Showing : SCRAN • reset
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310
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modelGeneVar in MulticoreParam: wrong args for environment subassignment
BiocParallel scran BiocParall
3 months ago Lluís Revilla Sancho ▴ 760
0
votes
5
replies
614
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modelGeneVarByPoisson error selecting bandwidth automatically
scran
updated 6 months ago by ▴ 740 • written 6 months ago by ▴ 760
0
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0
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233
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Differential Gene Wrapper for Propotion of Detected
scran
6 months ago Dario Strbenac ★ 1.5k
0
votes
4
replies
633
views
Single Cell Experiment : Differential Expression "List of length 0" - Help!
DifferentialExpression scran scater SingleCellExperiment edgeR
6 months ago vohara4 • 0
1
vote
2
replies
445
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Reproducibility issue with scran together with lapply and BiocParallel
scran BiocParallel bluster
8 months ago ATpoint ★ 4.6k
2
votes
1
reply
570
views
Existence of Bioconductor versus Seurat Software Ecosystems Quantitative Comparison
scran bluster scater scuttle
updated 9 months ago by ★ 4.6k • written 9 months ago by ★ 1.5k
0
votes
3
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938
views
scran package: quickCluster and calculateSumFactors parallelization
BiocParallel scran
updated 11 months ago by ★ 4.6k • written 11 months ago by • 0
1
vote
2
replies
1.5k
views
ScRNAseq analysis scran :: quickcluster Error
scRNAseq quickcluster scRNA scran
12 months ago ruba-mahmoud • 0
0
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1
reply
702
views
Speeding up large scale scRNAseq analyses in R and improve memory
scran
updated 16 months ago by ★ 4.6k • written 16 months ago by • 0
0
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2
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1.3k
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runPCA in a SingleCellExperiment results ina colMeans error
scran SingleCellExperiment
18 months ago Lluís Revilla Sancho ▴ 760
2
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2
replies
9.9k
views
scran ScoreMarkers throws a warning
scoreMarkers scran
updated 18 months ago by ▴ 740 • written 18 months ago by ★ 1.5k
2
votes
3
replies
1.7k
views
P-value histogram of testLinearModel is not uniform
smart-seq2 scRNAseq scran
18 months ago Lluís Revilla Sancho ▴ 760
0
votes
2
replies
1.1k
views
Scaling and normalization by deconvolution of SMART-Seq 2 data
scran Clustering SingleCell Normalization
21 months ago Assa Yeroslaviz ★ 1.5k
1
vote
0
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944
views
Use scran's normalization by deconvolution for each individual sample or over all samples
scran Normalization scRNA BatchEffect
24 months ago r_grau ▴ 10
4
votes
3
replies
2.1k
views
SingleCellExperiment: Edit cluster IDs in colLabels
scran Clustering SingleCellExperiment annotate cluster
updated 2.4 years ago by 67k • written 2.4 years ago by ▴ 10
1
vote
1
reply
1.1k
views
setting sizeFactors from scran :: caculateSumFactors.
scran DESeq2
updated 2.5 years ago by ★ 4.6k • written 2.5 years ago by • 0
3
votes
3
replies
1.4k
views
RFC: Inconsistent software license for scran & automated license checks
agpl license gpl scran
2.5 years ago • updated 2.4 years ago matthias-doering ▴ 40
2
votes
1
reply
1.5k
views
Getting error Creating SingleCellExperiment instances "all assays must have the same nrow and ncol"
SingleCellExperiment scran scater
updated 2.7 years ago by ▴ 780 • written 2.7 years ago by • 0
2
votes
2
replies
1.6k
views
scuttle:: librarySizeFactors returning non-finite values
normalizeCounts scran librarySizeFactors scuttle scRNAseq
2.8 years ago behr201 • 0
1
vote
2
replies
1.2k
views
How to answer reviewers question of physical cell size influencing single cell results?
SingleCellExperiment scater ExperimentalDesign scran
2.9 years ago • updated 2.8 years ago msn ▴ 10
2
votes
2
replies
1.2k
views
Block weights in scran::pairwiseTTests
scran
3.1 years ago Angelos Armen • 0
1
vote
1
reply
1.4k
views
scran computeSumFactors showing error
scran single cell
updated 3.1 years ago by ★ 28k • written 3.1 years ago by • 0
3
votes
3
replies
2.0k
views
Ensuring reproducibility in BiocParallel SingleCellExperiment workflows
scater SingleCellExperiment BiocParallel scuttle scran
3.2 years ago enricoferrero ▴ 660
2
votes
2
replies
2.2k
views
loading scran package
scran installation
3.9 years ago TJ • 0
5
votes
6
replies
2.1k
views
DE Analysis on Scran-Normalized Counts
DifferentialExpression scRNAseq scran
updated 3.9 years ago by ★ 28k • written 3.9 years ago by • 0
4
votes
5
replies
2.9k
views
scuttle::aggregateAcrossCells() crashes R on large SingleCellExperiment
scran SingleCellExperiment scuttle scater
updated 4.0 years ago by ★ 28k • written 4.0 years ago by ▴ 660
0
votes
0
replies
977
views
Creating a stable batch-corrected scRNA-Seq data with multiple datasets and multiple integrations
scater singlecell scran BatchEffect
4.1 years ago hamza_karakurt ▴ 60
1
vote
1
reply
1.2k
views
scran::computeSumFactors with single-cell ATAC-seq data
scran
updated 4.2 years ago by ★ 28k • written 4.2 years ago by • 0
1
vote
1
reply
2.3k
views
findMarkers() {scran} doesn't really find markers
findMarkers scran
updated 4.3 years ago by ★ 28k • written 4.3 years ago by • 0
2
votes
3
replies
2.2k
views
multiBatchNorm vs. calculateSumFactors on concatenated dataset
batchelor scran
updated 4.4 years ago by ★ 28k • written 4.4 years ago by • 0
5
votes
4
replies
7.1k
views
scRNA-seq pseudo-bulk differential expression analysis with pseudobulkDGE()
scran scater scuttle
updated 4.4 years ago by ★ 28k • written 4.4 years ago by ▴ 660
2
votes
6
replies
1.4k
views
Why is an averaged reference used in DESeq2 normalisation?
deseq2 scran batchelor
updated 4.5 years ago by ★ 28k • written 4.5 years ago by • 0
9
votes
4
replies
5.9k
views
Removing cell cycle genes in large data set integration
scran cyclone
updated 4.6 years ago by ★ 28k • written 4.6 years ago by ▴ 40
0
votes
4
replies
1.6k
views
scran's quickCluster error
scran
updated 4.6 years ago by ★ 28k • written 4.6 years ago by • 0
3
votes
1
reply
1.3k
views
Output lfc for Wilcox-based findMarkers
scran
updated 4.6 years ago by ★ 28k • written 4.6 years ago by ★ 4.6k
7
votes
5
replies
3.3k
views
Optimal cluster number identification using buildSNNgraph and igraph clusters
scran gap statistics single cell clustering
updated 4.6 years ago by ★ 28k • written 4.6 years ago by ▴ 40
7
votes
3
replies
6.6k
views
Downsample or not to downsample?
scrna-seq downsampleBatches scran
updated 4.7 years ago by ★ 28k • written 4.7 years ago by ▴ 40
0
votes
3
replies
1.2k
views
How can doubletCell() scores be converted to single/doublet annotation?
scran doublet
updated 4.8 years ago by ★ 28k • written 4.8 years ago by ▴ 10
2
votes
1
reply
2.4k
views
Batch Corrections (MNN) with TPM values
scRNA-Seq scater scran rna-seq MNN
updated 5.2 years ago by ★ 28k • written 5.2 years ago by ▴ 60
1
vote
1
reply
972
views
Stouffer's method weights in scran::pairwiseWilcox
scran
updated 5.2 years ago by ★ 28k • written 5.2 years ago by • 0
0
votes
5
replies
3.4k
views
Cannot install Bioconductor v3.9
scran cellassign bioconductor
updated 5.2 years ago by 25k • written 5.2 years ago by ▴ 10
1
vote
2
replies
1.5k
views
Mitigating cell cycle effect in scRNA-seq using a blocking factor or design matrix
scran
updated 5.3 years ago by ★ 28k • written 5.3 years ago by ▴ 20
2
votes
1
reply
1.7k
views
scran: excluding genes with extremely high expression during normalization?
single-cell RNA-seq scran normalization
updated 5.4 years ago by ★ 28k • written 5.4 years ago by • 0
1
vote
3
replies
1.2k
views
k argument in buildSNNGraph
scran
updated 5.4 years ago by ★ 28k • written 5.4 years ago by • 0
1
vote
5
replies
1.9k
views
Preprocessing in scran::doubletCells
scran simpleSingleCell
updated 5.4 years ago by ★ 28k • written 5.4 years ago by • 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 5.4 years ago by ★ 28k • written 5.4 years ago by ▴ 670
4
votes
4
replies
1.9k
views
scRNA-seq : Classification of cell cycle phase
scater scran
updated 5.5 years ago by ★ 28k • written 5.5 years ago by ▴ 670
3
votes
7
replies
2.4k
views
scRNA-seq : runPCA() and denoisePCA()
scater scran
updated 5.5 years ago by ★ 28k • written 5.5 years ago by ▴ 670
1
vote
4
replies
1.8k
views
number of cell clusters in scRNA-seq
scran scater sc3
updated 5.5 years ago by ★ 28k • written 5.5 years ago by ▴ 670
0
votes
7
replies
2.6k
views
differential expression between clusters (in distinct "treatments") in scRNAseq
scater limma scde scran sc3
5.5 years ago Bogdan ▴ 670
50 results • Page 1 of 1
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Comment: EuroBioC2024 abstract submission is open! by Alan Downey • 0
EuroBioC2024 has opened its abstract submission process, presenting an exciting opportunity for researchers to contribute to groundbreaking…
Comment: ChAMP.DMR error - Error in makeGenomicRatioSetFromMatrix by O'Brien • 0
Consult the ChAMP.DMR documentation for more information on supported array types and expected data formats: https://bioconductor.org/packa…
Answer: combining raw counts and estimated counts by O'Brien • 0
It is possible to combine raw counts from TCGA and estimated counts from GEO datasets (Kalisto pseudoalignment) while mitigating batch effe…
Comment: Packages don't update, but no error or warning is thrown by neighsanlo • 0
This is useful information.
Comment: Perform gene set enrichment analysis using fgsea on two conditions that don't ha by freemanmclaughlin9969289 • 0
Tools such as Pathway Analysis with Deweighting of Overlapping Genes ([block blast][1]) or Gene Set Enrichment Analysis for Single Cell RNA…
Votes
A: RNA-seq Normalisation - normalise all samples in experiment or only the ones use
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings?
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio
C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
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