Showing : SCRAN • reset
4
votes
15
replies
4.0k
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
0
votes
8
replies
2.0k
views
Using Scran with RSEM/DEseq
scran normalization deseq2 rsem edger
7.8 years ago a.guerra • 0
0
votes
5
replies
3.2k
views
Cannot install Bioconductor v3.9
scran cellassign bioconductor
updated 4.6 years ago by 25k • written 4.6 years ago by ▴ 10
4
votes
5
replies
2.3k
views
scuttle::aggregateAcrossCells() crashes R on large SingleCellExperiment
scran SingleCellExperiment scuttle scater
updated 3.4 years ago by ★ 28k • written 3.4 years ago by ▴ 660
0
votes
6
replies
1.6k
views
scran::trendVar throwing error
scran
6.4 years ago zhalehsafikhani • 0
2
votes
3
replies
3.2k
views
scran: question on minimum cluster size for computeSumFactors()
scran single cell normalization clustering
8.1 years ago • updated 8.0 years ago aatsmith • 0
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 ★ 28k • written 4.0 years ago by ▴ 40
1
vote
2
replies
1.3k
views
Should edgeR-GLM on single cell RNA data be performed on the counts or normalized data?
edger scran
updated 7.8 years ago by ▴ 90 • written 7.8 years ago by • 0
0
votes
3
replies
474
views
scran package: quickCluster and calculateSumFactors parallelization
BiocParallel scran
updated 4 months ago by ★ 4.1k • written 4 months ago by • 0
1
vote
3
replies
1.1k
views
Normalizing to multiple spike-in concentrations with scran
scran spike-in
6.2 years ago • updated 6.1 years ago supremerulersuraj • 0
2
votes
6
replies
1.2k
views
Why is an averaged reference used in DESeq2 normalisation?
deseq2 scran batchelor
updated 3.9 years ago by ★ 28k • written 3.9 years ago by • 0
5
votes
4
replies
6.1k
views
scRNA-seq pseudo-bulk differential expression analysis with pseudobulkDGE()
scran scater scuttle
updated 3.8 years ago by ★ 28k • written 3.8 years ago by ▴ 660
3
votes
3
replies
2.3k
views
is SCEset fully abandoned in scran?
scran scater splatter normalization
updated 6.6 years ago by ▴ 90 • written 6.6 years ago by • 0
2
votes
2
replies
1.0k
views
scran: trendVar() / lm.fit() fails in single-cell RNAseq experiment
scran
updated 6.4 years ago by ★ 28k • written 6.4 years ago by • 0
1
vote
3
replies
1.7k
views
scater/scran with TPMs from Salmon - counts?
scater salmon scran
updated 6.3 years ago by ★ 28k • written 6.3 years ago by • 0
6
votes
1
reply
3.1k
views
Downstream analysis after using mnnCorrect()
scran mnncorrect
updated 6.3 years ago by ★ 28k • written 6.3 years ago by ▴ 210
0
votes
1
reply
1.5k
views
Converting scater-normalized UMI data to Monocle CellDataSet
scater scran umi monocle
updated 6.1 years ago by ★ 28k • written 6.1 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 5.9 years ago by 25k • written 6.0 years ago by ▴ 10
6
votes
12
replies
3.7k
views
Merging RNAseq Datasets of Different Depths
singlecellexperiment scran sequencing depth batch effect scrnaseq
updated 5.9 years ago by ★ 28k • written 5.9 years ago by • 0
1
vote
2
replies
1.4k
views
SCRAN - Question: Error when calling cosineNorm through fastMNN
SCRAN fastMNN mnnCorrect
updated 5.8 years ago by ★ 28k • written 5.8 years ago by • 0
1
vote
1
reply
1.4k
views
Adjust number of clusters with scran/buildSNNGraph
scran buildsnngraph cluster_walktrap single-cell
updated 5.8 years ago by ★ 28k • written 5.8 years ago by • 0
0
votes
3
replies
984
views
Error of makeTechTrend() of Scran
scran single-cell seq.default
updated 5.8 years ago by ★ 28k • written 5.8 years ago by • 0
2
votes
6
replies
1.7k
views
Change the number of clusters with scater
scater scran scrnaseq clustering
updated 5.5 years ago by ★ 28k • written 5.5 years ago by ▴ 20
2
votes
2
replies
1.8k
views
[MnnCorrect] Remove batch effects but keep condition effects
single-cell scran mnncorrect rnaseq
updated 5.5 years ago by ★ 28k • written 5.5 years ago by ▴ 10
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
7
votes
5
replies
1.6k
views
scran: Are the log counts expression comparable among different genes within a sample/cell ?
scran scater
updated 5.4 years ago by ★ 28k • written 5.4 years ago by ▴ 30
1
vote
2
replies
1.1k
views
scran/scater Normalized matrix
scran scater normalized counts
updated 5.4 years ago by ★ 28k • written 5.4 years ago by ▴ 90
2
votes
2
replies
2.0k
views
Error in installation of scran
S4Vectors IRanges XVector GenomicRanges scran
updated 5.4 years ago by ★ 28k • written 5.4 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 21 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 5.2 years ago by ★ 28k • written 5.2 years ago by ▴ 50
2
votes
2
replies
1.0k
views
normalization for infected homogenious cell populations
normalization single cell scran
updated 5.2 years ago by ★ 28k • written 5.2 years ago by • 0
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 ▴ 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 5.1 years ago by ▴ 10
8
votes
4
replies
2.3k
views
Usage of doubletCells() function before or after the batch correction?
scater scran scRNA-Seq doubletCells
updated 5.1 years ago by ★ 28k • written 5.1 years ago by ▴ 50
4
votes
4
replies
1.8k
views
Some questions for remove batch effect by using mnnCorrect
batch effect single cells mnnCorrect scran
updated 5.1 years ago by ★ 28k • written 5.1 years ago by ▴ 20
3
votes
2
replies
1.2k
views
Is logFC a log2 fold change or some other base in scran::findMarkers
scran
updated 5.0 years ago by ★ 28k • written 5.0 years ago by • 0
0
votes
7
replies
2.2k
views
differential expression between clusters (in distinct "treatments") in scRNAseq
scater limma scde scran sc3
4.9 years ago Bogdan ▴ 670
1
vote
4
replies
1.5k
views
number of cell clusters in scRNA-seq
scran scater sc3
updated 4.9 years ago by ★ 28k • written 4.9 years ago by ▴ 670
4
votes
4
replies
1.5k
views
scRNA-seq : Classification of cell cycle phase
scater scran
updated 4.9 years ago by ★ 28k • written 4.9 years ago by ▴ 670
3
votes
7
replies
2.0k
views
scRNA-seq : runPCA() and denoisePCA()
scater scran
updated 4.9 years ago by ★ 28k • written 4.9 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
1
vote
5
replies
1.6k
views
Preprocessing in scran::doubletCells
scran simpleSingleCell
updated 4.8 years ago by ★ 28k • written 4.8 years ago by • 0
1
vote
3
replies
936
views
k argument in buildSNNGraph
scran
updated 4.8 years ago by ★ 28k • written 4.8 years ago by • 0
2
votes
1
reply
1.3k
views
scran: excluding genes with extremely high expression during normalization?
single-cell RNA-seq scran normalization
updated 4.8 years ago by ★ 28k • written 4.8 years ago by • 0
1
vote
2
replies
1.3k
views
Mitigating cell cycle effect in scRNA-seq using a blocking factor or design matrix
scran
updated 4.6 years ago by ★ 28k • written 4.6 years ago by ▴ 20
1
vote
1
reply
834
views
Stouffer's method weights in scran::pairwiseWilcox
scran
updated 4.6 years ago by ★ 28k • written 4.6 years ago by • 0
2
votes
1
reply
2.0k
views
Batch Corrections (MNN) with TPM values
scRNA-Seq scater scran rna-seq MNN
updated 4.6 years ago by ★ 28k • written 4.6 years ago by ▴ 50
0
votes
3
replies
974
views
How can doubletCell() scores be converted to single/doublet annotation?
scran doublet
updated 4.1 years ago by ★ 28k • written 4.1 years ago by ▴ 10
7
votes
3
replies
5.0k
views
Downsample or not to downsample?
scrna-seq downsampleBatches scran
updated 4.0 years ago by ★ 28k • written 4.0 years ago by ▴ 40
50 results • Page 1 of 1
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Replies
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by JKim • 0
The 1st model has an interaction term, but the 2nd model doesn't have the interaction term. That makes the difference.
Comment: Ensembl plants at annotationHub? by Daniele • 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by swbarnes2 ★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Comment: DESeq2- Mysterious interaction suppresses DEGs by shaunpeterson • 0
The images I tried to attach didn't attach. Here is the PCA (MDS) of all the samples, with the Cortex outlier highlighed. ![enter image de…
Comment: STRINGdb : error with string_db$plot_network() by damian.szk ▴ 80
ok. Forcing non-secure protocol should not be needed anymore, due to changes in the underlying library. However, I will look at why "HTTP" …
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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