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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
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3.4k
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Answer: A: Does Harmony batch correction for scRNA-seq require the same populations to be p
4.1 years ago by Lucy ▴ 140
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3
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3.4k
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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
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2
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2.1k
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Clustering resolution single-cell RNA-seq
scRNA-seq RNA-seq clustering single-cell
updated 6 weeks ago by ▴ 170 • written 4.1 years ago by ▴ 140
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0
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2.0k
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Downsampling reads vs. Seurat normalisation
RNA-Seq scRNA-seq DropletUtils single-cell
4.1 years ago by Lucy ▴ 140
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0
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6.4k
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Comment: C: Harmony batch correction vs. regressing out donor effect in Seurat
4.1 years ago by Lucy ▴ 140
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1
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6.4k
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Comment: C: Harmony batch correction vs. regressing out donor effect in Seurat
4.1 years ago by Lucy ▴ 140
9
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10
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6.4k
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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
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0
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1.3k
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Comment: C: ATAC-seq transcription factor binding prediction
4.1 years ago by Lucy ▴ 140
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0
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1.0k
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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
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4
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1.3k
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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
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1
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2.9k
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Homer annotatePeaks.pl custom GTF
Homer ATAC-seq GTF
4.8 years ago by Lucy ▴ 140
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1
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2.4k
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Comment: C: Aligning RNA-seq and ATAC-seq gene annotations
4.9 years ago by Lucy ▴ 140
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4
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2.4k
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Aligning RNA-seq and ATAC-seq gene annotations
Homer RNA-seq ATAC-seq Gene annotation
4.9 years ago by Lucy ▴ 140
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0
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13k
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Comment: C: FRIP score ATAC-seq
4.9 years ago by Lucy ▴ 140
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0
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810
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CENTIPEDE - values from fitCentipede
centipede R ATAC-seq
updated 4.9 years ago by 20 • written 5.1 years ago by ▴ 140
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3.8k
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Comment: A: HOMER de novo motif enrichment
5.0 years ago by Lucy ▴ 140
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2
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3.8k
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HOMER de novo motif enrichment
HOMER Motif enrichment
5.0 years ago by Lucy ▴ 140
0
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0
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689
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Error with fitCentipede
Centipede R
5.1 years ago by Lucy ▴ 140
0
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0
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1.5k
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featureCounts - how to make ATAC-seq cut-sites BAM
featureCounts bed
updated 8 months ago by 41k • written 5.2 years ago by ▴ 140
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0
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2.2k
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Comment: C: featureCounts allowMultiOverlap - fractional or not?
5.2 years ago by Lucy ▴ 140
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0
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1.6k
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Comment: C: When using MACS2 with -f BAM, it is possible to have a shift other than 0?
5.2 years ago by Lucy ▴ 140
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2
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2.2k
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featureCounts allowMultiOverlap - fractional or not?
featureCounts ATAC-seq
5.2 years ago by Lucy ▴ 140
0
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4
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1.6k
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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
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13k
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FRIP score ATAC-seq
ATAC-seq FRIP
updated 5.2 years ago by ▴ 20 • written 5.2 years ago by ▴ 140
0
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1
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2.2k
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Comment: C: Determine peak summits after IDR analysis
5.2 years ago by Lucy ▴ 140
3
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4
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2.2k
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Determine peak summits after IDR analysis
macs2 idr peak summits
updated 5.2 years ago by 35k • written 5.2 years ago by ▴ 140
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0
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2.2k
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Comment: C: Determine peak summits after IDR analysis
5.2 years ago by Lucy ▴ 140
0
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1
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1.6k
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Comment: C: When using MACS2 with -f BAM, it is possible to have a shift other than 0?
5.2 years ago by Lucy ▴ 140
0
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0
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35k
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Comment: C: ATAC-seq peak calling with MACS
5.3 years ago by Lucy ▴ 140
0
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1
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1.7k
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Comment: C: shift direction in ATAC/DNase data?
5.3 years ago by Lucy ▴ 140
0
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1
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1.0k
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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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