Showing : scater • reset
0
votes
7
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1.7k
views
error when installing beachmat
beachmat scater
updated 6.3 years ago by ▴ 10 • written 6.4 years ago by • 0
4
votes
3
replies
1.8k
views
using SC3 and scater for bulk-RNAseq
sc3 scater scRNAseq
updated 7.1 years ago by ▴ 150 • written 7.1 years ago by ★ 1.5k
4
votes
15
replies
3.9k
views
Warning: negative size factors
size factor negative scran singlecellexperiment scater
updated 6.2 years ago by ★ 28k • written 6.2 years ago by • 0
1
vote
8
replies
2.3k
views
SC3_estimate_k formatting error?
sc3 scater
updated 6.4 years ago by ▴ 150 • written 6.4 years ago by ▴ 10
4
votes
7
replies
6.3k
views
BiocParallel/scater warning after move to R 3.4.0
biocparallel scater
updated 6.8 years ago by ▴ 40 • written 7.0 years ago by • 0
1
vote
7
replies
6.4k
views
scater runUMAP fails with error "function 'as_cholmod_sparse' not provided by package 'Matrix'"
runUMAP scater Matrix
updated 7 weeks ago by 16k • written 5 months ago by ▴ 10
3
votes
3
replies
335
views
plotUMAP Gene Set Faceted
scater
updated 12 weeks ago by ▴ 160 • written 12 weeks ago by ★ 1.5k
0
votes
4
replies
4.8k
views
Change point size and remove outline in scater's plotPCA
scater rnaseq single-cell
updated 6.0 years ago by • 0 • written 7.0 years ago by ▴ 70
1
vote
2
replies
1.4k
views
plotRLE not working in scater
software error scater plotRLE
7.0 years ago ian.oslo • 0
0
votes
2
replies
3.9k
views
problems when working with SingleCellExperiment object in scater
scater SingleCellExperiment
updated 6.6 years ago by ▴ 90 • written 6.6 years ago by ▴ 10
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
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 ★ 28k • written 3.7 years ago by ▴ 660
0
votes
16
replies
2.4k
views
How does newSCESet calculate expression matrix
scater
updated 6.9 years ago by ▴ 90 • written 6.9 years ago by • 0
5
votes
2
replies
5.9k
views
Raw count data for SC3 and SingleCellExperiment set problem
singlecellexperiment sc3 scater
updated 6.4 years ago by ▴ 150 • written 6.4 years ago by ▴ 10
0
votes
1
reply
667
views
calculateQCmetrics doesn't accept `numeric` `feature_controls` in scater 1.6.2
scater
updated 6.2 years ago by ★ 28k • written 6.2 years ago by ▴ 270
1
vote
2
replies
1.8k
views
SingleCellExperiment object cannot be used by Scater package?
scater singlecellexperiment simplesinglecell
updated 6.2 years ago by ★ 28k • written 6.2 years ago by • 0
1
vote
2
replies
871
views
Inserting "Biotype" into scater SCE objects
scater sce biotype R
updated 6.1 years ago by ★ 28k • written 6.1 years ago by • 0
5
votes
2
replies
1.6k
views
Accessing normalized counts
splatter singlecellexperiment scater
6.0 years ago luke.zappia ▴ 50
0
votes
1
reply
1.4k
views
Converting scater-normalized UMI data to Monocle CellDataSet
scater scran umi monocle
updated 6.0 years ago by ★ 28k • written 6.0 years ago by • 0
3
votes
3
replies
7.1k
views
rowSums() rowMeans() don't work on sparse matrix "dgCMatrix"
scater scran single-cell
updated 5.8 years ago by 25k • written 6.0 years ago by ▴ 10
0
votes
1
reply
987
views
RNAseq scater error in plotQC()
scater plotQC scRNAseq
updated 5.7 years ago by ★ 28k • written 5.7 years ago by ▴ 90
0
votes
6
replies
1.6k
views
Scater package PlotExpression
scater
5.7 years ago mayank.geit89 • 0
1
vote
5
replies
2.5k
views
newSCESet and SingleCellExperiment basic differences and TMM Normalization
singlecellexperiment single-cell rnaseq seurat scater
5.5 years ago hamza_karakurt ▴ 50
2
votes
6
replies
1.7k
views
Change the number of clusters with scater
scater scran scrnaseq clustering
updated 5.4 years ago by ★ 28k • written 5.4 years ago by ▴ 20
0
votes
2
replies
2.8k
views
Problem installing scater
scater R biocmanager bioconductor
updated 5.4 years ago by ★ 28k • written 5.4 years ago by • 0
3
votes
5
replies
1.2k
views
plotPlatePosition and plate_position
scater R singlecellexperiment
updated 5.4 years ago by ★ 28k • written 5.4 years ago by • 0
2
votes
1
reply
1.2k
views
Top variable features used by 'runPCA' in scater
scater pca features
updated 5.4 years ago by ★ 28k • written 5.4 years ago by • 0
1
vote
3
replies
1.1k
views
How to resolve these trendVar() warnings and errors
scater scran singlecellexperiment
updated 5.4 years ago by ★ 28k • written 5.4 years ago by ▴ 20
0
votes
1
reply
2.5k
views
Deconvolution Method in Seurat and convert from SingleCellExperiment
scater seurat singlecellexperiment rnaseq
updated 5.4 years ago by 50k • written 5.4 years ago by ▴ 50
3
votes
3
replies
2.7k
views
Gene ID to Gene Name/Symbol in loom files
Scater LoomR SCopeloomR
updated 5.3 years ago by ★ 28k • written 5.3 years ago by ▴ 20
7
votes
5
replies
1.6k
views
scran: Are the log counts expression comparable among different genes within a sample/cell ?
scran scater
updated 5.3 years ago by ★ 28k • written 5.3 years ago by ▴ 30
1
vote
2
replies
1.1k
views
scran/scater Normalized matrix
scran scater normalized counts
updated 5.3 years ago by ★ 28k • written 5.3 years ago by ▴ 90
2
votes
2
replies
1.4k
views
scater error: invalid rownames length
scater
updated 5.2 years ago by ★ 28k • written 5.2 years ago by • 0
2
votes
5
replies
3.8k
views
Adding labels on clusters in a t-SNE plot and changing colors
scran scater Rtsne ggplot2 scRNA-Seq
updated 20 months ago by ▴ 60 • written 5.2 years ago by ▴ 50
2
votes
5
replies
1.4k
views
Modularity values of clusters and Differential Expression in scRNA-Seq
scater scran igraph scRNA-Seq rots
updated 5.2 years ago by ★ 28k • written 5.2 years ago by ▴ 50
1
vote
2
replies
1.4k
views
Dunn Index for Clusters from scRNA-Seq
scRNA-Seq clustering scater scran dunn index
updated 5.1 years ago by ★ 28k • written 5.1 years ago by ▴ 50
7
votes
3
replies
3.2k
views
Log2(RPKM) counts in Bioconductor
rpkm scater calcaverage R expression
updated 5.1 years ago by ★ 28k • written 5.1 years ago by ▴ 10
4
votes
5
replies
1.7k
views
Using SC3 with batch corrected MNN values
SC3 Scater Scran scRNA-Seq Batch Correction
updated 5.1 years ago by ▴ 150 • written 5.1 years ago by ▴ 50
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 5.0 years ago by ▴ 10
2
votes
3
replies
1.6k
views
Unable to change point size in plotExpression()
scater plotexpression singlecellexperiment plotting
updated 5.0 years ago by ★ 28k • written 5.0 years ago by ▴ 10
8
votes
4
replies
2.2k
views
Usage of doubletCells() function before or after the batch correction?
scater scran scRNA-Seq doubletCells
updated 5.0 years ago by ★ 28k • written 5.0 years ago by ▴ 50
2
votes
1
reply
1.2k
views
scater::runPCA() errors on DelayedMatrix (DelayedArray:::.check_Ops_vector_arg_length)
scater BiocSingular DelayedArray
updated 4.9 years ago by ★ 28k • written 4.9 years ago by ▴ 350
0
votes
7
replies
2.1k
views
differential expression between clusters (in distinct "treatments") in scRNAseq
scater limma scde scran sc3
4.9 years ago • updated 4.8 years ago 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 ★ 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
1.9k
views
scRNA-seq : runPCA() and denoisePCA()
scater scran
updated 4.8 years ago by ★ 28k • written 4.8 years ago by ▴ 670
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
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 ★ 28k • written 4.5 years ago by ▴ 50
4
votes
1
reply
1.2k
views
could not find function "plotQC" in scater package
scater
updated 4.5 years ago by ★ 28k • written 4.5 years ago by ▴ 20
0
votes
1
reply
993
views
scater cbind for singlecellexperiment objects problem
scater SingleCellExperiment
updated 4.4 years ago by ★ 28k • written 4.4 years ago by • 0
50 results • Page 1 of 1
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Comment: How to retrieve gene ontology GO class from gene list? by bandconductor • 0
Thanks, this is potentially a much faster way than parsing BiomRt. However, it is only returning one GO term right now (biomaRt returns a f…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
Both `RUVseq` and `sva` are meant to be used to remove technical variability. The problem is the identification of variability that is tech…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0
Hello James, Thank you very much for your answer and taking the time to read my post. I understand your remark, but isn't the approach o…
Comment: PCA plot suggestions by JKim • 0
cross post: https://www.biostars.org/p/9593486/
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
You cannot correct for technical variability due to batch if samples are nested in batch. The technical and biological differences are comp…
Votes
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
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