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SCRAN
•
reset
9
votes
4
replies
5.0k
views
Removing cell cycle genes in large data set integration
scran
cyclone
updated 3.9 years ago by
Aaron Lun
★ 28k • written 3.9 years ago by
p.joshi
▴ 40
8
votes
4
replies
2.3k
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
4.8k
views
Downsample or not to downsample?
scrna-seq
downsampleBatches
scran
updated 4.0 years ago by
Aaron Lun
★ 28k • written 4.0 years ago by
p.joshi
▴ 40
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
Aaron Lun
★ 28k • written 5.3 years ago by
heyao
▴ 30
7
votes
5
replies
2.5k
views
Optimal cluster number identification using buildSNNgraph and igraph clusters
scran
gap statistics
single cell clustering
updated 4.0 years ago by
Aaron Lun
★ 28k • written 4.0 years ago by
p.joshi
▴ 40
6
votes
1
reply
3.1k
views
Downstream analysis after using mnnCorrect()
scran
mnncorrect
updated 6.2 years ago by
Aaron Lun
★ 28k • written 6.2 years ago by
Dave Tang
▴ 210
6
votes
12
replies
3.6k
views
Merging RNAseq Datasets of Different Depths
singlecellexperiment
scran
sequencing depth
batch effect
scrnaseq
updated 5.9 years ago by
Aaron Lun
★ 28k • written 5.9 years ago by
liam.salleh
• 0
5
votes
4
replies
6.1k
views
scRNA-seq pseudo-bulk differential expression analysis with pseudobulkDGE()
scran
scater
scuttle
updated 3.7 years ago by
Aaron Lun
★ 28k • written 3.7 years ago by
enricoferrero
▴ 660
5
votes
6
replies
1.6k
views
DE Analysis on Scran-Normalized Counts
DifferentialExpression
scRNAseq
scran
updated 3.2 years ago by
Aaron Lun
★ 28k • written 3.2 years ago by
LUCIA
• 0
4
votes
4
replies
1.8k
views
Some questions for remove batch effect by using mnnCorrect
batch effect
single cells
mnnCorrect
scran
updated 5.0 years ago by
Aaron Lun
★ 28k • written 5.0 years ago by
xingxd16
▴ 20
4
votes
15
replies
3.9k
views
Warning: negative size factors
size factor
negative
scran
singlecellexperiment
scater
updated 6.2 years ago by
Aaron Lun
★ 28k • written 6.2 years ago by
Marina V.V.
• 0
4
votes
3
replies
1.5k
views
SingleCellExperiment: Edit cluster IDs in colLabels
scran
Clustering
SingleCellExperiment
annotate
cluster
updated 21 months ago by
James W. MacDonald
65k • written 21 months ago by
achoppe
▴ 10
4
votes
5
replies
1.8k
views
Using SC3 with batch corrected MNN values
SC3
Scater
Scran
scRNA-Seq
Batch Correction
updated 5.1 years ago by
Vladimir Kiselev
▴ 150 • written 5.1 years ago by
hamza_karakurt
▴ 50
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
Aaron Lun
★ 28k • written 4.8 years ago by
Bogdan
▴ 670
4
votes
5
replies
2.3k
views
scuttle::aggregateAcrossCells() crashes R on large SingleCellExperiment
scran
SingleCellExperiment
scuttle
scater
updated 3.3 years ago by
Aaron Lun
★ 28k • written 3.3 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
7.7 years ago
Aaron Lun
★ 28k
4
votes
2
replies
1.6k
views
single cell data: adding random effects for subject with multilevel experiment design
SingleCellExperiment
scran
limma
simpleSingleCell
updated 4.9 years ago by
Aaron Lun
★ 28k • written 4.9 years ago by
Matt Mulé
• 0
4
votes
4
replies
1.5k
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
6.7 years ago
ravi_patel_4
▴ 10
3
votes
1
reply
1.0k
views
Output lfc for Wilcox-based findMarkers
scran
updated 4.0 years ago by
Aaron Lun
★ 28k • written 4.0 years ago by
ATpoint
★ 4.1k
3
votes
3
replies
2.3k
views
is SCEset fully abandoned in scran?
scran
scater
splatter
normalization
updated 6.5 years ago by
davis
▴ 90 • written 6.5 years ago by
wt215
• 0
3
votes
3
replies
1.7k
views
Ensuring reproducibility in BiocParallel SingleCellExperiment workflows
scater
SingleCellExperiment
BiocParallel
scuttle
scran
2.5 years ago
enricoferrero
▴ 660
3
votes
5
replies
2.1k
views
Using Scran normalization with in edgeR
edger
estimatedisp
scran
sizefactors
updated 7.8 years ago by
Aaron Lun
★ 28k • written 7.8 years ago by
mnaymik
▴ 10
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
Martin Morgan
25k • written 6.0 years ago by
MengChun Tseng
▴ 10
3
votes
4
replies
1.8k
views
Scran normalization error with computeSumFactors
scran
scater
updated 7.3 years ago by
Aaron Lun
★ 28k • written 7.3 years ago by
hrishi27n
▴ 20
3
votes
9
replies
4.1k
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
1.2k
views
Is logFC a log2 fold change or some other base in scran::findMarkers
scran
updated 4.9 years ago by
Aaron Lun
★ 28k • written 4.9 years ago by
Chris Conley
• 0
3
votes
3
replies
1.2k
views
RFC: Inconsistent software license for scran & automated license checks
agpl
license
gpl
scran
22 months ago • updated 21 months ago
matthias-doering
▴ 40
3
votes
1
reply
1.1k
views
Normalizing vs RNA content in scRNAseq data
monocle
scran
updated 6.8 years ago by
Aaron Lun
★ 28k • written 6.8 years ago by
ankur.chakravarthy.10
▴ 40
3
votes
7
replies
2.0k
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
1.8k
views
[MnnCorrect] Remove batch effects but keep condition effects
single-cell
scran
mnncorrect
rnaseq
updated 5.4 years ago by
Aaron Lun
★ 28k • written 5.4 years ago by
John Reid
▴ 10
2
votes
3
replies
1.8k
views
multiBatchNorm vs. calculateSumFactors on concatenated dataset
batchelor
scran
updated 3.7 years ago by
Aaron Lun
★ 28k • written 3.7 years ago by
Angelos Armen
• 0
2
votes
6
replies
1.2k
views
Why is an averaged reference used in DESeq2 normalisation?
deseq2
scran
batchelor
updated 3.8 years ago by
Aaron Lun
★ 28k • written 3.9 years ago by
Angelos Armen
• 0
2
votes
1
reply
1.1k
views
Getting error Creating SingleCellExperiment instances "all assays must have the same nrow and ncol"
SingleCellExperiment
scran
scater
updated 2.1 years ago by
Basti
▴ 780 • written 2.1 years ago by
Lucky
• 0
2
votes
2
replies
2.0k
views
Error in installation of scran
S4Vectors
IRanges
XVector
GenomicRanges
scran
updated 5.3 years ago by
Aaron Lun
★ 28k • written 5.3 years ago by
Momo
• 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
jamie.gearing
▴ 60 • written 5.2 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 5.2 years ago by
Aaron Lun
★ 28k • written 5.2 years ago by
hamza_karakurt
▴ 50
2
votes
1
reply
1.3k
views
scran: excluding genes with extremely high expression during normalization?
single-cell RNA-seq
scran
normalization
updated 4.7 years ago by
Aaron Lun
★ 28k • written 4.7 years ago by
daniel.borshagovski
• 0
2
votes
2
replies
1.2k
views
scuttle:: librarySizeFactors returning non-finite values
normalizeCounts
scran
librarySizeFactors
scuttle
scRNAseq
2.2 years ago
behr201
• 0
2
votes
2
replies
1.0k
views
normalization for infected homogenious cell populations
normalization
single cell
scran
updated 5.1 years ago by
Aaron Lun
★ 28k • written 5.1 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 4.6 years ago by
Aaron Lun
★ 28k • written 4.6 years ago by
hamza_karakurt
▴ 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
Dayme
• 0 • written 5.1 years ago by
kushshah
▴ 10
2
votes
5
replies
5.8k
views
RNA-Seq Batch correction negative values
rna-seq
batch-effect
combat
scran
sva
updated 6.6 years ago by
Aaron Lun
★ 28k • written 6.6 years ago by
rmf
▴ 20
2
votes
2
replies
1.8k
views
loading scran package
scran
installation
3.2 years ago
TJ
• 0
2
votes
3
replies
1.3k
views
Scran functions not found
single-cell
scran
updated 6.7 years ago by
Aaron Lun
★ 28k • written 6.7 years ago by
alva.james
• 0
2
votes
2
replies
1.0k
views
Block weights in scran::pairwiseTTests
scran
2.5 years ago • updated 2.4 years ago
Angelos Armen
• 0
2
votes
3
replies
1.3k
views
P-value histogram of testLinearModel is not uniform
smart-seq2
scRNAseq
scran
11 months ago • updated 10 months ago
Lluís Revilla Sancho
▴ 730
2
votes
2
replies
1.0k
views
scran: trendVar() / lm.fit() fails in single-cell RNAseq experiment
scran
updated 6.3 years ago by
Aaron Lun
★ 28k • written 6.3 years ago by
roman.hillje
• 0
2
votes
2
replies
5.4k
views
scran ScoreMarkers throws a warning
scoreMarkers
scran
updated 10 months ago by
Peter Hickey
▴ 740 • written 10 months ago by
Assa Yeroslaviz
★ 1.5k
2
votes
3
replies
3.2k
views
scran: question on minimum cluster size for computeSumFactors()
scran
single cell
normalization
clustering
8.0 years ago
aatsmith
• 0
50 results • Page
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Comment: Deseq2 and Normalization of RNA sequencing data
by
kcarey
• 0
Noise in terms of expression...to make sure that the information reported is not due to artifacts and actually expression. When I had FPKM …
Answer: NEED FOR NESSASORY HELP
by
Gordon Smyth
50k
Is this quesion related to your earlier question? https://support.bioconductor.org/p/9157127/ If you've already done an edgeR analysis, yo…
Answer: Gene-by-sample covariates in limma
by
Gordon Smyth
50k
Your first method would be valid if, instead of taking ratios, you instead used the differences between the log-transformed 13C and 12C int…
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
by
Gordon Smyth
50k
You have discovered something that I have pointed out many times on this forum. fgsea does not implement the classic GSEA method published …
Comment: Once again a "Model matrix not full rank"
by
James W. MacDonald
65k
In that case both time and treatment are identical things, so choose one and go with it.
Votes
Bioconductor 3.19 is Released!
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
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