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Answer: Answer: How to obtain distinct/uniqe rows from GenomicRanges object
5 months ago by jon.klonowski ▴ 150
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5.5k
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Comment: Comment: How to obtain distinct/uniqe rows from GenomicRanges object
5 months ago by jon.klonowski ▴ 150
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0
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686
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Comment: Comment: Mapping Mutations, Protein Domains, Exon structure on a Protein Figure/Visualiza
6 months ago by jon.klonowski ▴ 150
1
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3
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686
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Mapping Mutations, Protein Domains, Exon structure on a Protein Figure/Visualization with annoations
mutation protein domain structure
6 months ago by jon.klonowski ▴ 150
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1.0k
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Comment: Comment: Sample Level Filtering During GATK Germline Short Variant Discovery
14 months ago by jon.klonowski ▴ 150
2
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3
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1.0k
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Sample Level Filtering During GATK Germline Short Variant Discovery
Genotyping genomics vcf GATK germline
14 months ago by jon.klonowski ▴ 150
1
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3.3k
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Comment: Comment: bcftools query add header
16 months ago by jon.klonowski ▴ 150
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1
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777
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Comment: Comment: Purpose of Seqinfo Circularity Attribute in GenomicRanges Objects
17 months ago by jon.klonowski ▴ 150
4
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4
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777
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Purpose of Seqinfo Circularity Attribute in GenomicRanges Objects
Seqinfo GenomeInfoDb Circularity GenomicRanges
updated 17 months ago by 11k • written 17 months ago by ▴ 150
0
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1
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27k
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Answer: Answer: Best way to query VCF for specific variants
19 months ago by jon.klonowski ▴ 150
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2.0k
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Comment: Comment: biomaRt: Timeout on getBM().
23 months ago by jon.klonowski ▴ 150
4
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5
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2.0k
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biomaRt: Timeout on getBM().
ensembl biomart
23 months ago by jon.klonowski ▴ 150
0
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1
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2.0k
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Comment: Comment: biomaRt: Timeout on getBM().
23 months ago by jon.klonowski ▴ 150
1
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0
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9.4k
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Comment: Comment: biomaRt: Timeout on getBM().
23 months ago by jon.klonowski ▴ 150
0
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0
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894
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VEP verisoning and GRCh37 vs GRCh38. conda/mamba/anaconda
ensembl genomics VEP GRCh37 conda
2.1 years ago by jon.klonowski ▴ 150
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0
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1.9k
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Comment: Comment: Installing VEP in conda
2.1 years ago by jon.klonowski ▴ 150
3
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5
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1.5k
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How to choose output when using a "By" function from a TxDb object; GenomicFeatures R
TxDb GenomicFeatures genomics R
2.3 years ago by jon.klonowski ▴ 150
2
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0
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1.5k
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Answer: Answer: How to choose output when using a "By" function from a TxDb object; GenomicFeatu
2.3 years ago by jon.klonowski ▴ 150
0
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1
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1.5k
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Comment: Comment: How to choose output when using a "By" function from a TxDb object; GenomicFeatu
2.4 years ago by jon.klonowski ▴ 150
0
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0
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482
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How to check for the most recent EnsDb Hsapiens verison?
genomics ensembl ensdb ensembldb
2.4 years ago by jon.klonowski ▴ 150
0
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0
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979
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Comment: Comment: Command line VEP "Amino_acid" Output Column Inturperation: AA / AA * AA
2.4 years ago by jon.klonowski ▴ 150
2
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3
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979
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Command line VEP "Amino_acid" Output Column Inturperation: AA / AA * AA
VEP ensembl genetics genomics annotation
2.4 years ago by jon.klonowski ▴ 150
0
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0
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2.2k
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Comment: Comment: How do I split a genomicrange on chromosome and strand?
2.5 years ago by jon.klonowski ▴ 150
0
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0
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972
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Comment: Comment: how do you get an IN-FRAME deletion stop gain variant?
2.5 years ago by jon.klonowski ▴ 150
1
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3
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972
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how do you get an IN-FRAME deletion stop gain variant?
genomics annotation ensembl VEP genetics
2.5 years ago by jon.klonowski ▴ 150
1
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1
reply
972
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Answer: Answer: how do you get an IN-FRAME deletion stop gain variant?
2.5 years ago by jon.klonowski ▴ 150
0
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0
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657
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What is a good Standardized Beta/standardized regression coefficient in a genetics study?
regression genetics genomics
updated 14 months ago by 44k • written 2.8 years ago by ▴ 150
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0
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16k
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Comment: Comment: Pararellization in GATK 4
3.0 years ago by jon.klonowski ▴ 150
0
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1
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1.2k
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gnomAD AF = 0 vs gnomAD AF = NA (gnomad V2)
annontation rare genomics variant gnomad
3.1 years ago by jon.klonowski ▴ 150
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0
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1.2k
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Answer: Answer: gnomAD AF = 0 vs gnomAD AF = NA (gnomad V2)
3.1 years ago by jon.klonowski ▴ 150
1
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0
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1000
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Answer: Answer: Merged Reference Panel using WES data
3.1 years ago by jon.klonowski ▴ 150
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0
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1.1k
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Comment: Comment: gnomAD reports variants with "NA" allele count and allele frequency
3.1 years ago by jon.klonowski ▴ 150
0
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0
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737
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UCSC parameters for converting between human genome builds
genomics bed ucsc genotyping
3.1 years ago by jon.klonowski ▴ 150
0
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0
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489
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How important is aligning BAM files to the appropriate design file?
gatk sequencing genomics wes bam
3.2 years ago by jon.klonowski ▴ 150
0
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1
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4.9k
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Comment: C: Version history and design files for exome kits from Agilent, Roche(Nimblegen),
3.2 years ago by jon.klonowski ▴ 150
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1
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4.9k
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Comment: A: Version history and design files for exome kits from Agilent, Roche(Nimblegen),
3.2 years ago by jon.klonowski ▴ 150
0
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0
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467
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Multiple Sequencing Platforms, One Interval File?
WES sequencing GATK
3.2 years ago by jon.klonowski ▴ 150
1
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1
reply
1.1k
views
Considerations when merging a gVCF with a VCF?
vcf bcftools gvcf gatk WES
updated 3.4 years ago by • 0 • written 3.4 years ago by ▴ 150
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0
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1.6k
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Comment: C: plink2: no file/directory libgfortran, search has found libgfortran
3.5 years ago by jon.klonowski ▴ 150
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0
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1.6k
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Comment: C: plink2: no file/directory libgfortran, search has found libgfortran
3.5 years ago by jon.klonowski ▴ 150
1
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4
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1.6k
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plink2: no file/directory libgfortran, search has found libgfortran
plink genetics vcf sequencing WES
updated 3.5 years ago by ★ 27k • written 3.5 years ago by ▴ 150
0
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1
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2.3k
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Comment: A: join vcf file with annotations file?
3.5 years ago by jon.klonowski ▴ 150
0
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2
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763
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Gene Location File - One Gene One Genomic Interval
genomics genome sequencing SNP burden
3.5 years ago by jon.klonowski ▴ 150
0
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0
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763
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Answer: A: Gene Location File - One Gene One Genomic Interval
3.5 years ago by jon.klonowski ▴ 150
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0
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4.3k
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Comment: C: Downloadable File With Gene Locations
3.5 years ago by jon.klonowski ▴ 150
0
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2
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2.5k
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gatk SelectVariants odd behavior
gatk selectvariants vcf filtering SNP
updated 4.5 years ago by • 0 • written 5.1 years ago by ▴ 150
8
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10
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3.5k
views
6 follow
Is Ingenuity Pathway Analysis still relevant for analyzing RNA-seq data?
IPA RNA-Seq NGS dataanalysis
updated 4.9 years ago by ▴ 360 • written 4.9 years ago by ▴ 150
1
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1
reply
2.3k
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Comment: C: BCF Tools Filter on 1000Genomes Annotation
updated 5.1 years ago by 16k • written 5.1 years ago by ▴ 150
0
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1
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2.3k
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Comment: C: BCF Tools Filter on 1000Genomes Annotation
updated 5.1 years ago by 16k • written 5.1 years ago by ▴ 150
0
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0
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1.4k
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Comment: C: BCFTools Query: Avoid grouping Alt Alleles
5.1 years ago by jon.klonowski ▴ 150
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