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211
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Transcript feature coverage with coverage of each feature shown like e.g. UTR's CDS, exons etc
rseqc transcript-featurecoverage gene_body_coverage
3 months ago by Saad Khan ▴ 420
5
votes
3
replies
2.1k
views
How to visualize the co-occupancy of one set of genomic data with another.
TFBS methylation co-occupancy Histone
updated 14 months ago by 39k • written 8.6 years ago by ▴ 420
0
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1
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2.5k
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Comment: C: Normalization scheme to use for upstream sequences read count in (Chip-seq histo
updated 3.4 years ago by 39k • written 7.3 years ago by ▴ 420
0
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0
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2.4k
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Comment: C: chain files for mouse mm9 to ensembl version 75
updated 3.4 years ago by 39k • written 7.4 years ago by ▴ 420
0
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1
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2.4k
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Comment: C: chain files for mouse mm9 to ensembl version 75
updated 3.4 years ago by 39k • written 7.4 years ago by ▴ 420
0
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0
replies
845
views
Is it possible to introduce mutations (SNV/Indels) in precomputed lastz alignments
FastaAlternateReferenceMaker lastz pairwise_align
3.8 years ago by Saad Khan ▴ 420
0
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0
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3.5k
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Comment: C: how to get all gc/cpg positions in the latest human genome (gencode hg19)
updated 4.0 years ago by 39k • written 8.9 years ago by ▴ 420
0
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0
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3.5k
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Comment: C: how to get all gc/cpg positions in the latest human genome (gencode hg19)
updated 4.0 years ago by 39k • written 8.9 years ago by ▴ 420
0
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0
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995
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Comment: C: Merging variant calls of whole exome and RNA-seq
4.2 years ago by Saad Khan ▴ 420
0
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2
replies
995
views
Merging variant calls of whole exome and RNA-seq
GATK RNA-seq variants indels SNVs
updated 4.2 years ago by ▴ 220 • written 4.2 years ago by ▴ 420
0
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2
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1.3k
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Comment: C: Negative dataset selection
4.3 years ago by Saad Khan ▴ 420
1
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4
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1.3k
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Negative dataset selection
machine-learning sequence classification RNA DNA
4.3 years ago by Saad Khan ▴ 420
0
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1
reply
3.4k
views
How to do gene enrichment analysis using only GO-slim terma
GO-slim gene enrichment
updated 4.5 years ago by ▴ 90 • written 6.7 years ago by ▴ 420
0
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1
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1.1k
views
Which tool to use to get all citations of a pmid paper?
entrez eutils efetch
updated 4.7 years ago by 34k • written 4.7 years ago by ▴ 420
0
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0
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1.7k
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Comment: C: What are some of the state of the art approaches for prediction of origins of re
updated 4.7 years ago by 39k • written 7.3 years ago by ▴ 420
0
votes
0
replies
957
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Tool for generating Physicochemical properties from sequence of RNA/DNA
mRNA DNA Sequence physicochemical properties
5.1 years ago by Saad Khan ▴ 420
0
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0
replies
1.4k
views
Comment: C: Most genes with entrez id in KEGG database don't have a pathway assigned. Is the
5.2 years ago by Saad Khan ▴ 420
0
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3
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1.4k
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Most genes with entrez id in KEGG database don't have a pathway assigned. Is there a tool already available that uses textmining to assign pathway to…
kegg reactome keggrest
5.2 years ago by Saad Khan ▴ 420
0
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6
replies
4.0k
views
Where all can I find Histone Modification data for certain Human and Mouse cells
histone-modification Human Mouse
updated 2.1 years ago by 39k • written 8.6 years ago by ▴ 420
1
vote
13
replies
2.5k
views
Normalization scheme to use for upstream sequences read count in (Chip-seq histones)
normalization RPKM histones
updated 10 months ago by 39k • written 7.4 years ago by ▴ 420
0
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0
replies
1.2k
views
Comment: C: Protein protein interaction conservation scores
6.2 years ago by Saad Khan ▴ 420
0
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2
replies
1.2k
views
Protein protein interaction conservation scores
PPI conservation scores
6.2 years ago by Saad Khan ▴ 420
0
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1
reply
1.4k
views
Cancer data for histone Chip-seq in human and mouse
cancer chip-seq histone GEO SRA
updated 6.2 years ago by ▴ 60 • written 6.2 years ago by ▴ 420
2
votes
4
replies
2.1k
views
Clustering using codon usage similarity
codon usage clustering
updated 6.5 years ago by 20 • written 6.7 years ago by ▴ 420
0
votes
0
replies
1.5k
views
What does mm10-minimal mean in encode files
metadata encode mm10-minimal
6.6 years ago by Saad Khan ▴ 420
0
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0
replies
2.1k
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Comment: C: Clustering using codon usage similarity
6.7 years ago by Saad Khan ▴ 420
0
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0
replies
1.1k
views
Segment genes into functional subsets
gene ontology functions subsets
6.8 years ago by Saad Khan ▴ 420
1
vote
0
replies
1.6k
views
Top 20% expressed orthologus genes in two species
RNA-seq RPKM FPKM
updated 6.8 years ago by 20 • written 7.0 years ago by ▴ 420
1
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0
replies
1.5k
views
Comparing features of high expression genes vs low expression genes in two species
rpkm gene expression RNA-Seq
7.0 years ago by Saad Khan ▴ 420
0
votes
2
replies
2.5k
views
Comment: C: NIH roadmap epigenomics data Bam files
7.0 years ago by Saad Khan ▴ 420
1
vote
4
replies
2.5k
views
NIH roadmap epigenomics data Bam files
NIH roadmap-epigenomics
updated 7.0 years ago by ★ 5.2k • written 7.0 years ago by ▴ 420
1
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0
replies
1.6k
views
Statistically robust approach of assigning presence or absence of Histone peaks
Histone Peaks cross-species orthologus regions
7.2 years ago by Saad Khan ▴ 420
0
votes
2
replies
1.7k
views
What are some of the state of the art approaches for prediction of origins of replication in vertebrates
Machine learning ORiC origin of replication
updated 7.3 years ago by 7.7k • written 7.3 years ago by ▴ 420
0
votes
1
reply
2.5k
views
Comment: Comment: Normalization scheme to use for upstream sequences read count in (Chip-seq histo
updated 11 months ago by 39k • written 7.3 years ago by ▴ 420
0
votes
1
reply
2.5k
views
Comment: C: Normalization scheme to use for upstream sequences read count in (Chip-seq histo
7.3 years ago by Saad Khan ▴ 420
0
votes
1
reply
2.5k
views
Comment: C: Normalization scheme to use for upstream sequences read count in (Chip-seq histo
7.3 years ago by Saad Khan ▴ 420
0
votes
0
replies
2.5k
views
Comment: C: Normalization scheme to use for upstream sequences read count in (Chip-seq histo
7.3 years ago by Saad Khan ▴ 420
0
votes
0
replies
2.5k
views
Comment: C: Normalization scheme to use for upstream sequences read count in (Chip-seq histo
7.3 years ago by Saad Khan ▴ 420
0
votes
1
reply
2.5k
views
Comment: C: Normalization scheme to use for upstream sequences read count in (Chip-seq histo
7.3 years ago by Saad Khan ▴ 420
0
votes
6
replies
2.4k
views
chain files for mouse mm9 to ensembl version 75
bed liftover ucsc chain-files ensembl
updated 10 months ago by 39k • written 7.4 years ago by ▴ 420
0
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1
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2.4k
views
Comment: C: chain files for mouse mm9 to ensembl version 75
7.4 years ago by Saad Khan ▴ 420
0
votes
0
replies
3.1k
views
Comment: Comment: liftover chain files for mouse mm9 to ensembl version 75
updated 10 months ago by 39k • written 7.4 years ago by ▴ 420
0
votes
4
replies
3.1k
views
liftover chain files for mouse mm9 to ensembl version 75
lift-over chain-file mm9 ensembl
updated 10 months ago by 39k • written 7.4 years ago by ▴ 420
2
votes
0
replies
25k
views
Comment: C: What is the difference between narrow peak, Broad peak and a gapped peak of a c
7.6 years ago by Saad Khan ▴ 420
0
votes
1
reply
25k
views
Comment: C: What is the difference between narrow peak, Broad peak and a gapped peak of a c
7.6 years ago by Saad Khan ▴ 420
0
votes
1
reply
3.0k
views
Comment: C: Where are the actual transcription factor binding sites located in the CHIP-seq
7.6 years ago by Saad Khan ▴ 420
5
votes
5
replies
3.0k
views
Where are the actual transcription factor binding sites located in the CHIP-seq peaks
CHIP-seq-peaks MACS peak-calls TFBS
updated 9 months ago by 39k • written 7.6 years ago by ▴ 420
0
votes
1
reply
25k
views
Comment: C: What is the difference between narrow peak, Broad peak and a gapped peak of a c
7.7 years ago by Saad Khan ▴ 420
20
votes
8
replies
25k
views
What is the difference between narrow peak, Broad peak and a gapped peak of a chip-seq experiment and is it okay to use all of these regions for dow…
peaks broad gapped chip-seq narrow
updated 9 months ago by 39k • written 7.7 years ago by ▴ 420
1
vote
4
replies
2.0k
views
Can something like this be done in IGV or other better browsers
coverage ggbio exome SNV
updated 9 months ago by 39k • written 7.7 years ago by ▴ 420
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