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Scran
•
reset
9
votes
4
replies
4.9k
views
Removing cell cycle genes in large data set integration
scran
cyclone
updated 3.8 years ago by
Aaron Lun
★ 28k • written 3.8 years ago by
p.joshi
▴ 40
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
Aaron Lun
★ 28k • written 5.0 years ago by
hamza_karakurt
▴ 50
7
votes
3
replies
4.6k
views
Downsample or not to downsample?
scrna-seq
downsampleBatches
scran
updated 3.9 years ago by
Aaron Lun
★ 28k • written 3.9 years ago by
p.joshi
▴ 40
7
votes
5
replies
1.5k
views
scran: Are the log counts expression comparable among different genes within a sample/cell ?
scran
scater
updated 5.2 years ago by
Aaron Lun
★ 28k • written 5.2 years ago by
heyao
▴ 30
7
votes
5
replies
2.4k
views
Optimal cluster number identification using buildSNNgraph and igraph clusters
scran
gap statistics
single cell clustering
updated 3.9 years ago by
Aaron Lun
★ 28k • written 3.9 years ago by
p.joshi
▴ 40
6
votes
1
reply
3.0k
views
Downstream analysis after using mnnCorrect()
scran
mnncorrect
updated 6.1 years ago by
Aaron Lun
★ 28k • written 6.1 years ago by
Dave Tang
▴ 210
6
votes
12
replies
3.5k
views
Merging RNAseq Datasets of Different Depths
singlecellexperiment
scran
sequencing depth
batch effect
scrnaseq
updated 5.8 years ago by
Aaron Lun
★ 28k • written 5.8 years ago by
liam.salleh
• 0
5
votes
4
replies
5.9k
views
scRNA-seq pseudo-bulk differential expression analysis with pseudobulkDGE()
scran
scater
scuttle
updated 3.6 years ago by
Aaron Lun
★ 28k • written 3.6 years ago by
enricoferrero
▴ 660
5
votes
6
replies
1.5k
views
DE Analysis on Scran-Normalized Counts
DifferentialExpression
scRNAseq
scran
updated 3.1 years ago by
Aaron Lun
★ 28k • written 3.1 years ago by
LUCIA
• 0
4
votes
4
replies
1.7k
views
Some questions for remove batch effect by using mnnCorrect
batch effect
single cells
mnnCorrect
scran
updated 4.9 years ago by
Aaron Lun
★ 28k • written 4.9 years ago by
xingxd16
▴ 20
4
votes
15
replies
3.8k
views
Warning: negative size factors
size factor
negative
scran
singlecellexperiment
scater
updated 6.1 years ago by
Aaron Lun
★ 28k • written 6.1 years ago by
Marina V.V.
• 0
4
votes
3
replies
1.4k
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
4
votes
5
replies
1.7k
views
Using SC3 with batch corrected MNN values
SC3
Scater
Scran
scRNA-Seq
Batch Correction
updated 5.0 years ago by
Vladimir Kiselev
▴ 150 • written 5.0 years ago by
hamza_karakurt
▴ 50
4
votes
4
replies
2.7k
views
using limma and edgeR for differential expression of Drop-seq/10xGenomics scRNA-seq data
limma
edgeR
simplesingleCell
scran
scater
updated 4.7 years ago by
Aaron Lun
★ 28k • written 4.7 years ago by
Bogdan
▴ 670
4
votes
5
replies
2.2k
views
scuttle::aggregateAcrossCells() crashes R on large SingleCellExperiment
scran
SingleCellExperiment
scuttle
scater
updated 3.2 years ago by
Aaron Lun
★ 28k • written 3.2 years ago by
enricoferrero
▴ 660
4
votes
0
replies
3.4k
views
Tutorial:
Workflow for low-level analysis of single-cell RNA-seq data
scran
scater
single cell
Tutorial
7.6 years ago
Aaron Lun
★ 28k
4
votes
2
replies
1.5k
views
single cell data: adding random effects for subject with multilevel experiment design
SingleCellExperiment
scran
limma
simpleSingleCell
updated 4.8 years ago by
Aaron Lun
★ 28k • written 4.8 years ago by
Matt Mulé
• 0
4
votes
4
replies
1.4k
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
2.7k
views
Error: could not find function "findMarkers"
scran
6.6 years ago
ravi_patel_4
▴ 10
3
votes
1
reply
1.0k
views
Output lfc for Wilcox-based findMarkers
scran
updated 3.9 years ago by
Aaron Lun
★ 28k • written 3.9 years ago by
ATpoint
★ 4.0k
3
votes
3
replies
2.3k
views
is SCEset fully abandoned in scran?
scran
scater
splatter
normalization
updated 6.4 years ago by
davis
▴ 90 • written 6.4 years ago by
wt215
• 0
3
votes
3
replies
1.6k
views
Ensuring reproducibility in BiocParallel SingleCellExperiment workflows
scater
SingleCellExperiment
BiocParallel
scuttle
scran
2.4 years ago
enricoferrero
▴ 660
3
votes
5
replies
2.1k
views
Using Scran normalization with in edgeR
edger
estimatedisp
scran
sizefactors
updated 7.7 years ago by
Aaron Lun
★ 28k • written 7.7 years ago by
mnaymik
▴ 10
3
votes
3
replies
7.0k
views
rowSums() rowMeans() don't work on sparse matrix "dgCMatrix"
scater
scran
single-cell
updated 5.8 years ago by
Martin Morgan
25k • written 5.9 years ago by
MengChun Tseng
▴ 10
3
votes
4
replies
1.8k
views
Scran normalization error with computeSumFactors
scran
scater
updated 7.2 years ago by
Aaron Lun
★ 28k • written 7.2 years ago by
hrishi27n
▴ 20
3
votes
9
replies
4.0k
views
Why does scran's computeSumFactors produce different size factors for cells with the exact same gene counts?
scran
scater
drop-seq
scrnaseq
updated 7.0 years ago by
Aaron Lun
★ 28k • written 7.0 years ago by
Friederike
▴ 10
3
votes
2
replies
1.1k
views
Is logFC a log2 fold change or some other base in scran::findMarkers
scran
updated 4.8 years ago by
Aaron Lun
★ 28k • written 4.8 years ago by
Chris Conley
• 0
3
votes
3
replies
1.1k
views
RFC: Inconsistent software license for scran & automated license checks
agpl
license
gpl
scran
21 months ago • updated 19 months ago
matthias-doering
▴ 40
3
votes
1
reply
1.1k
views
Normalizing vs RNA content in scRNAseq data
monocle
scran
updated 6.7 years ago by
Aaron Lun
★ 28k • written 6.7 years ago by
ankur.chakravarthy.10
▴ 40
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
2
votes
2
replies
1.7k
views
[MnnCorrect] Remove batch effects but keep condition effects
single-cell
scran
mnncorrect
rnaseq
updated 5.3 years ago by
Aaron Lun
★ 28k • written 5.3 years ago by
John Reid
▴ 10
2
votes
3
replies
1.7k
views
multiBatchNorm vs. calculateSumFactors on concatenated dataset
batchelor
scran
updated 3.6 years ago by
Aaron Lun
★ 28k • written 3.6 years ago by
Angelos Armen
• 0
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
2
votes
1
reply
1.0k
views
Getting error Creating SingleCellExperiment instances "all assays must have the same nrow and ncol"
SingleCellExperiment
scran
scater
updated 24 months ago by
Basti
▴ 750 • written 24 months ago by
Lucky
• 0
2
votes
2
replies
2.0k
views
Error in installation of scran
S4Vectors
IRanges
XVector
GenomicRanges
scran
updated 5.2 years ago by
Aaron Lun
★ 28k • written 5.2 years ago by
Momo
• 0
2
votes
5
replies
3.7k
views
Adding labels on clusters in a t-SNE plot and changing colors
scran
scater
Rtsne
ggplot2
scRNA-Seq
updated 19 months ago by
jamie.gearing
▴ 60 • written 5.1 years ago by
hamza_karakurt
▴ 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 5.1 years ago by
Aaron Lun
★ 28k • written 5.1 years ago by
hamza_karakurt
▴ 50
2
votes
1
reply
1.2k
views
scran: excluding genes with extremely high expression during normalization?
single-cell RNA-seq
scran
normalization
updated 4.6 years ago by
Aaron Lun
★ 28k • written 4.6 years ago by
daniel.borshagovski
• 0
2
votes
2
replies
1.2k
views
scuttle:: librarySizeFactors returning non-finite values
normalizeCounts
scran
librarySizeFactors
scuttle
scRNAseq
2.1 years ago
behr201
• 0
2
votes
2
replies
991
views
normalization for infected homogenious cell populations
normalization
single cell
scran
updated 5.0 years ago by
Aaron Lun
★ 28k • written 5.0 years ago by
jcvera
• 0
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
2
votes
4
replies
3.5k
views
ERROR - Size factors should be positive real numbers (using normalize() function)
scater
scran
singlecellexperiment
normalize
qc
updated 2.0 years ago by
Dayme
• 0 • written 5.0 years ago by
kushshah
▴ 10
2
votes
5
replies
5.7k
views
RNA-Seq Batch correction negative values
rna-seq
batch-effect
combat
scran
sva
updated 6.5 years ago by
Aaron Lun
★ 28k • written 6.5 years ago by
rmf
▴ 20
2
votes
2
replies
1.7k
views
loading scran package
scran
installation
3.1 years ago
TJ
• 0
2
votes
3
replies
1.2k
views
Scran functions not found
single-cell
scran
updated 6.6 years ago by
Aaron Lun
★ 28k • written 6.6 years ago by
alva.james
• 0
2
votes
2
replies
961
views
Block weights in scran::pairwiseTTests
scran
2.4 years ago • updated 2.3 years ago
Angelos Armen
• 0
2
votes
3
replies
1.2k
views
P-value histogram of testLinearModel is not uniform
smart-seq2
scRNAseq
scran
9 months ago
Lluís Revilla Sancho
▴ 730
2
votes
2
replies
994
views
scran: trendVar() / lm.fit() fails in single-cell RNAseq experiment
scran
updated 6.2 years ago by
Aaron Lun
★ 28k • written 6.2 years ago by
roman.hillje
• 0
2
votes
2
replies
4.7k
views
scran ScoreMarkers throws a warning
scoreMarkers
scran
updated 9 months ago by
Peter Hickey
▴ 670 • written 9 months ago by
Assa Yeroslaviz
★ 1.5k
2
votes
3
replies
3.1k
views
scran: question on minimum cluster size for computeSumFactors()
scran
single cell
normalization
clustering
7.9 years ago
aatsmith
• 0
50 results • Page
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Answer: New genes that did not exist in dds object suddenly showed up after degPatterns
by
Michael Love
41k
May be documented by the software you are using? https://github.com/lpantano/DEGreport
Answer: Doing comparison of RNA-seq data using Deseq2
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Michael Love
41k
Take a look at our workflow, this starts from a beginner's level. You could export from Excel using CSV or TSV, then read into R. htt…
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This support site is meant to help people with questions about Bioconductor packages (WGCNA is not a Bioconductor package). You might try o…
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Yes that is correct
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It is the minimum group size rather than the total number of samples that is relevant. `min.prop` is more a biological parameter rather th…
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Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
DESeq2 normalization vs VST vs rlog
Answer: DESeq2 "Contrast" option
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