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0
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5.6k
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Answer:
Answer: How to obtain distinct/uniqe rows from GenomicRanges object
5 months ago by
jon.klonowski
▴ 150
0
votes
0
replies
5.6k
views
Comment:
Comment: How to obtain distinct/uniqe rows from GenomicRanges object
5 months ago by
jon.klonowski
▴ 150
0
votes
0
replies
697
views
Comment:
Comment: Mapping Mutations, Protein Domains, Exon structure on a Protein Figure/Visualiza
7 months ago by
jon.klonowski
▴ 150
1
vote
3
replies
697
views
Mapping Mutations, Protein Domains, Exon structure on a Protein Figure/Visualization with annoations
mutation
protein
domain
structure
7 months ago by
jon.klonowski
▴ 150
0
votes
0
replies
1.1k
views
Comment:
Comment: Sample Level Filtering During GATK Germline Short Variant Discovery
15 months ago by
jon.klonowski
▴ 150
2
votes
3
replies
1.1k
views
Sample Level Filtering During GATK Germline Short Variant Discovery
Genotyping
genomics
vcf
GATK
germline
15 months ago by
jon.klonowski
▴ 150
1
vote
0
replies
3.4k
views
Comment:
Comment: bcftools query add header
17 months ago by
jon.klonowski
▴ 150
0
votes
1
reply
796
views
Comment:
Comment: Purpose of Seqinfo Circularity Attribute in GenomicRanges Objects
18 months ago by
jon.klonowski
▴ 150
4
votes
4
replies
796
views
Purpose of Seqinfo Circularity Attribute in GenomicRanges Objects
Seqinfo
GenomeInfoDb
Circularity
GenomicRanges
updated 18 months ago by
seidel
11k • written 18 months ago by
jon.klonowski
▴ 150
0
votes
1
reply
27k
views
Answer:
Answer: Best way to query VCF for specific variants
20 months ago by
jon.klonowski
▴ 150
0
votes
0
replies
2.0k
views
Comment:
Comment: biomaRt: Timeout on getBM().
23 months ago by
jon.klonowski
▴ 150
4
votes
5
replies
2.0k
views
biomaRt: Timeout on getBM().
ensembl
biomart
23 months ago by
jon.klonowski
▴ 150
0
votes
1
reply
2.0k
views
Comment:
Comment: biomaRt: Timeout on getBM().
23 months ago by
jon.klonowski
▴ 150
1
vote
0
replies
9.5k
views
Comment:
Comment: biomaRt: Timeout on getBM().
23 months ago by
jon.klonowski
▴ 150
0
votes
0
replies
909
views
VEP verisoning and GRCh37 vs GRCh38. conda/mamba/anaconda
ensembl
genomics
VEP
GRCh37
conda
2.1 years ago by
jon.klonowski
▴ 150
0
votes
0
replies
1.9k
views
Comment:
Comment: Installing VEP in conda
2.1 years ago by
jon.klonowski
▴ 150
3
votes
5
replies
1.5k
views
How to choose output when using a "By" function from a TxDb object; GenomicFeatures R
TxDb
GenomicFeatures
genomics
R
2.4 years ago by
jon.klonowski
▴ 150
2
votes
0
replies
1.5k
views
Answer:
Answer: How to choose output when using a "By" function from a TxDb object; GenomicFeatu
2.4 years ago by
jon.klonowski
▴ 150
0
votes
1
reply
1.5k
views
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
votes
0
replies
497
views
How to check for the most recent EnsDb Hsapiens verison?
genomics
ensembl
ensdb
ensembldb
2.4 years ago by
jon.klonowski
▴ 150
0
votes
0
replies
993
views
Comment:
Comment: Command line VEP "Amino_acid" Output Column Inturperation: AA / AA * AA
2.4 years ago by
jon.klonowski
▴ 150
2
votes
3
replies
993
views
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
votes
0
replies
2.2k
views
Comment:
Comment: How do I split a genomicrange on chromosome and strand?
2.5 years ago by
jon.klonowski
▴ 150
0
votes
0
replies
987
views
Comment:
Comment: how do you get an IN-FRAME deletion stop gain variant?
2.5 years ago by
jon.klonowski
▴ 150
1
vote
3
replies
987
views
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
vote
1
reply
987
views
Answer:
Answer: how do you get an IN-FRAME deletion stop gain variant?
2.5 years ago by
jon.klonowski
▴ 150
0
votes
0
replies
665
views
What is a good Standardized Beta/standardized regression coefficient in a genetics study?
regression
genetics
genomics
updated 14 months ago by
Ram
44k • written 2.8 years ago by
jon.klonowski
▴ 150
0
votes
0
replies
16k
views
Comment:
Comment: Pararellization in GATK 4
3.0 years ago by
jon.klonowski
▴ 150
0
votes
1
reply
1.2k
views
gnomAD AF = 0 vs gnomAD AF = NA (gnomad V2)
annontation
rare
genomics
variant
gnomad
3.1 years ago by
jon.klonowski
▴ 150
0
votes
0
replies
1.2k
views
Answer:
Answer: gnomAD AF = 0 vs gnomAD AF = NA (gnomad V2)
3.1 years ago by
jon.klonowski
▴ 150
1
vote
0
replies
1.0k
views
Answer:
Answer: Merged Reference Panel using WES data
3.1 years ago by
jon.klonowski
▴ 150
0
votes
0
replies
1.2k
views
Comment:
Comment: gnomAD reports variants with "NA" allele count and allele frequency
3.1 years ago by
jon.klonowski
▴ 150
0
votes
0
replies
741
views
UCSC parameters for converting between human genome builds
genomics
bed
ucsc
genotyping
3.2 years ago by
jon.klonowski
▴ 150
0
votes
0
replies
494
views
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
votes
1
reply
4.9k
views
Comment:
C: Version history and design files for exome kits from Agilent, Roche(Nimblegen),
3.3 years ago by
jon.klonowski
▴ 150
0
votes
1
reply
4.9k
views
Comment:
A: Version history and design files for exome kits from Agilent, Roche(Nimblegen),
3.3 years ago by
jon.klonowski
▴ 150
0
votes
0
replies
471
views
Multiple Sequencing Platforms, One Interval File?
WES
sequencing
GATK
3.3 years ago by
jon.klonowski
▴ 150
1
vote
1
reply
1.1k
views
Considerations when merging a gVCF with a VCF?
vcf
bcftools
gvcf
gatk
WES
updated 3.5 years ago by
kreenaijuriya
• 0 • written 3.5 years ago by
jon.klonowski
▴ 150
0
votes
0
replies
1.6k
views
Comment:
C: plink2: no file/directory libgfortran, search has found libgfortran
3.5 years ago by
jon.klonowski
▴ 150
0
votes
0
replies
1.6k
views
Comment:
C: plink2: no file/directory libgfortran, search has found libgfortran
3.5 years ago by
jon.klonowski
▴ 150
1
vote
4
replies
1.6k
views
plink2: no file/directory libgfortran, search has found libgfortran
plink
genetics
vcf
sequencing
WES
updated 3.5 years ago by
Mensur Dlakic
★ 27k • written 3.5 years ago by
jon.klonowski
▴ 150
0
votes
1
reply
2.3k
views
Comment:
A: join vcf file with annotations file?
3.5 years ago by
jon.klonowski
▴ 150
0
votes
2
replies
770
views
Gene Location File - One Gene One Genomic Interval
genomics
genome
sequencing
SNP
burden
3.5 years ago by
jon.klonowski
▴ 150
0
votes
0
replies
770
views
Answer:
A: Gene Location File - One Gene One Genomic Interval
3.5 years ago by
jon.klonowski
▴ 150
0
votes
0
replies
4.4k
views
Comment:
C: Downloadable File With Gene Locations
3.5 years ago by
jon.klonowski
▴ 150
0
votes
2
replies
2.5k
views
gatk SelectVariants odd behavior
gatk
selectvariants
vcf
filtering
SNP
updated 4.6 years ago by
cricgpu
• 0 • written 5.2 years ago by
jon.klonowski
▴ 150
8
votes
10
replies
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
Morris_Chair
▴ 360 • written 4.9 years ago by
jon.klonowski
▴ 150
1
vote
1
reply
2.3k
views
Comment:
C: BCF Tools Filter on 1000Genomes Annotation
updated 5.1 years ago by
finswimmer
16k • written 5.2 years ago by
jon.klonowski
▴ 150
0
votes
1
reply
2.3k
views
Comment:
C: BCF Tools Filter on 1000Genomes Annotation
updated 5.1 years ago by
finswimmer
16k • written 5.2 years ago by
jon.klonowski
▴ 150
0
votes
0
replies
1.4k
views
Comment:
C: BCFTools Query: Avoid grouping Alt Alleles
5.2 years ago by
jon.klonowski
▴ 150
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