Showing : SCRAN • reset
0
votes
5
replies
243
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modelGeneVarByPoisson error selecting bandwidth automatically
scran
updated 7 days ago by ▴ 740 • written 10 days ago by ▴ 730
0
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0
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85
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Differential Gene Wrapper for Propotion of Detected
scran
11 days ago Dario Strbenac ★ 1.5k
0
votes
4
replies
259
views
Single Cell Experiment : Differential Expression "List of length 0" - Help!
DifferentialExpression scran scater SingleCellExperiment edgeR
23 days ago • updated 22 days ago vohara4 • 0
1
vote
2
replies
240
views
Reproducibility issue with scran together with lapply and BiocParallel
scran BiocParallel bluster
10 weeks ago ATpoint ★ 4.2k
2
votes
1
reply
337
views
Existence of Bioconductor versus Seurat Software Ecosystems Quantitative Comparison
scran bluster scater scuttle
updated 3 months ago by ★ 4.2k • written 3 months ago by ★ 1.5k
0
votes
3
replies
558
views
scran package: quickCluster and calculateSumFactors parallelization
BiocParallel scran
updated 5 months ago by ★ 4.2k • written 5 months ago by • 0
1
vote
2
replies
1.1k
views
ScRNAseq analysis scran :: quickcluster Error
scRNAseq quickcluster scRNA scran
7 months ago ruba-mahmoud • 0
0
votes
1
reply
450
views
Speeding up large scale scRNAseq analyses in R and improve memory
scran
updated 10 months ago by ★ 4.2k • written 10 months ago by • 0
0
votes
2
replies
958
views
runPCA in a SingleCellExperiment results ina colMeans error
scran SingleCellExperiment
12 months ago Lluís Revilla Sancho ▴ 730
2
votes
2
replies
6.8k
views
scran ScoreMarkers throws a warning
scoreMarkers scran
updated 12 months ago by ▴ 740 • written 12 months ago by ★ 1.5k
2
votes
3
replies
1.4k
views
P-value histogram of testLinearModel is not uniform
smart-seq2 scRNAseq scran
13 months ago • updated 12 months ago Lluís Revilla Sancho ▴ 730
0
votes
2
replies
835
views
Scaling and normalization by deconvolution of SMART-Seq 2 data
scran Clustering SingleCell Normalization
15 months ago Assa Yeroslaviz ★ 1.5k
1
vote
0
replies
751
views
Use scran's normalization by deconvolution for each individual sample or over all samples
scran Normalization scRNA BatchEffect
18 months ago r_grau ▴ 10
4
votes
3
replies
1.7k
views
SingleCellExperiment: Edit cluster IDs in colLabels
scran Clustering SingleCellExperiment annotate cluster
updated 23 months ago by 66k • written 23 months ago by ▴ 10
1
vote
1
reply
891
views
setting sizeFactors from scran :: caculateSumFactors.
scran DESeq2
updated 2.0 years ago by ★ 4.2k • written 2.0 years ago by • 0
3
votes
3
replies
1.2k
views
RFC: Inconsistent software license for scran & automated license checks
agpl license gpl scran
2.1 years ago • updated 23 months ago matthias-doering ▴ 40
2
votes
1
reply
1.2k
views
Getting error Creating SingleCellExperiment instances "all assays must have the same nrow and ncol"
SingleCellExperiment scran scater
updated 2.3 years ago by ▴ 780 • written 2.3 years ago by • 0
2
votes
2
replies
1.3k
views
scuttle:: librarySizeFactors returning non-finite values
normalizeCounts scran librarySizeFactors scuttle scRNAseq
2.4 years ago behr201 • 0
1
vote
2
replies
988
views
How to answer reviewers question of physical cell size influencing single cell results?
SingleCellExperiment scater ExperimentalDesign scran
2.4 years ago msn ▴ 10
2
votes
2
replies
1.1k
views
Block weights in scran::pairwiseTTests
scran
2.6 years ago Angelos Armen • 0
1
vote
1
reply
1.2k
views
scran computeSumFactors showing error
scran single cell
updated 2.6 years ago by ★ 28k • written 2.6 years ago by • 0
3
votes
3
replies
1.8k
views
Ensuring reproducibility in BiocParallel SingleCellExperiment workflows
scater SingleCellExperiment BiocParallel scuttle scran
2.7 years ago enricoferrero ▴ 660
2
votes
2
replies
1.9k
views
loading scran package
scran installation
3.4 years ago TJ • 0
5
votes
6
replies
1.8k
views
DE Analysis on Scran-Normalized Counts
DifferentialExpression scRNAseq scran
updated 3.4 years ago by ★ 28k • written 3.4 years ago by • 0
4
votes
5
replies
2.4k
views
scuttle::aggregateAcrossCells() crashes R on large SingleCellExperiment
scran SingleCellExperiment scuttle scater
updated 3.5 years ago by ★ 28k • written 3.5 years ago by ▴ 660
0
votes
0
replies
809
views
Creating a stable batch-corrected scRNA-Seq data with multiple datasets and multiple integrations
scater singlecell scran BatchEffect
3.7 years ago hamza_karakurt ▴ 60
1
vote
1
reply
1.0k
views
scran::computeSumFactors with single-cell ATAC-seq data
scran
updated 3.7 years ago by ★ 28k • written 3.7 years ago by • 0
1
vote
1
reply
1.9k
views
findMarkers() {scran} doesn't really find markers
findMarkers scran
updated 3.8 years ago by ★ 28k • written 3.8 years ago by • 0
2
votes
3
replies
1.9k
views
multiBatchNorm vs. calculateSumFactors on concatenated dataset
batchelor scran
updated 3.9 years ago by ★ 28k • written 3.9 years ago by • 0
5
votes
4
replies
6.3k
views
scRNA-seq pseudo-bulk differential expression analysis with pseudobulkDGE()
scran scater scuttle
updated 3.9 years ago by ★ 28k • written 3.9 years ago by ▴ 660
2
votes
6
replies
1.2k
views
Why is an averaged reference used in DESeq2 normalisation?
deseq2 scran batchelor
updated 4.0 years ago by ★ 28k • written 4.0 years ago by • 0
9
votes
4
replies
5.3k
views
Removing cell cycle genes in large data set integration
scran cyclone
updated 4.1 years ago by ★ 28k • written 4.1 years ago by ▴ 40
0
votes
4
replies
1.4k
views
scran's quickCluster error
scran
updated 4.1 years ago by ★ 28k • written 4.1 years ago by • 0
3
votes
1
reply
1.1k
views
Output lfc for Wilcox-based findMarkers
scran
updated 4.2 years ago by ★ 28k • written 4.2 years ago by ★ 4.2k
7
votes
5
replies
2.7k
views
Optimal cluster number identification using buildSNNgraph and igraph clusters
scran gap statistics single cell clustering
updated 4.2 years ago by ★ 28k • written 4.2 years ago by ▴ 40
7
votes
3
replies
5.3k
views
Downsample or not to downsample?
scrna-seq downsampleBatches scran
updated 4.2 years ago by ★ 28k • written 4.2 years ago by ▴ 40
0
votes
3
replies
1.0k
views
How can doubletCell() scores be converted to single/doublet annotation?
scran doublet
updated 4.3 years ago by ★ 28k • written 4.3 years ago by ▴ 10
2
votes
1
reply
2.1k
views
Batch Corrections (MNN) with TPM values
scRNA-Seq scater scran rna-seq MNN
updated 4.7 years ago by ★ 28k • written 4.7 years ago by ▴ 60
1
vote
1
reply
858
views
Stouffer's method weights in scran::pairwiseWilcox
scran
updated 4.8 years ago by ★ 28k • written 4.8 years ago by • 0
0
votes
5
replies
3.3k
views
Cannot install Bioconductor v3.9
scran cellassign bioconductor
updated 4.8 years ago by 25k • written 4.8 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 4.8 years ago by ★ 28k • written 4.8 years ago by ▴ 20
2
votes
1
reply
1.4k
views
scran: excluding genes with extremely high expression during normalization?
single-cell RNA-seq scran normalization
updated 4.9 years ago by ★ 28k • written 4.9 years ago by • 0
1
vote
3
replies
976
views
k argument in buildSNNGraph
scran
updated 4.9 years ago by ★ 28k • written 4.9 years ago by • 0
1
vote
5
replies
1.7k
views
Preprocessing in scran::doubletCells
scran simpleSingleCell
updated 4.9 years ago by ★ 28k • written 4.9 years ago by • 0
4
votes
4
replies
2.9k
views
using limma and edgeR for differential expression of Drop-seq/10xGenomics scRNA-seq data
limma edgeR simplesingleCell scran scater
updated 5.0 years ago by ★ 28k • written 5.0 years ago by ▴ 670
4
votes
4
replies
1.6k
views
scRNA-seq : Classification of cell cycle phase
scater scran
updated 5.0 years ago by ★ 28k • written 5.0 years ago by ▴ 670
3
votes
7
replies
2.1k
views
scRNA-seq : runPCA() and denoisePCA()
scater scran
updated 5.0 years ago by ★ 28k • written 5.0 years ago by ▴ 670
1
vote
4
replies
1.6k
views
number of cell clusters in scRNA-seq
scran scater sc3
updated 5.0 years ago by ★ 28k • written 5.0 years ago by ▴ 670
0
votes
7
replies
2.3k
views
differential expression between clusters (in distinct "treatments") in scRNAseq
scater limma scde scran sc3
5.0 years ago Bogdan ▴ 670
0
votes
1
reply
875
views
emptyDrops result is full NAs
scran dropletUtils scater scRNA-Seq
5.1 years ago hamza_karakurt ▴ 60
50 results • Page 1 of 1
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Comment: Mapping Between GenBank ID's and Uniprot by James W. MacDonald 66k
Also, ``` > result <- mapUniProt( from = "EMBL-GenBank-DDBJ_CDS", to = "UniProtKB", query = c("ACF95883.1") ) > result From…
Comment: Mapping Between GenBank ID's and Uniprot by James W. MacDonald 66k
Ugh, here's the link https://www.uniprot.org/id-mapping/uniprotkb/dd08aa16774d98ef087dc3bd708582012bba49e2/overview?fields=accession%2Cre…
Answer: Mapping Between GenBank ID's and Uniprot by James W. MacDonald 66k
The input should be 'EMBL-GenBank-DDBJ_CDS", as that is a GenBank ID.
Answer: XCMS2 of orbitrap data by Elodie • 0
Hi, I have the same question, I have acquired MS2 data with PRM analysis and inclusion lists of several ions. I have a list of product ion…
Answer: unreal negative log2fc values by ATpoint ★ 4.2k
I don't see why this is unrealistic. A logFC of -10 is about -1000 on normal scale. The rough difference between the mean of these counts p…
Votes
Answer: EPIC array hg38 annotation?
Answer: Why does DESeq2 give negative log2 fold change in treatment vs control for some
Comment: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: Ranking the GSEA Results
Error in `$<-.data.frame`(`*tmp*`, "dispersion", value = NA)
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