Showing : Scran • reset
9
votes
4
replies
3.1k
views
Removing cell cycle genes in large data set integration
scran cyclone
updated 2.7 years ago by ★ 28k • written 2.7 years ago by ▴ 30
8
votes
4
replies
1.2k
views
Usage of doubletCells() function before or after the batch correction?
scater scran scRNA-Seq doubletCells
updated 3.8 years ago by ★ 28k • written 3.8 years ago by ▴ 50
7
votes
5
replies
932
views
scran: Are the log counts expression comparable among different genes within a sample/cell ?
scran scater
updated 4.1 years ago by ★ 28k • written 4.1 years ago by ▴ 30
7
votes
5
replies
1.3k
views
Optimal cluster number identification using buildSNNgraph and igraph clusters
scran gap statistics single cell clustering
updated 2.7 years ago by ★ 28k • written 2.7 years ago by ▴ 30
6
votes
12
replies
2.6k
views
Merging RNAseq Datasets of Different Depths
singlecellexperiment scran sequencing depth batch effect scrnaseq
updated 4.6 years ago by ★ 28k • written 4.6 years ago by • 0
6
votes
1
reply
2.5k
views
Downstream analysis after using mnnCorrect()
scran mnncorrect
updated 5.0 years ago by ★ 28k • written 5.0 years ago by ▴ 210
5
votes
6
replies
884
views
DE Analysis on Scran-Normalized Counts
DifferentialExpression scRNAseq scran
updated 23 months ago by ★ 28k • written 23 months ago by • 0
4
votes
4
replies
1.0k
views
Some questions for remove batch effect by using mnnCorrect
batch effect single cells mnnCorrect scran
updated 3.7 years ago by ★ 28k • written 3.7 years ago by ▴ 20
4
votes
0
replies
2.8k
views
Tutorial: Workflow for low-level analysis of single-cell RNA-seq data
scran scater single cell Tutorial
6.4 years ago Aaron Lun ★ 28k
4
votes
4
replies
1.9k
views
using limma and edgeR for differential expression of Drop-seq/10xGenomics scRNA-seq data
limma edgeR simplesingleCell scran scater
updated 3.5 years ago by ★ 28k • written 3.5 years ago by ▴ 660
4
votes
3
replies
2.1k
views
Downsample or not to downsample?
scrna-seq downsampleBatches scran
updated 2.7 years ago by ★ 28k • written 2.7 years ago by ▴ 30
4
votes
5
replies
1.1k
views
scuttle::aggregateAcrossCells() crashes R on large SingleCellExperiment
scran SingleCellExperiment scuttle scater
updated 2.0 years ago by ★ 28k • written 2.1 years ago by ▴ 650
4
votes
4
replies
877
views
scRNA-seq : Classification of cell cycle phase
scater scran
updated 3.6 years ago by ★ 28k • written 3.6 years ago by ▴ 660
4
votes
5
replies
1.1k
views
Using SC3 with batch corrected MNN values
SC3 Scater Scran scRNA-Seq Batch Correction
updated 3.8 years ago by ▴ 150 • written 3.8 years ago by ▴ 50
4
votes
3
replies
343
views
SingleCellExperiment: Edit cluster IDs in colLabels
scran Clustering SingleCellExperiment annotate cluster
updated 5 months ago by 62k • written 5 months ago by • 0
4
votes
15
replies
2.8k
views
Warning: negative size factors
size factor negative scran singlecellexperiment scater
updated 4.9 years ago by ★ 28k • written 4.9 years ago by • 0
3
votes
7
replies
1.1k
views
scRNA-seq : runPCA() and denoisePCA()
scater scran
updated 3.6 years ago by ★ 28k • written 3.6 years ago by ▴ 660
3
votes
3
replies
797
views
Ensuring reproducibility in BiocParallel SingleCellExperiment workflows
scater SingleCellExperiment BiocParallel scuttle scran
15 months ago enricoferrero ▴ 650
3
votes
7
replies
1.9k
views
Error: could not find function "findMarkers"
scran
5.4 years ago ravi_patel_4 ▴ 10
3
votes
4
replies
3.2k
views
scRNA-seq pseudo-bulk differential expression analysis with pseudobulkDGE()
scran scater scuttle
updated 2.5 years ago by ★ 28k • written 2.5 years ago by ▴ 650
3
votes
1
reply
605
views
Output lfc for Wilcox-based findMarkers
scran
updated 2.7 years ago by ★ 28k • written 2.7 years ago by ★ 2.0k
3
votes
3
replies
1.9k
views
is SCEset fully abandoned in scran?
scran scater splatter normalization
updated 5.3 years ago by ▴ 90 • written 5.3 years ago by • 0
3
votes
5
replies
1.7k
views
Using Scran normalization with in edgeR
edger estimatedisp scran sizefactors
updated 6.5 years ago by ★ 28k • written 6.5 years ago by ▴ 10
3
votes
3
replies
5.8k
views
rowSums() rowMeans() don't work on sparse matrix "dgCMatrix"
scater scran single-cell
updated 4.6 years ago by 25k • written 4.7 years ago by ▴ 10
3
votes
2
replies
912
views
single cell data: adding random effects for subject with multilevel experiment design
SingleCellExperiment scran limma simpleSingleCell
updated 3.6 years ago by ★ 28k • written 3.6 years ago by • 0
3
votes
3
replies
449
views
RFC: Inconsistent software license for scran & automated license checks
agpl license gpl scran
7 months ago • updated 5 months ago matthias-doering ▴ 30
3
votes
4
replies
1.5k
views
Scran normalization error with computeSumFactors
scran scater
updated 6.0 years ago by ★ 28k • written 6.0 years ago by ▴ 20
3
votes
9
replies
3.0k
views
Why does scran's computeSumFactors produce different size factors for cells with the exact same gene counts?
scran scater drop-seq scrnaseq
updated 5.8 years ago by ★ 28k • written 5.8 years ago by ▴ 10
3
votes
2
replies
688
views
Is logFC a log2 fold change or some other base in scran::findMarkers
scran
updated 3.6 years ago by ★ 28k • written 3.6 years ago by • 0
3
votes
1
reply
765
views
Normalizing vs RNA content in scRNAseq data
monocle scran
updated 5.5 years ago by ★ 28k • written 5.5 years ago by ▴ 40
2
votes
2
replies
1.2k
views
[MnnCorrect] Remove batch effects but keep condition effects
single-cell scran mnncorrect rnaseq
updated 4.2 years ago by ★ 28k • written 4.2 years ago by ▴ 10
2
votes
2
replies
784
views
scran: trendVar() / lm.fit() fails in single-cell RNAseq experiment
scran
updated 5.1 years ago by ★ 28k • written 5.1 years ago by • 0
2
votes
3
replies
2.5k
views
scran: question on minimum cluster size for computeSumFactors()
scran single cell normalization clustering
6.7 years ago aatsmith • 0
2
votes
3
replies
1.0k
views
multiBatchNorm vs. calculateSumFactors on concatenated dataset
batchelor scran
updated 2.4 years ago by ★ 28k • written 2.4 years ago by • 0
2
votes
2
replies
1.3k
views
Error in installation of scran
S4Vectors IRanges XVector GenomicRanges scran
updated 4.0 years ago by ★ 28k • written 4.0 years ago by • 0
2
votes
5
replies
2.4k
views
Adding labels on clusters in a t-SNE plot and changing colors
scran scater Rtsne ggplot2 scRNA-Seq
updated 5 months ago by ▴ 60 • written 3.9 years ago by ▴ 50
2
votes
5
replies
835
views
Modularity values of clusters and Differential Expression in scRNA-Seq
scater scran igraph scRNA-Seq rots
updated 3.9 years ago by ★ 28k • written 3.9 years ago by ▴ 50
2
votes
3
replies
948
views
Scran functions not found
single-cell scran
updated 5.4 years ago by ★ 28k • written 5.4 years ago by • 0
2
votes
2
replies
1.0k
views
loading scran package
scran installation
23 months ago TJ • 0
2
votes
2
replies
621
views
normalization for infected homogenious cell populations
normalization single cell scran
updated 3.9 years ago by ★ 28k • written 3.9 years ago by • 0
2
votes
6
replies
633
views
Why is an averaged reference used in DESeq2 normalisation?
deseq2 scran batchelor
updated 2.6 years ago by ★ 28k • written 2.6 years ago by • 0
2
votes
4
replies
2.4k
views
ERROR - Size factors should be positive real numbers (using normalize() function)
scater scran singlecellexperiment normalize qc
updated 10 months ago by • 0 • written 3.8 years ago by ▴ 10
2
votes
2
replies
458
views
scuttle:: librarySizeFactors returning non-finite values
normalizeCounts scran librarySizeFactors scuttle scRNAseq
11 months ago behr201 • 0
2
votes
1
reply
1.1k
views
Batch Corrections (MNN) with TPM values
scRNA-Seq scater scran rna-seq MNN
updated 3.3 years ago by ★ 28k • written 3.3 years ago by ▴ 50
2
votes
2
replies
420
views
Block weights in scran::pairwiseTTests
scran
14 months ago Angelos Armen • 0
2
votes
1
reply
377
views
Getting error Creating SingleCellExperiment instances "all assays must have the same nrow and ncol"
SingleCellExperiment scran scater
updated 9 months ago by ▴ 530 • written 9 months ago by • 0
2
votes
5
replies
4.1k
views
RNA-Seq Batch correction negative values
rna-seq batch-effect combat scran sva
updated 5.3 years ago by ★ 28k • written 5.3 years ago by ▴ 20
2
votes
1
reply
611
views
scran: excluding genes with extremely high expression during normalization?
single-cell RNA-seq scran normalization
updated 3.4 years ago by ★ 28k • written 3.4 years ago by • 0
2
votes
6
replies
990
views
Change the number of clusters with scater
scater scran scrnaseq clustering
updated 4.2 years ago by ★ 28k • written 4.2 years ago by ▴ 20
1
vote
5
replies
1.0k
views
Preprocessing in scran::doubletCells
scran simpleSingleCell
updated 3.5 years ago by ★ 28k • written 3.5 years ago by • 0
50 results • Page 1 of 1
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Replies
Comment: Empty ChipQC Report by Okan • 0
Hi, I have the same issue. Have you found any solution or any reason why this is happening?
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper by Gordon Smyth 47k
Am I understanding correctly that you have 24 RNA-seq libraries in total, 6 from the pooled samples and 18 from regular samples with biolog…
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper by k.roelfs • 0
I'm sorry, I know it is kinda confusing... We have 6 pools in total: Phenotype A: T1a, T2, T1b, T1c Phenotype B: T1, T2 Each pool consist…
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper by Gordon Smyth 47k
Sorry, I don't understand your experiment. You are reading the edgeR Section on on what to do without replicates, but your experiment appe…
Answer: MA plot by Nathalie • 0
Thank you very much for your help and comments. There is errors in my file. BaseMean is BaseMeanLog2. I don't know how insert a file.
Votes
Volcano Plot in R
Answer: Replicating iDEP parameters in DESeq2; two conditions and an interaction term.
Answer: Replicating iDEP parameters in DESeq2; two conditions and an interaction term.
Answer: MA plot
Answer: MA plot
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