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Showing :
scran
•
reset
0
votes
0
replies
163
views
modelGeneVar in MulticoreParam: wrong args for environment subassignment
BiocParallel
scran
BiocParall
28 days ago
Lluís Revilla Sancho
▴ 750
0
votes
5
replies
512
views
modelGeneVarByPoisson error selecting bandwidth automatically
scran
updated 3 months ago by
Peter Hickey
▴ 740 • written 3 months ago by
Lluís Revilla Sancho
▴ 750
0
votes
0
replies
196
views
Differential Gene Wrapper for Propotion of Detected
scran
3 months ago
Dario Strbenac
★ 1.5k
0
votes
4
replies
514
views
Single Cell Experiment : Differential Expression "List of length 0" - Help!
DifferentialExpression
scran
scater
SingleCellExperiment
edgeR
4 months ago
vohara4
• 0
1
vote
2
replies
367
views
Reproducibility issue with scran together with lapply and BiocParallel
scran
BiocParallel
bluster
5 months ago
ATpoint
★ 4.5k
2
votes
1
reply
471
views
Existence of Bioconductor versus Seurat Software Ecosystems Quantitative Comparison
scran
bluster
scater
scuttle
updated 6 months ago by
ATpoint
★ 4.5k • written 6 months ago by
Dario Strbenac
★ 1.5k
0
votes
3
replies
785
views
scran package: quickCluster and calculateSumFactors parallelization
BiocParallel
scran
updated 9 months ago by
ATpoint
★ 4.5k • written 9 months ago by
qwang178
• 0
1
vote
2
replies
1.4k
views
ScRNAseq analysis scran :: quickcluster Error
scRNAseq
quickcluster
scRNA
scran
10 months ago
ruba-mahmoud
• 0
0
votes
1
reply
609
views
Speeding up large scale scRNAseq analyses in R and improve memory
scran
updated 13 months ago by
ATpoint
★ 4.5k • written 13 months ago by
Maximilian
• 0
0
votes
2
replies
1.2k
views
runPCA in a SingleCellExperiment results ina colMeans error
scran
SingleCellExperiment
16 months ago
Lluís Revilla Sancho
▴ 750
2
votes
2
replies
8.7k
views
scran ScoreMarkers throws a warning
scoreMarkers
scran
updated 16 months ago by
Peter Hickey
▴ 740 • written 16 months ago by
Assa Yeroslaviz
★ 1.5k
2
votes
3
replies
1.6k
views
P-value histogram of testLinearModel is not uniform
smart-seq2
scRNAseq
scran
16 months ago
Lluís Revilla Sancho
▴ 750
0
votes
2
replies
1.0k
views
Scaling and normalization by deconvolution of SMART-Seq 2 data
scran
Clustering
SingleCell
Normalization
18 months ago
Assa Yeroslaviz
★ 1.5k
1
vote
0
replies
876
views
Use scran's normalization by deconvolution for each individual sample or over all samples
scran
Normalization
scRNA
BatchEffect
21 months ago
r_grau
▴ 10
4
votes
3
replies
1.9k
views
SingleCellExperiment: Edit cluster IDs in colLabels
scran
Clustering
SingleCellExperiment
annotate
cluster
updated 2.2 years ago by
James W. MacDonald
67k • written 2.2 years ago by
achoppe
▴ 10
1
vote
1
reply
1.0k
views
setting sizeFactors from scran :: caculateSumFactors.
scran
DESeq2
updated 2.3 years ago by
ATpoint
★ 4.5k • written 2.3 years ago by
OE
• 0
3
votes
3
replies
1.4k
views
RFC: Inconsistent software license for scran & automated license checks
agpl
license
gpl
scran
2.3 years ago • updated 2.2 years ago
matthias-doering
▴ 40
2
votes
1
reply
1.4k
views
Getting error Creating SingleCellExperiment instances "all assays must have the same nrow and ncol"
SingleCellExperiment
scran
scater
updated 2.5 years ago by
Basti
▴ 780 • written 2.5 years ago by
Lucky
• 0
2
votes
2
replies
1.5k
views
scuttle:: librarySizeFactors returning non-finite values
normalizeCounts
scran
librarySizeFactors
scuttle
scRNAseq
2.6 years ago
behr201
• 0
1
vote
2
replies
1.1k
views
How to answer reviewers question of physical cell size influencing single cell results?
SingleCellExperiment
scater
ExperimentalDesign
scran
2.7 years ago • updated 2.6 years ago
msn
▴ 10
2
votes
2
replies
1.2k
views
Block weights in scran::pairwiseTTests
scran
2.9 years ago
Angelos Armen
• 0
1
vote
1
reply
1.3k
views
scran computeSumFactors showing error
scran
single
cell
updated 2.9 years ago by
Aaron Lun
★ 28k • written 2.9 years ago by
hemantcnaik
• 0
3
votes
3
replies
1.9k
views
Ensuring reproducibility in BiocParallel SingleCellExperiment workflows
scater
SingleCellExperiment
BiocParallel
scuttle
scran
3.0 years ago
enricoferrero
▴ 660
2
votes
2
replies
2.1k
views
loading scran package
scran
installation
3.7 years ago
TJ
• 0
5
votes
6
replies
2.0k
views
DE Analysis on Scran-Normalized Counts
DifferentialExpression
scRNAseq
scran
updated 3.7 years ago by
Aaron Lun
★ 28k • written 3.7 years ago by
LUCIA
• 0
4
votes
5
replies
2.8k
views
scuttle::aggregateAcrossCells() crashes R on large SingleCellExperiment
scran
SingleCellExperiment
scuttle
scater
updated 3.8 years ago by
Aaron Lun
★ 28k • written 3.8 years ago by
enricoferrero
▴ 660
0
votes
0
replies
899
views
Creating a stable batch-corrected scRNA-Seq data with multiple datasets and multiple integrations
scater
singlecell
scran
BatchEffect
3.9 years ago
hamza_karakurt
▴ 60
1
vote
1
reply
1.1k
views
scran::computeSumFactors with single-cell ATAC-seq data
scran
updated 4.0 years ago by
Aaron Lun
★ 28k • written 4.0 years ago by
Angelos Armen
• 0
1
vote
1
reply
2.1k
views
findMarkers() {scran} doesn't really find markers
findMarkers
scran
updated 4.1 years ago by
Aaron Lun
★ 28k • written 4.1 years ago by
paula.vaccarello
• 0
2
votes
3
replies
2.1k
views
multiBatchNorm vs. calculateSumFactors on concatenated dataset
batchelor
scran
updated 4.2 years ago by
Aaron Lun
★ 28k • written 4.2 years ago by
Angelos Armen
• 0
5
votes
4
replies
6.8k
views
scRNA-seq pseudo-bulk differential expression analysis with pseudobulkDGE()
scran
scater
scuttle
updated 4.2 years ago by
Aaron Lun
★ 28k • written 4.2 years ago by
enricoferrero
▴ 660
2
votes
6
replies
1.3k
views
Why is an averaged reference used in DESeq2 normalisation?
deseq2
scran
batchelor
updated 4.3 years ago by
Aaron Lun
★ 28k • written 4.3 years ago by
Angelos Armen
• 0
9
votes
4
replies
5.7k
views
Removing cell cycle genes in large data set integration
scran
cyclone
updated 4.4 years ago by
Aaron Lun
★ 28k • written 4.4 years ago by
p.joshi
▴ 40
0
votes
4
replies
1.6k
views
scran's quickCluster error
scran
updated 4.4 years ago by
Aaron Lun
★ 28k • written 4.4 years ago by
marc.tormo
• 0
3
votes
1
reply
1.2k
views
Output lfc for Wilcox-based findMarkers
scran
updated 4.4 years ago by
Aaron Lun
★ 28k • written 4.4 years ago by
ATpoint
★ 4.5k
7
votes
5
replies
3.0k
views
Optimal cluster number identification using buildSNNgraph and igraph clusters
scran
gap statistics
single cell clustering
updated 4.4 years ago by
Aaron Lun
★ 28k • written 4.4 years ago by
p.joshi
▴ 40
7
votes
3
replies
6.1k
views
Downsample or not to downsample?
scrna-seq
downsampleBatches
scran
updated 4.5 years ago by
Aaron Lun
★ 28k • written 4.5 years ago by
p.joshi
▴ 40
0
votes
3
replies
1.2k
views
How can doubletCell() scores be converted to single/doublet annotation?
scran
doublet
updated 4.6 years ago by
Aaron Lun
★ 28k • written 4.6 years ago by
thkapell
▴ 10
2
votes
1
reply
2.3k
views
Batch Corrections (MNN) with TPM values
scRNA-Seq
scater
scran
rna-seq
MNN
updated 5.0 years ago by
Aaron Lun
★ 28k • written 5.0 years ago by
hamza_karakurt
▴ 60
1
vote
1
reply
935
views
Stouffer's method weights in scran::pairwiseWilcox
scran
updated 5.0 years ago by
Aaron Lun
★ 28k • written 5.0 years ago by
Angelos Armen
• 0
0
votes
5
replies
3.4k
views
Cannot install Bioconductor v3.9
scran
cellassign
bioconductor
updated 5.0 years ago by
Martin Morgan
25k • written 5.0 years ago by
thkapell
▴ 10
1
vote
2
replies
1.5k
views
Mitigating cell cycle effect in scRNA-seq using a blocking factor or design matrix
scran
updated 5.0 years ago by
Aaron Lun
★ 28k • written 5.1 years ago by
s1437643
▴ 20
2
votes
1
reply
1.5k
views
scran: excluding genes with extremely high expression during normalization?
single-cell RNA-seq
scran
normalization
updated 5.2 years ago by
Aaron Lun
★ 28k • written 5.2 years ago by
daniel.borshagovski
• 0
1
vote
3
replies
1.1k
views
k argument in buildSNNGraph
scran
updated 5.2 years ago by
Aaron Lun
★ 28k • written 5.2 years ago by
Angelos Armen
• 0
1
vote
5
replies
1.9k
views
Preprocessing in scran::doubletCells
scran
simpleSingleCell
updated 5.2 years ago by
Aaron Lun
★ 28k • written 5.2 years ago by
Angelos Armen
• 0
4
votes
4
replies
3.1k
views
using limma and edgeR for differential expression of Drop-seq/10xGenomics scRNA-seq data
limma
edgeR
simplesingleCell
scran
scater
updated 5.2 years ago by
Aaron Lun
★ 28k • written 5.2 years ago by
Bogdan
▴ 670
4
votes
4
replies
1.8k
views
scRNA-seq : Classification of cell cycle phase
scater
scran
updated 5.3 years ago by
Aaron Lun
★ 28k • written 5.3 years ago by
Bogdan
▴ 670
3
votes
7
replies
2.3k
views
scRNA-seq : runPCA() and denoisePCA()
scater
scran
updated 5.3 years ago by
Aaron Lun
★ 28k • written 5.3 years ago by
Bogdan
▴ 670
1
vote
4
replies
1.7k
views
number of cell clusters in scRNA-seq
scran
scater
sc3
updated 5.3 years ago by
Aaron Lun
★ 28k • written 5.3 years ago by
Bogdan
▴ 670
0
votes
7
replies
2.5k
views
differential expression between clusters (in distinct "treatments") in scRNAseq
scater
limma
scde
scran
sc3
5.3 years ago
Bogdan
▴ 670
50 results • Page
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Recent ...
Replies
Comment: How to reverse complement some elements of a DNAStringSet
by
Christine Jones
• 0
Fantastic, thank you
Comment: When running contrasts, does it use normalized read counts?
by
Katherine
• 0
Ok, so the comment I was given where they said DeSeq2 should be with normalized counts is incorrect. the ```normalized_counts``` variable …
Answer: How to reverse complement some elements of a DNAStringSet
by
James W. MacDonald
67k
You should always try the vectorized method first, rather than looping. ``` > myFasta[myFasta_rc] <- reverseComplement(myFasta[myFasta_…
Answer: When running contrasts, does it use normalized read counts?
by
James W. MacDonald
67k
A contrast is a comparison of two or more coefficients. When you run `nbiomWaldTest` you are fitting the GLM and estimating coefficients. T…
Comment: Too much data for Diffbind
by
Ou, Jianhong
★ 1.3k
Just in case if somebody still want to apply summits greater than 0 and got the same error, you can filter out the peaks with start positio…
Votes
Comment: featureCounts fails to load annotation file
Answer: How to reverse complement some elements of a DNAStringSet
Answer: KEGGgraph result difference
Answer: What should be the normalization protocol for RNA seq data for WGCNA?
What should be the normalization protocol for RNA seq data for WGCNA?
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