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0
votes
0
replies
340
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Specify the order of the sets in VennDiagram R?
VennDiagram R
9 months ago by Lucy ▴ 140
0
votes
2
replies
559
views
Move Cytoscape "CytoscapeConfiguration" directory
cytoscape
9 months ago by Lucy ▴ 140
0
votes
2
replies
442
views
How does --primary work with -M and --fractional options featureCounts?
RNA-seq subread mapping featureCounts STAR
20 months ago by Lucy ▴ 140
1
vote
7
replies
1.7k
views
featureCounts parameters
RNA-seq featureCounts RNA-Seq
updated 19 months ago by 78k • written 21 months ago by ▴ 140
6
votes
2
replies
1.9k
views
Seurat sctransform - does anyone know of a good explanation for biologists?
Seurat scRNA-seq normalization
updated 2.0 years ago by ▴ 50 • written 2.0 years ago by ▴ 140
0
votes
0
replies
697
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Why do we log transform and scale data prior to PCA for scRNA-seq analysis
Seurat log transformation scaling scRNA-seq
updated 2.1 years ago by 99k • written 2.1 years ago by ▴ 140
0
votes
0
replies
378
views
Goodness-of-fit test - observed vs. expected (some expected values < 5)
R stats goodness-of-fit
2.1 years ago by Lucy ▴ 140
5
votes
9
replies
4.3k
views
Which counts to use for RNA-seq heatmap and PCA?
RNA-seq heatmap EdgeR PCA
updated 2.3 years ago by 78k • written 4.0 years ago by ▴ 140
0
votes
0
replies
412
views
Add SM group STAR
samtools variant RNA-seq calling GATK STAR
2.3 years ago by Lucy ▴ 140
1
vote
3
replies
2.7k
views
Error with Seurat subset function
Seurat scRNA-seq RNA-seq
2.4 years ago by Lucy ▴ 140
1
vote
4
replies
1.6k
views
Gini coefficient TCR repertoire
TCR-sequencing Gini
10 months ago by Lucy ▴ 140
4
votes
3
replies
1.4k
views
Identification of modules of genes that vary over pseudotime (scRNA-seq pseudotime analysis)
modules scRNA-seq singlecell pseudotime RNA-seq
updated 2.6 years ago by ★ 16k • written 2.6 years ago by ▴ 140
0
votes
1
reply
875
views
Negbinom vs. logistic regression for Seurat FindMarkers()
scRNA-seq RNA-seq Seurat
2.9 years ago by Lucy ▴ 140
2
votes
3
replies
3.7k
views
Differential expression analysis in Seurat
RNA-Seq scRNA-seq Seurat
updated 3.0 years ago by 12k • written 3.0 years ago by ▴ 140
3
votes
11
replies
1.5k
views
Correlation plot sized by another variable
ggplot2 correlation plot corrplot
updated 3.3 years ago by 4.2k • written 3.3 years ago by ▴ 140
0
votes
4
replies
14k
views
biplot scaling options (ggbiplot)
biplot PCA ggbiplot
4.0 years ago by Lucy ▴ 140
3
votes
4
replies
1.1k
views
DEsingle differential-expression analysis
differential-expression analysis scRNA-seq
4.0 years ago by Lucy ▴ 140
4
votes
5
replies
3.2k
views
Seurat sctransform return.only.var.genes = FALSE
scRNA-seq Seurat sctransform
updated 4.1 years ago by ★ 16k • written 4.1 years ago by ▴ 140
5
votes
6
replies
5.0k
views
RNA velocity on 5' 10x data?
RNA-Seq scRNA-seq RNA velocity
updated 2.0 years ago by ▴ 10 • written 4.1 years ago by ▴ 140
1
vote
2
replies
2.2k
views
Differential-expression analysis using logistic regression in Seurat - glm.fit warning message
scRNA-seq Seurat Differential-expression analysis
updated 4.1 years ago by ★ 16k • written 4.1 years ago by ▴ 140
0
votes
3
replies
3.4k
views
Does Harmony batch correction for scRNA-seq require the same populations to be present in all samples?
scRNA-seq single-cell batch correction Harmony
4.1 years ago by Lucy ▴ 140
7
votes
2
replies
2.1k
views
Clustering resolution single-cell RNA-seq
scRNA-seq RNA-seq clustering single-cell
updated 5 weeks ago by ▴ 170 • written 4.1 years ago by ▴ 140
0
votes
0
replies
2.0k
views
Downsampling reads vs. Seurat normalisation
RNA-Seq scRNA-seq DropletUtils single-cell
4.1 years ago by Lucy ▴ 140
9
votes
10
replies
6.4k
views
Harmony batch correction vs. regressing out donor effect in Seurat
scRNA-seq Seurat Harmony RNA-seq batch correction
updated 4.1 years ago by ★ 16k • written 4.1 years ago by ▴ 140
0
votes
0
replies
1.0k
views
Should batch correction be performed before or after feature selection in scRNA-seq
scRNA-seq feature selection batch effect
4.5 years ago by Lucy ▴ 140
0
votes
4
replies
1.3k
views
ATAC-seq transcription factor binding prediction
ATAC-seq RNA-seq transcription factor
updated 4.8 years ago by • 0 • written 5.0 years ago by ▴ 140
2
votes
1
reply
2.9k
views
Homer annotatePeaks.pl custom GTF
Homer ATAC-seq GTF
4.8 years ago by Lucy ▴ 140
0
votes
4
replies
2.4k
views
Aligning RNA-seq and ATAC-seq gene annotations
Homer RNA-seq ATAC-seq Gene annotation
4.9 years ago by Lucy ▴ 140
0
votes
0
replies
809
views
CENTIPEDE - values from fitCentipede
centipede R ATAC-seq
updated 4.9 years ago by 20 • written 5.1 years ago by ▴ 140
0
votes
2
replies
3.8k
views
HOMER de novo motif enrichment
HOMER Motif enrichment
5.0 years ago by Lucy ▴ 140
0
votes
0
replies
687
views
Error with fitCentipede
Centipede R
5.1 years ago by Lucy ▴ 140
0
votes
0
replies
1.5k
views
featureCounts - how to make ATAC-seq cut-sites BAM
featureCounts bed
updated 8 months ago by 41k • written 5.2 years ago by ▴ 140
0
votes
2
replies
2.2k
views
featureCounts allowMultiOverlap - fractional or not?
featureCounts ATAC-seq
5.2 years ago by Lucy ▴ 140
0
votes
4
replies
1.5k
views
When using MACS2 with -f BAM, it is possible to have a shift other than 0?
macs2 macs
updated 5.2 years ago by 20 • written 5.3 years ago by ▴ 140
14
votes
12
replies
13k
views
FRIP score ATAC-seq
ATAC-seq FRIP
updated 5.2 years ago by ▴ 20 • written 5.2 years ago by ▴ 140
3
votes
4
replies
2.2k
views
Determine peak summits after IDR analysis
macs2 idr peak summits
updated 5.2 years ago by 35k • written 5.2 years ago by ▴ 140
0
votes
1
reply
1.0k
views
Should --very-sensitive be combined with -no-1mm-upfront?
bowtie2 bowtie
updated 5.3 years ago by 104k • written 5.3 years ago by ▴ 140
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