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Shared pathways up in disease blood and tissue relative to healthy blood (scRNA-seq)
scRNA-seq
updated 24 days ago by 82k • written 25 days ago by ▴ 140
0
votes
0
replies
455
views
Specify the order of the sets in VennDiagram R?
VennDiagram R
14 months ago by Lucy ▴ 140
0
votes
2
replies
683
views
Move Cytoscape "CytoscapeConfiguration" directory
cytoscape
14 months ago by Lucy ▴ 140
0
votes
2
replies
544
views
How does --primary work with -M and --fractional options featureCounts?
RNA-seq subread mapping featureCounts STAR
2.2 years ago by Lucy ▴ 140
1
vote
7
replies
2.0k
views
featureCounts parameters
RNA-seq featureCounts RNA-Seq
updated 2.1 years ago by 82k • written 2.2 years ago by ▴ 140
6
votes
2
replies
2.5k
views
Seurat sctransform - does anyone know of a good explanation for biologists?
Seurat scRNA-seq normalization
updated 2.5 years ago by ▴ 50 • written 2.5 years ago by ▴ 140
0
votes
0
replies
830
views
Why do we log transform and scale data prior to PCA for scRNA-seq analysis
Seurat log transformation scaling scRNA-seq
updated 2.5 years ago by 100k • written 2.5 years ago by ▴ 140
0
votes
0
replies
442
views
Goodness-of-fit test - observed vs. expected (some expected values < 5)
R stats goodness-of-fit
2.6 years ago by Lucy ▴ 140
5
votes
9
replies
4.7k
views
Which counts to use for RNA-seq heatmap and PCA?
RNA-seq heatmap EdgeR PCA
updated 2.7 years ago by 82k • written 4.4 years ago by ▴ 140
0
votes
0
replies
464
views
Add SM group STAR
samtools variant RNA-seq calling GATK STAR
2.8 years ago by Lucy ▴ 140
1
vote
3
replies
3.1k
views
Error with Seurat subset function
Seurat scRNA-seq RNA-seq
2.8 years ago by Lucy ▴ 140
1
vote
4
replies
1.8k
views
Gini coefficient TCR repertoire
TCR-sequencing Gini
15 months ago by Lucy ▴ 140
4
votes
3
replies
1.5k
views
Identification of modules of genes that vary over pseudotime (scRNA-seq pseudotime analysis)
modules scRNA-seq singlecell pseudotime RNA-seq
updated 3.0 years ago by ★ 16k • written 3.0 years ago by ▴ 140
0
votes
1
reply
995
views
Negbinom vs. logistic regression for Seurat FindMarkers()
scRNA-seq RNA-seq Seurat
3.4 years ago by Lucy ▴ 140
2
votes
3
replies
3.9k
views
Differential expression analysis in Seurat
RNA-Seq scRNA-seq Seurat
updated 3.4 years ago by 13k • written 3.4 years ago by ▴ 140
3
votes
11
replies
1.7k
views
Correlation plot sized by another variable
ggplot2 correlation plot corrplot
updated 3.8 years ago by 4.6k • written 3.8 years ago by ▴ 140
0
votes
4
replies
14k
views
biplot scaling options (ggbiplot)
biplot PCA ggbiplot
4.4 years ago by Lucy ▴ 140
3
votes
4
replies
1.2k
views
DEsingle differential-expression analysis
differential-expression analysis scRNA-seq
4.4 years ago by Lucy ▴ 140
4
votes
5
replies
3.5k
views
Seurat sctransform return.only.var.genes = FALSE
scRNA-seq Seurat sctransform
updated 4.5 years ago by ★ 16k • written 4.5 years ago by ▴ 140
5
votes
6
replies
5.3k
views
RNA velocity on 5' 10x data?
RNA-Seq scRNA-seq RNA velocity
updated 2.5 years ago by ▴ 10 • written 4.5 years ago by ▴ 140
1
vote
2
replies
2.4k
views
Differential-expression analysis using logistic regression in Seurat - glm.fit warning message
scRNA-seq Seurat Differential-expression analysis
updated 4.5 years ago by ★ 16k • written 4.5 years ago by ▴ 140
1
vote
3
replies
3.6k
views
Does Harmony batch correction for scRNA-seq require the same populations to be present in all samples?
Harmony single-cell scRNA-seq batch-effect
updated 16 days ago by 43k • written 4.5 years ago by ▴ 140
7
votes
2
replies
2.3k
views
Clustering resolution single-cell RNA-seq
scRNA-seq RNA-seq clustering single-cell
updated 6 months ago by ▴ 210 • written 4.6 years ago by ▴ 140
0
votes
0
replies
2.1k
views
Downsampling reads vs. Seurat normalisation
RNA-Seq scRNA-seq DropletUtils single-cell
4.6 years ago by Lucy ▴ 140
9
votes
10
replies
6.9k
views
Harmony batch correction vs. regressing out donor effect in Seurat
Seurat scRNA-seq Harmony RNA-seq batch-effect
updated 16 days ago by 43k • written 4.6 years ago by ▴ 140
0
votes
0
replies
1.1k
views
Should batch correction be performed before or after feature selection in scRNA-seq
batch-effect scRNA-seq feature-selection
updated 17 days ago by 43k • written 4.9 years ago by ▴ 140
0
votes
4
replies
1.4k
views
ATAC-seq transcription factor binding prediction
ATAC-seq RNA-seq transcription factor
updated 5.2 years ago by • 0 • written 5.5 years ago by ▴ 140
2
votes
1
reply
3.1k
views
Homer annotatePeaks.pl custom GTF
Homer ATAC-seq GTF
5.3 years ago by Lucy ▴ 140
0
votes
4
replies
2.6k
views
Aligning RNA-seq and ATAC-seq gene annotations
Homer RNA-seq ATAC-seq Gene annotation
5.3 years ago by Lucy ▴ 140
0
votes
0
replies
853
views
CENTIPEDE - values from fitCentipede
centipede R ATAC-seq
updated 5.4 years ago by 20 • written 5.5 years ago by ▴ 140
0
votes
2
replies
4.0k
views
HOMER de novo motif enrichment
HOMER Motif enrichment
5.4 years ago by Lucy ▴ 140
0
votes
0
replies
737
views
Error with fitCentipede
Centipede R
5.5 years ago by Lucy ▴ 140
0
votes
0
replies
1.6k
views
featureCounts - how to make ATAC-seq cut-sites BAM
featureCounts bed
updated 13 months ago by 43k • written 5.6 years ago by ▴ 140
0
votes
2
replies
2.3k
views
featureCounts allowMultiOverlap - fractional or not?
featureCounts ATAC-seq
5.6 years ago by Lucy ▴ 140
0
votes
4
replies
1.7k
views
When using MACS2 with -f BAM, it is possible to have a shift other than 0?
macs2 macs
updated 5.6 years ago by 20 • written 5.7 years ago by ▴ 140
16
votes
12
replies
14k
views
FRIP score ATAC-seq
ATAC-seq FRIP
updated 5.6 years ago by ▴ 20 • written 5.6 years ago by ▴ 140
3
votes
4
replies
2.4k
views
Determine peak summits after IDR analysis
macs2 idr peak summits
updated 5.6 years ago by 35k • written 5.6 years ago by ▴ 140
0
votes
1
reply
1.1k
views
Should --very-sensitive be combined with -no-1mm-upfront?
bowtie2 bowtie
updated 5.7 years ago by 104k • written 5.7 years ago by ▴ 140
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