Showing : SCRAN • reset
1
vote
2
replies
139
views
Reproducibility issue with scran together with lapply and BiocParallel
scran BiocParallel bluster
8 days ago • updated 7 days ago ATpoint ★ 4.1k
2
votes
1
reply
231
views
Existence of Bioconductor versus Seurat Software Ecosystems Quantitative Comparison
scran bluster scater scuttle
updated 5 weeks ago by ★ 4.1k • written 5 weeks ago by ★ 1.5k
0
votes
3
replies
431
views
scran package: quickCluster and calculateSumFactors parallelization
BiocParallel scran
updated 3 months ago by ★ 4.1k • written 3 months ago by • 0
1
vote
2
replies
798
views
ScRNAseq analysis scran :: quickcluster Error
scRNAseq quickcluster scRNA scran
4 months ago ruba-mahmoud • 0
0
votes
1
reply
354
views
Speeding up large scale scRNAseq analyses in R and improve memory
scran
updated 8 months ago by ★ 4.1k • written 8 months ago by • 0
0
votes
2
replies
821
views
runPCA in a SingleCellExperiment results ina colMeans error
scran SingleCellExperiment
10 months ago Lluís Revilla Sancho ▴ 730
2
votes
2
replies
5.4k
views
scran ScoreMarkers throws a warning
scoreMarkers scran
updated 10 months ago by ▴ 740 • written 10 months ago by ★ 1.5k
2
votes
3
replies
1.3k
views
P-value histogram of testLinearModel is not uniform
smart-seq2 scRNAseq scran
11 months ago • updated 10 months ago Lluís Revilla Sancho ▴ 730
0
votes
2
replies
709
views
Scaling and normalization by deconvolution of SMART-Seq 2 data
scran Clustering SingleCell Normalization
13 months ago Assa Yeroslaviz ★ 1.5k
1
vote
0
replies
668
views
Use scran's normalization by deconvolution for each individual sample or over all samples
scran Normalization scRNA BatchEffect
16 months ago r_grau ▴ 10
4
votes
3
replies
1.5k
views
SingleCellExperiment: Edit cluster IDs in colLabels
scran Clustering SingleCellExperiment annotate cluster
updated 21 months ago by 65k • written 21 months ago by ▴ 10
1
vote
1
reply
798
views
setting sizeFactors from scran :: caculateSumFactors.
scran DESeq2
updated 22 months ago by ★ 4.1k • written 22 months ago by • 0
3
votes
3
replies
1.2k
views
RFC: Inconsistent software license for scran & automated license checks
agpl license gpl scran
22 months ago • updated 21 months ago matthias-doering ▴ 40
2
votes
1
reply
1.1k
views
Getting error Creating SingleCellExperiment instances "all assays must have the same nrow and ncol"
SingleCellExperiment scran scater
updated 2.1 years ago by ▴ 780 • written 2.1 years ago by • 0
2
votes
2
replies
1.2k
views
scuttle:: librarySizeFactors returning non-finite values
normalizeCounts scran librarySizeFactors scuttle scRNAseq
2.2 years ago behr201 • 0
1
vote
2
replies
923
views
How to answer reviewers question of physical cell size influencing single cell results?
SingleCellExperiment scater ExperimentalDesign scran
2.2 years ago msn ▴ 10
2
votes
2
replies
1.0k
views
Block weights in scran::pairwiseTTests
scran
2.5 years ago • updated 2.4 years ago Angelos Armen • 0
1
vote
1
reply
1.1k
views
scran computeSumFactors showing error
scran single cell
updated 2.5 years ago by ★ 28k • written 2.5 years ago by • 0
3
votes
3
replies
1.7k
views
Ensuring reproducibility in BiocParallel SingleCellExperiment workflows
scater SingleCellExperiment BiocParallel scuttle scran
2.5 years ago enricoferrero ▴ 660
2
votes
2
replies
1.8k
views
loading scran package
scran installation
3.2 years ago TJ • 0
5
votes
6
replies
1.6k
views
DE Analysis on Scran-Normalized Counts
DifferentialExpression scRNAseq scran
updated 3.2 years ago by ★ 28k • written 3.2 years ago by • 0
4
votes
5
replies
2.3k
views
scuttle::aggregateAcrossCells() crashes R on large SingleCellExperiment
scran SingleCellExperiment scuttle scater
updated 3.3 years ago by ★ 28k • written 3.3 years ago by ▴ 660
0
votes
0
replies
765
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
1
vote
1
reply
972
views
scran::computeSumFactors with single-cell ATAC-seq data
scran
updated 3.5 years ago by ★ 28k • written 3.5 years ago by • 0
1
vote
1
reply
1.9k
views
findMarkers() {scran} doesn't really find markers
findMarkers scran
updated 3.7 years ago by ★ 28k • written 3.7 years ago by • 0
2
votes
3
replies
1.8k
views
multiBatchNorm vs. calculateSumFactors on concatenated dataset
batchelor scran
updated 3.7 years ago by ★ 28k • written 3.7 years ago by • 0
5
votes
4
replies
6.1k
views
scRNA-seq pseudo-bulk differential expression analysis with pseudobulkDGE()
scran scater scuttle
updated 3.7 years ago by ★ 28k • written 3.7 years ago by ▴ 660
2
votes
6
replies
1.2k
views
Why is an averaged reference used in DESeq2 normalisation?
deseq2 scran batchelor
updated 3.8 years ago by ★ 28k • written 3.9 years ago by • 0
9
votes
4
replies
5.0k
views
Removing cell cycle genes in large data set integration
scran cyclone
updated 3.9 years ago by ★ 28k • written 3.9 years ago by ▴ 40
0
votes
4
replies
1.3k
views
scran's quickCluster error
scran
updated 4.0 years ago by ★ 28k • written 4.0 years ago by • 0
3
votes
1
reply
1.0k
views
Output lfc for Wilcox-based findMarkers
scran
updated 4.0 years ago by ★ 28k • written 4.0 years ago by ★ 4.1k
7
votes
5
replies
2.5k
views
Optimal cluster number identification using buildSNNgraph and igraph clusters
scran gap statistics single cell clustering
updated 4.0 years ago by ★ 28k • written 4.0 years ago by ▴ 40
7
votes
3
replies
4.8k
views
Downsample or not to downsample?
scrna-seq downsampleBatches scran
updated 4.0 years ago by ★ 28k • written 4.0 years ago by ▴ 40
0
votes
3
replies
960
views
How can doubletCell() scores be converted to single/doublet annotation?
scran doublet
updated 4.1 years ago by ★ 28k • written 4.1 years ago by ▴ 10
2
votes
1
reply
1.9k
views
Batch Corrections (MNN) with TPM values
scRNA-Seq scater scran rna-seq MNN
updated 4.6 years ago by ★ 28k • written 4.6 years ago by ▴ 50
1
vote
1
reply
822
views
Stouffer's method weights in scran::pairwiseWilcox
scran
updated 4.6 years ago by ★ 28k • written 4.6 years ago by • 0
0
votes
5
replies
3.2k
views
Cannot install Bioconductor v3.9
scran cellassign bioconductor
updated 4.6 years ago by 25k • written 4.6 years ago by ▴ 10
1
vote
2
replies
1.3k
views
Mitigating cell cycle effect in scRNA-seq using a blocking factor or design matrix
scran
updated 4.6 years ago by ★ 28k • written 4.6 years ago by ▴ 20
2
votes
1
reply
1.3k
views
scran: excluding genes with extremely high expression during normalization?
single-cell RNA-seq scran normalization
updated 4.7 years ago by ★ 28k • written 4.7 years ago by • 0
1
vote
3
replies
923
views
k argument in buildSNNGraph
scran
updated 4.7 years ago by ★ 28k • written 4.7 years ago by • 0
1
vote
5
replies
1.6k
views
Preprocessing in scran::doubletCells
scran simpleSingleCell
updated 4.8 years ago by ★ 28k • written 4.8 years ago by • 0
4
votes
4
replies
2.8k
views
using limma and edgeR for differential expression of Drop-seq/10xGenomics scRNA-seq data
limma edgeR simplesingleCell scran scater
updated 4.8 years ago by ★ 28k • written 4.8 years ago by ▴ 670
4
votes
4
replies
1.5k
views
scRNA-seq : Classification of cell cycle phase
scater scran
updated 4.8 years ago by ★ 28k • written 4.8 years ago by ▴ 670
3
votes
7
replies
2.0k
views
scRNA-seq : runPCA() and denoisePCA()
scater scran
updated 4.8 years ago by ★ 28k • written 4.8 years ago by ▴ 670
1
vote
4
replies
1.5k
views
number of cell clusters in scRNA-seq
scran scater sc3
updated 4.8 years ago by ★ 28k • written 4.8 years ago by ▴ 670
0
votes
7
replies
2.2k
views
differential expression between clusters (in distinct "treatments") in scRNAseq
scater limma scde scran sc3
4.9 years ago Bogdan ▴ 670
0
votes
1
reply
832
views
emptyDrops result is full NAs
scran dropletUtils scater scRNA-Seq
4.9 years ago hamza_karakurt ▴ 50
3
votes
2
replies
1.2k
views
Is logFC a log2 fold change or some other base in scran::findMarkers
scran
updated 4.9 years ago by ★ 28k • written 4.9 years ago by • 0
4
votes
2
replies
1.6k
views
single cell data: adding random effects for subject with multilevel experiment design
SingleCellExperiment scran limma simpleSingleCell
updated 4.9 years ago by ★ 28k • written 4.9 years ago by • 0
2
votes
4
replies
3.6k
views
ERROR - Size factors should be positive real numbers (using normalize() function)
scater scran singlecellexperiment normalize qc
updated 2.1 years ago by • 0 • written 5.1 years ago by ▴ 10
50 results • Page 1 of 1
Recent ...
Replies
Answer: DESeq2 v1.35.0 by Michael Love 41k
That is not a release (odd 'y' digit). See Bioconductor help pages: https://contributions.bioconductor.org/description.html#description-ver…
Comment: Although I successfully installed the package "simpleaffy'' , I cannot library i by James W. MacDonald 65k
Please don't piggyback on posts from 2.3 years ago. If you have a question, post as a new question.
Answer: DESeq2 v1.35.0 by James W. MacDonald 65k
Odd release versions indicate a devel version, which upon release is incremented to the next even version, so you won't be able to find tha…
Comment: Although I successfully installed the package "simpleaffy'' , I cannot library i by fatinataly • 0
I tried also with oligo does not work, any other suggestion?
Comment: More regions in union when increasing DBA$config$mergeOverlap by Ian D. ▴ 70
Hello. Thanks for the reply. Sorry about this. My testing is telling me that 1 is the default (a gap), not -1 (1bp overlap). Negative …
Votes
Bioconductor 3.19 is Released!
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
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