Showing : scran • reset
3
votes
7
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2.8k
views
scRNA-seq : runPCA() and denoisePCA()
scater scran
updated 6.2 years ago by ★ 29k • written 6.2 years ago by ▴ 670
1
vote
4
replies
2.2k
views
number of cell clusters in scRNA-seq
scran scater sc3
updated 6.2 years ago by ★ 29k • written 6.2 years ago by ▴ 670
0
votes
7
replies
3.0k
views
differential expression between clusters (in distinct "treatments") in scRNAseq
scater limma scde scran sc3
6.2 years ago Bogdan ▴ 670
0
votes
1
reply
1.2k
views
emptyDrops result is full NAs
scran dropletUtils scater scRNA-Seq
6.2 years ago hamza_karakurt ▴ 60
4
votes
2
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1.6k
views
Is logFC a log2 fold change or some other base in scran::findMarkers
scran
updated 6.2 years ago by ★ 29k • written 6.2 years ago by • 0
4
votes
2
replies
2.2k
views
single cell data: adding random effects for subject with multilevel experiment design
SingleCellExperiment scran limma simpleSingleCell
updated 6.2 years ago by ★ 29k • written 6.2 years ago by • 0
2
votes
4
replies
4.7k
views
ERROR - Size factors should be positive real numbers (using normalize() function)
scater scran singlecellexperiment normalize qc
updated 3.4 years ago by • 0 • written 6.4 years ago by ▴ 10
5
votes
4
replies
2.7k
views
Some questions for remove batch effect by using mnnCorrect
batch effect single cells mnnCorrect scran
updated 6.3 years ago by ★ 29k • written 6.3 years ago by ▴ 20
8
votes
4
replies
3.8k
views
Usage of doubletCells() function before or after the batch correction?
scater scran scRNA-Seq doubletCells
updated 6.4 years ago by ★ 29k • written 6.4 years ago by ▴ 60
4
votes
5
replies
2.5k
views
Using SC3 with batch corrected MNN values
SC3 Scater Scran scRNA-Seq Batch Correction
updated 6.4 years ago by ▴ 150 • written 6.4 years ago by ▴ 60
2
votes
2
replies
1.4k
views
normalization for infected homogenious cell populations
normalization single cell scran
updated 6.5 years ago by ★ 29k • written 6.5 years ago by • 0
0
votes
1
reply
1.4k
views
Scran: Performing DE after cell-typle identifaction on the corrected and integrated datasets
Scran MNN_correct Differential expression single-cell
6.5 years ago baldissera152 • 0
1
vote
2
replies
2.0k
views
Dunn Index for Clusters from scRNA-Seq
scRNA-Seq clustering scater scran dunn index
updated 6.5 years ago by ★ 29k • written 6.5 years ago by ▴ 60
2
votes
5
replies
2.3k
views
Modularity values of clusters and Differential Expression in scRNA-Seq
scater scran igraph scRNA-Seq rots
updated 6.5 years ago by ★ 29k • written 6.5 years ago by ▴ 60
2
votes
5
replies
5.2k
views
Adding labels on clusters in a t-SNE plot and changing colors
scran scater Rtsne ggplot2 scRNA-Seq
updated 3.0 years ago by ▴ 60 • written 6.5 years ago by ▴ 60
2
votes
2
replies
2.7k
views
Error in installation of scran
S4Vectors IRanges XVector GenomicRanges scran
updated 6.6 years ago by ★ 29k • written 6.6 years ago by • 0
1
vote
2
replies
1.5k
views
scran/scater Normalized matrix
scran scater normalized counts
updated 6.7 years ago by ★ 29k • written 6.7 years ago by ▴ 90
7
votes
5
replies
2.2k
views
scran: Are the log counts expression comparable among different genes within a sample/cell ?
scran scater
updated 6.7 years ago by ★ 29k • written 6.7 years ago by ▴ 30
1
vote
3
replies
1.5k
views
How to resolve these trendVar() warnings and errors
scater scran singlecellexperiment
updated 6.7 years ago by ★ 29k • written 6.7 years ago by ▴ 20
2
votes
2
replies
2.3k
views
[MnnCorrect] Remove batch effects but keep condition effects
single-cell scran mnncorrect rnaseq
updated 6.8 years ago by ★ 29k • written 6.8 years ago by ▴ 10
2
votes
6
replies
2.4k
views
Change the number of clusters with scater
scater scran scrnaseq clustering
updated 6.8 years ago by ★ 29k • written 6.8 years ago by ▴ 20
0
votes
3
replies
1.3k
views
Error of makeTechTrend() of Scran
scran single-cell seq.default
updated 7.0 years ago by ★ 29k • written 7.0 years ago by • 0
1
vote
1
reply
2.0k
views
Adjust number of clusters with scran/buildSNNGraph
scran buildsnngraph cluster_walktrap single-cell
updated 7.1 years ago by ★ 29k • written 7.1 years ago by • 0
1
vote
2
replies
1.7k
views
SCRAN - Question: Error when calling cosineNorm through fastMNN
SCRAN fastMNN mnnCorrect
updated 7.1 years ago by ★ 29k • written 7.1 years ago by • 0
1
vote
2
replies
3.4k
views
keep getting this error "number of rows is not the same across batches" even though my 2 matrices have the same row number
mnncorrect batch effect scran
updated 7.1 years ago by ★ 29k • written 7.1 years ago by • 0
3
votes
3
replies
8.4k
views
rowSums() rowMeans() don't work on sparse matrix "dgCMatrix"
scater scran single-cell
updated 7.2 years ago by 25k • written 7.3 years ago by ▴ 10
6
votes
12
replies
5.1k
views
Merging RNAseq Datasets of Different Depths
singlecellexperiment scran sequencing depth batch effect scrnaseq
updated 7.2 years ago by ★ 29k • written 7.2 years ago by • 0
0
votes
1
reply
2.0k
views
Converting scater-normalized UMI data to Monocle CellDataSet
scater scran umi monocle
updated 7.4 years ago by ★ 29k • written 7.4 years ago by • 0
1
vote
3
replies
1.6k
views
Normalizing to multiple spike-in concentrations with scran
scran spike-in
7.5 years ago • updated 7.4 years ago supremerulersuraj • 0
4
votes
15
replies
5.1k
views
Warning: negative size factors
size factor negative scran singlecellexperiment scater
updated 7.5 years ago by ★ 29k • written 7.5 years ago by • 0
6
votes
1
reply
3.6k
views
Downstream analysis after using mnnCorrect()
scran mnncorrect
updated 7.6 years ago by ★ 29k • written 7.6 years ago by ▴ 210
2
votes
3
replies
2.3k
views
scater/scran with TPMs from Salmon - counts?
scater salmon scran
updated 7.6 years ago by ★ 29k • written 7.6 years ago by ▴ 10
2
votes
2
replies
1.4k
views
scran: trendVar() / lm.fit() fails in single-cell RNAseq experiment
scran
updated 7.7 years ago by ★ 29k • written 7.7 years ago by • 0
0
votes
6
replies
2.0k
views
scran::trendVar throwing error
scran
7.7 years ago zhalehsafikhani • 0
3
votes
3
replies
2.7k
views
is SCEset fully abandoned in scran?
scran scater splatter normalization
updated 7.9 years ago by ▴ 90 • written 7.9 years ago by • 0
1
vote
4
replies
1.3k
views
Missing design when using Scran to create a DESeqDataSet
deseq2 Scran
updated 7.9 years ago by ★ 29k • written 7.9 years ago by • 0
2
votes
5
replies
7.7k
views
RNA-Seq Batch correction negative values
rna-seq batch-effect combat scran sva
updated 7.9 years ago by ★ 29k • written 7.9 years ago by ▴ 20
2
votes
3
replies
1.7k
views
Scran functions not found
single-cell scran
updated 8.0 years ago by ★ 29k • written 8.0 years ago by • 0
3
votes
7
replies
3.7k
views
Error: could not find function "findMarkers"
scran
8.0 years ago ravi_patel_4 ▴ 10
0
votes
5
replies
2.7k
views
[MnnCorrect] In case of known subpopulations
scran single-cell mnncorrect rnaseq
8.1 years ago Jens Preussner ▴ 30
3
votes
1
reply
1.5k
views
Normalizing vs RNA content in scRNAseq data
monocle scran
updated 8.1 years ago by ★ 29k • written 8.1 years ago by ▴ 40
3
votes
9
replies
5.3k
views
Why does scran's computeSumFactors produce different size factors for cells with the exact same gene counts?
scran scater drop-seq scrnaseq
updated 8.4 years ago by ★ 29k • written 8.4 years ago by ▴ 10
3
votes
4
replies
2.4k
views
Scran normalization error with computeSumFactors
scran scater
updated 8.6 years ago by ★ 29k • written 8.6 years ago by ▴ 20
4
votes
0
replies
4.2k
views
Tutorial: Workflow for low-level analysis of single-cell RNA-seq data
scran scater single cell Tutorial
9.0 years ago Aaron Lun ★ 29k
1
vote
2
replies
1.7k
views
Should edgeR-GLM on single cell RNA data be performed on the counts or normalized data?
edger scran
updated 9.1 years ago by ▴ 90 • written 9.1 years ago by • 0
0
votes
1
reply
1.3k
views
Does the normalization pipeline for scran include filtering out genes with low counts?
filtering scran
updated 9.1 years ago by ★ 29k • written 9.1 years ago by • 0
0
votes
8
replies
2.5k
views
Using Scran with RSEM/DEseq
scran normalization deseq2 rsem edger
9.1 years ago a.guerra • 0
3
votes
5
replies
2.6k
views
Using Scran normalization with in edgeR
edger estimatedisp scran sizefactors
updated 9.1 years ago by ★ 29k • written 9.1 years ago by ▴ 10
2
votes
3
replies
3.7k
views
scran: question on minimum cluster size for computeSumFactors()
scran single cell normalization clustering
9.3 years ago aatsmith • 0
99 results • Page 2 of 2
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Replies
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by snijesh ▴ 200
I would like to clarify whether the command `res <- results(dds, name = "phaseLP.conditionTreated")` is the correct approach to generate …
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by James W. MacDonald 68k
Not sure I understand. You ask how to do something and then show how one would do so.
Comment: DiffBind getting Fold values of near 0 by littlefishes20 ▴ 10
Same issues. All peaks return to a fold near 0, although they are significant when visualizing in IGV. Please find the MAplot and volcanoPl…
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by snijesh ▴ 200
I have checked DEGs between Solvent Control (SC) of FP and LP and there are noticebale differences in terms of DEGs. ``` # Checking SC in …
Answer: A0A287BB68 not recognized as UNPROT key in org.Ss.eg.db using AnnotationDbi::sel by James W. MacDonald 68k
Apparently it's been over-ridden by a different UniProtKB ID ``` > select(org.Ss.eg.db, "MYH11", "UNIPROT", "SYMBOL") 'select()' retu…
Votes
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Comment: Using DESeq2 on single cell RNA Seq data of same cell type but different conditi
Can NanoString data be analyzed using DESeq2?
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