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Scran
•
reset
0
votes
0
replies
8
views
Reproducibility issue with scran together with lapply and BiocParallel
scran
BiocParallel
bluster
1 hour ago
ATpoint
★ 4.0k
2
votes
1
reply
217
views
Existence of Bioconductor versus Seurat Software Ecosystems Quantitative Comparison
scran
bluster
scater
scuttle
updated 4 weeks ago by
ATpoint
★ 4.0k • written 4 weeks ago by
Dario Strbenac
★ 1.5k
0
votes
3
replies
398
views
scran package: quickCluster and calculateSumFactors parallelization
BiocParallel
scran
updated 3 months ago by
ATpoint
★ 4.0k • written 3 months ago by
qwang178
• 0
1
vote
2
replies
764
views
ScRNAseq analysis scran :: quickcluster Error
scRNAseq
quickcluster
scRNA
scran
4 months ago
ruba-mahmoud
• 0
0
votes
1
reply
346
views
Speeding up large scale scRNAseq analyses in R and improve memory
scran
updated 8 months ago by
ATpoint
★ 4.0k • written 8 months ago by
Maximilian
• 0
0
votes
2
replies
796
views
runPCA in a SingleCellExperiment results ina colMeans error
scran
SingleCellExperiment
10 months ago
Lluís Revilla Sancho
▴ 730
2
votes
2
replies
5.2k
views
scran ScoreMarkers throws a warning
scoreMarkers
scran
updated 10 months ago by
Peter Hickey
▴ 740 • written 10 months ago by
Assa Yeroslaviz
★ 1.5k
2
votes
3
replies
1.3k
views
P-value histogram of testLinearModel is not uniform
smart-seq2
scRNAseq
scran
10 months ago
Lluís Revilla Sancho
▴ 730
0
votes
2
replies
697
views
Scaling and normalization by deconvolution of SMART-Seq 2 data
scran
Clustering
SingleCell
Normalization
12 months ago
Assa Yeroslaviz
★ 1.5k
1
vote
0
replies
648
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 20 months ago by
James W. MacDonald
65k • written 20 months ago by
achoppe
▴ 10
1
vote
1
reply
782
views
setting sizeFactors from scran :: caculateSumFactors.
scran
DESeq2
updated 22 months ago by
ATpoint
★ 4.0k • written 22 months ago by
OE
• 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 20 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
Basti
▴ 780 • written 2.1 years ago by
Lucky
• 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
913
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
996
views
Block weights in scran::pairwiseTTests
scran
2.4 years ago
Angelos Armen
• 0
1
vote
1
reply
1.1k
views
scran computeSumFactors showing error
scran
single
cell
updated 2.4 years ago by
Aaron Lun
★ 28k • written 2.4 years ago by
hemantcnaik
• 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
1.7k
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
Aaron Lun
★ 28k • written 3.2 years ago by
LUCIA
• 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
Aaron Lun
★ 28k • written 3.3 years ago by
enricoferrero
▴ 660
0
votes
0
replies
757
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
968
views
scran::computeSumFactors with single-cell ATAC-seq data
scran
updated 3.5 years ago by
Aaron Lun
★ 28k • written 3.5 years ago by
Angelos Armen
• 0
1
vote
1
reply
1.8k
views
findMarkers() {scran} doesn't really find markers
findMarkers
scran
updated 3.6 years ago by
Aaron Lun
★ 28k • written 3.6 years ago by
paula.vaccarello
• 0
2
votes
3
replies
1.8k
views
multiBatchNorm vs. calculateSumFactors on concatenated dataset
batchelor
scran
updated 3.7 years ago by
Aaron Lun
★ 28k • written 3.7 years ago by
Angelos Armen
• 0
5
votes
4
replies
6.0k
views
scRNA-seq pseudo-bulk differential expression analysis with pseudobulkDGE()
scran
scater
scuttle
updated 3.7 years ago by
Aaron Lun
★ 28k • written 3.7 years ago by
enricoferrero
▴ 660
2
votes
6
replies
1.1k
views
Why is an averaged reference used in DESeq2 normalisation?
deseq2
scran
batchelor
updated 3.8 years ago by
Aaron Lun
★ 28k • written 3.8 years ago by
Angelos Armen
• 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
Aaron Lun
★ 28k • written 3.9 years ago by
p.joshi
▴ 40
0
votes
4
replies
1.3k
views
scran's quickCluster error
scran
updated 3.9 years ago by
Aaron Lun
★ 28k • written 3.9 years ago by
marc.tormo
• 0
3
votes
1
reply
1.0k
views
Output lfc for Wilcox-based findMarkers
scran
updated 4.0 years ago by
Aaron Lun
★ 28k • written 4.0 years ago by
ATpoint
★ 4.0k
7
votes
5
replies
2.4k
views
Optimal cluster number identification using buildSNNgraph and igraph clusters
scran
gap statistics
single cell clustering
updated 4.0 years ago by
Aaron Lun
★ 28k • written 4.0 years ago by
p.joshi
▴ 40
7
votes
3
replies
4.8k
views
Downsample or not to downsample?
scrna-seq
downsampleBatches
scran
updated 4.0 years ago by
Aaron Lun
★ 28k • written 4.0 years ago by
p.joshi
▴ 40
0
votes
3
replies
955
views
How can doubletCell() scores be converted to single/doublet annotation?
scran
doublet
updated 4.1 years ago by
Aaron Lun
★ 28k • written 4.1 years ago by
thkapell
▴ 10
2
votes
1
reply
1.9k
views
Batch Corrections (MNN) with TPM values
scRNA-Seq
scater
scran
rna-seq
MNN
updated 4.5 years ago by
Aaron Lun
★ 28k • written 4.5 years ago by
hamza_karakurt
▴ 50
1
vote
1
reply
818
views
Stouffer's method weights in scran::pairwiseWilcox
scran
updated 4.6 years ago by
Aaron Lun
★ 28k • written 4.6 years ago by
Angelos Armen
• 0
0
votes
5
replies
3.2k
views
Cannot install Bioconductor v3.9
scran
cellassign
bioconductor
updated 4.6 years ago by
Martin Morgan
25k • written 4.6 years ago by
thkapell
▴ 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
Aaron Lun
★ 28k • written 4.6 years ago by
s1437643
▴ 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
Aaron Lun
★ 28k • written 4.7 years ago by
daniel.borshagovski
• 0
1
vote
3
replies
918
views
k argument in buildSNNGraph
scran
updated 4.7 years ago by
Aaron Lun
★ 28k • written 4.7 years ago by
Angelos Armen
• 0
1
vote
5
replies
1.6k
views
Preprocessing in scran::doubletCells
scran
simpleSingleCell
updated 4.7 years ago by
Aaron Lun
★ 28k • written 4.7 years ago by
Angelos Armen
• 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
Aaron Lun
★ 28k • written 4.8 years ago by
Bogdan
▴ 670
4
votes
4
replies
1.5k
views
scRNA-seq : Classification of cell cycle phase
scater
scran
updated 4.8 years ago by
Aaron Lun
★ 28k • written 4.8 years ago by
Bogdan
▴ 670
3
votes
7
replies
1.9k
views
scRNA-seq : runPCA() and denoisePCA()
scater
scran
updated 4.8 years ago by
Aaron Lun
★ 28k • written 4.8 years ago by
Bogdan
▴ 670
1
vote
4
replies
1.5k
views
number of cell clusters in scRNA-seq
scran
scater
sc3
updated 4.8 years ago by
Aaron Lun
★ 28k • written 4.8 years ago by
Bogdan
▴ 670
0
votes
7
replies
2.1k
views
differential expression between clusters (in distinct "treatments") in scRNAseq
scater
limma
scde
scran
sc3
4.8 years ago
Bogdan
▴ 670
0
votes
1
reply
823
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
Aaron Lun
★ 28k • written 4.9 years ago by
Chris Conley
• 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
Aaron Lun
★ 28k • written 4.9 years ago by
Matt Mulé
• 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
Dayme
• 0 • written 5.0 years ago by
kushshah
▴ 10
50 results • Page
1 of 1
Recent ...
Replies
Comment: How to tell and visualize up/down regulation of pathways from clusterprofiler gs
by
Guangchuang Yu
★ 1.2k
an example is also presented in <https://pubmed.ncbi.nlm.nih.gov/34557778/>.
Comment: Trying to use enrichGO
by
Guido Hooiveld
★ 3.9k
Nothing would prevent you from using the `enrichGO` function (or any other function for over-representation analysis [ORA]) with only 14 ge…
Comment: Different Shrunk Log2FC according with reference
by
andrebolerbarros
▴ 20
Thanks @atpoint for your answer! The issue with that is then it severely hinders the possiblity of using `apeglm` shrinking approach, sinc…
Comment: featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_ge
by
ATpoint
★ 4.0k
The error that is relevant is `Aborted (core dumped)`. This line 2890 refers to the C source code that throws the error, it is not relevant…
Answer: Different Shrunk Log2FC according with reference
by
ATpoint
★ 4.0k
Please see: https://support.bioconductor.org/p/p134551/ I asked basically the same before. In short, reference level might have an influ…
Votes
C: SGSeq: moving toward diffex from SGSeq analysis
DEXSeq-Error in FUN(X[[i]], ...) : subscript out of bounds
Subset DEXSeqDataSet In DEXSeq
How to get all possible comparisons in DiffBind
Comment: get BM error
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