
0
votes
0
replies
715
views
Job: PhD student position: Vertebrate brain origins and evolution
PhD single-cell ComparativeGenomics evolution
2.5 years ago henrik.kaessmann • 0
0
votes
1
reply
1.1k
views
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
0
votes
0
replies
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
42 results • Page 1 of 1
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Comment: DESeq2 setting significant p-value by Michael Love 41k
It does not resort. Also the dataset and results will have the same row names from object creation throughout the analysis.
Comment: Input Question for deseq.r by ATpoint ★ 4.0k
It is unclear what "deseq.r" is. It is not part of DESeq2, and almost certainly no part of RSeqAn. Please add details, and keep in mind tha…
Answer: DESEQ2 output gives multiple groups when only 2 groups are present by ATpoint ★ 4.0k
In the first PCA plot there is almost certainly some hidden character like whitespaces in the column from colData that encodes this group. …
Answer: A ComBat-seq issue: the covariates are confounded by ATpoint ★ 4.0k
```r > table(batch, group) group batch egfr gfp her2 1 0 12 5 2 6 6 0 ``` All of her2 is batch2, all of egfr i…
Comment: DESeq2 setting significant p-value by Dev • 0
after running DESeq2 does it sort the value on the basis of pvalue, or anything, or does it give the data back in the input format I have …
Votes
Using GRanges and IRanges to simply get all chromosome data
A: Using GRanges and IRanges to simply get all chromosome data
Comment: Reading huge bismark coverage files using bbseq::read.bismark
Answer: Reading huge bismark coverage files using bbseq::read.bismark
Answer: Reading huge bismark coverage files using bbseq::read.bismark
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