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412
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How to speed up pileup from Rsamtools?
Rsamtools pileup
11 months ago alexandr.gopanenko ▴ 50
1
vote
0
replies
581
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Over Representation Analysis using PFAM/InterPro database
PFAM.db clusterProfiler
17 months ago alexandr.gopanenko ▴ 50
0
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0
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2.2k
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Comment: Comment: fgsea usage question - what gene set to use?
3.1 years ago alexandr.gopanenko ▴ 50
2
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2
replies
2.2k
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fgsea usage question - what gene set to use?
fgsea
3.1 years ago alexandr.gopanenko ▴ 50
0
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0
replies
985
views
Comment: Comment: ribosomeProfilingQC - countReads function - is it possible to consider library
3.1 years ago alexandr.gopanenko ▴ 50
1
vote
4
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985
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ribosomeProfilingQC - countReads function - is it possible to consider library type - non-stranded, forward-stranded or rev-stransded?
ribosomeProfilingQC countReads
3.1 years ago alexandr.gopanenko ▴ 50
0
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0
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985
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Comment: Comment: ribosomeProfilingQC - countReads function - is it possible to consider library
3.1 years ago alexandr.gopanenko ▴ 50
0
votes
1
reply
924
views
DESeq2 - shrunken LFC calculation
apeglm DESeq2
updated 3.3 years ago by 41k • written 3.3 years ago by ▴ 50
0
votes
1
reply
611
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Subsetting the bamfile by readlength and extracting the information about distribution the SNV across these reads length
Rsamtools
updated 4.1 years ago by 25k • written 4.1 years ago by ▴ 50
0
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0
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694
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Comment: C: RNA-seq analysis with DESeq2
4.1 years ago alexandr.gopanenko ▴ 50
2
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2
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694
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RNA-seq analysis with DESeq2
deseq2
updated 4.1 years ago by ▴ 270 • written 4.1 years ago by ▴ 50
0
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1
reply
966
views
What tool for reads alignment are prefereble for wavClusteR input bams?
wavcluster
updated 7.4 years ago by ▴ 100 • written 7.4 years ago by ▴ 50
0
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0
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1.9k
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Comment: C: How to extract only mRNA from TxDb object?
7.4 years ago alexandr.gopanenko ▴ 50
4
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3
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1.9k
views
How to extract only mRNA from TxDb object?
genomicfeatures
updated 21 months ago by ▴ 40 • written 7.5 years ago by ▴ 50
0
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0
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2.2k
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Comment: C: How to combine replicates creating heatmap?
7.5 years ago alexandr.gopanenko ▴ 50
1
vote
3
replies
2.2k
views
How to combine replicates creating heatmap?
deseq2 edgeR heatmap.2
updated 7.5 years ago by 41k • written 7.5 years ago by ▴ 50
0
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0
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1.2k
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Comment: C: Analysis of Ribo-seq with poly(A) mRNA RNA-seq
7.5 years ago alexandr.gopanenko ▴ 50
2
votes
2
replies
1.2k
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Analysis of Ribo-seq with poly(A) mRNA RNA-seq
deseq2 genomicfeatures genomicalignments
updated 7.5 years ago by 41k • written 7.5 years ago by ▴ 50
0
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0
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2.0k
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Comment: C: Problem with systemPipeR package: run_edgeR or run_DESeq2 functions don't work
7.5 years ago alexandr.gopanenko ▴ 50
1
vote
2
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2.0k
views
Problem with systemPipeR package: run_edgeR or run_DESeq2 functions don't work
systempiper run_edgeR
updated 7.5 years ago by ★ 1.7k • written 7.5 years ago by ▴ 50
0
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0
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856
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Comment: C: How to extract transcripts from Txdb with length >100
7.5 years ago alexandr.gopanenko ▴ 50
4
votes
2
replies
856
views
How to extract transcripts from Txdb with length >100
genomicfeatures rtracklayer
updated 7.5 years ago by 25k • written 7.5 years ago by ▴ 50
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