Showing : Scran • reset
0
votes
8
replies
1.5k
views
Using Scran with RSEM/DEseq
scran normalization deseq2 rsem edger
6.5 years ago a.guerra • 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
0
votes
5
replies
2.4k
views
Cannot install Bioconductor v3.9
scran cellassign bioconductor
updated 3.3 years ago by 25k • written 3.3 years ago by ▴ 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
1
vote
3
replies
678
views
Normalizing to multiple spike-in concentrations with scran
scran spike-in
4.9 years ago • updated 4.8 years ago supremerulersuraj • 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
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
1
vote
2
replies
1.0k
views
Should edgeR-GLM on single cell RNA data be performed on the counts or normalized data?
edger scran
updated 6.5 years ago by ▴ 90 • written 6.5 years ago by • 0
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
0
votes
6
replies
1.1k
views
scran::trendVar throwing error
scran
5.1 years ago zhalehsafikhani • 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
1
vote
4
replies
721
views
Missing design when using Scran to create a DESeqDataSet
deseq2 Scran
updated 5.3 years ago by ★ 28k • written 5.3 years ago by • 0
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
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
1
vote
3
replies
1.2k
views
scater/scran with TPMs from Salmon - counts?
scater salmon scran
updated 5.0 years ago by ★ 28k • written 5.0 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
0
votes
1
reply
932
views
Converting scater-normalized UMI data to Monocle CellDataSet
scater scran umi monocle
updated 4.8 years ago by ★ 28k • written 4.8 years ago by • 0
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
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
1
vote
2
replies
1.1k
views
SCRAN - Question: Error when calling cosineNorm through fastMNN
SCRAN fastMNN mnnCorrect
updated 4.5 years ago by ★ 28k • written 4.5 years ago by • 0
1
vote
1
reply
966
views
Adjust number of clusters with scran/buildSNNGraph
scran buildsnngraph cluster_walktrap single-cell
updated 4.5 years ago by ★ 28k • written 4.5 years ago by • 0
0
votes
3
replies
606
views
Error of makeTechTrend() of Scran
scran single-cell seq.default
updated 4.4 years ago by ★ 28k • written 4.4 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
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
1
vote
3
replies
723
views
How to resolve these trendVar() warnings and errors
scater scran singlecellexperiment
updated 4.1 years ago by ★ 28k • written 4.1 years ago by ▴ 20
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
1
vote
2
replies
686
views
scran/scater Normalized matrix
scran scater normalized counts
updated 4.1 years ago by ★ 28k • written 4.1 years ago by ▴ 90
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
1
vote
2
replies
884
views
Dunn Index for Clusters from scRNA-Seq
scRNA-Seq clustering scater scran dunn index
updated 3.9 years ago by ★ 28k • written 3.9 years ago by ▴ 50
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
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
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
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
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
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
0
votes
7
replies
933
views
differential expression between clusters (in distinct "treatments") in scRNAseq
scater limma scde scran sc3
3.6 years ago Bogdan ▴ 660
1
vote
4
replies
826
views
number of cell clusters in scRNA-seq
scran scater sc3
updated 3.6 years ago by ★ 28k • written 3.6 years ago by ▴ 660
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
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
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
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
1
vote
3
replies
507
views
k argument in buildSNNGraph
scran
updated 3.5 years ago by ★ 28k • written 3.5 years ago by • 0
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
1
vote
2
replies
765
views
Mitigating cell cycle effect in scRNA-seq using a blocking factor or design matrix
scran
updated 3.3 years ago by ★ 28k • written 3.3 years ago by ▴ 10
1
vote
1
reply
434
views
Stouffer's method weights in scran::pairwiseWilcox
scran
updated 3.3 years ago by ★ 28k • written 3.3 years ago by • 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
0
votes
3
replies
444
views
How can doubletCell() scores be converted to single/doublet annotation?
scran doublet
updated 2.8 years ago by ★ 28k • written 2.8 years ago by ▴ 10
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
50 results • Page 1 of 1
Recent ...
Replies
Comment: How to normalize long-read RNA-seq data for comparison with short-reads by Bernardo • 0
Just did that, thank you for the suggestion.
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…
Votes
Comment: How to normalize long-read RNA-seq data for comparison with short-reads
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
Awards • All
Teacher to Michael Love 39k
Teacher to James W. MacDonald 62k
Popular Question to Assa Yeroslaviz ★ 1.5k
Scholar to ATpoint ★ 2.0k
Popular Question to adR ▴ 20
Locations • All
United States, just now
WEHI, Melbourne, Australia, 16 minutes ago
United States, 17 minutes ago
United States, 17 minutes ago
United States, 33 minutes ago
Traffic: 375 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6