User: Jimbou

gravatar for Jimbou
Jimbou730
Reputation:
730
Status:
Trusted
Location:
Germany
Last seen:
3 days, 19 hours ago
Joined:
6 years, 4 months ago
Email:
r************@gmail.com

about me

Posts by Jimbou

<prev • 78 results • page 1 of 8 • next >
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Comment: C: Partial or complete overlap of two genomic ranges
... check the `valr` package ...
written 4 days ago by Jimbou730
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Comment: C: Snptest association test results OR and BETA difference
... I'm pretty sure that the calculation for both differs. But unfortunatly I can't figure it out yet. ...
written 16 days ago by Jimbou730
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Comment: C: Snpsift to filter a number of genes
... old questioun, but I need exactly the same and get it to work using `ANN[*].GENE ` ...
written 9 weeks ago by Jimbou730
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Comment: C: how to find haplotype of SNPs
... try haplo.stat in R? ...
written 3 months ago by Jimbou730
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SnpSift Annotate replace ID column
... Is it possible to use [SnpSift Annotate][1] function to replace values already existing in the ID column? java -jar SnpSift.jar annotate -id 00-common_all.vcf.gz my_sample.vcf #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 22 16050435 22:16050435 ...
snpsift annotation snps snpeff written 3 months ago by Jimbou730 • updated 3 months ago by Nicholas Mancuso70
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Comment: C: Pathway Enrichment Analysis, Clustering and Scoring with pathfindR
... So the logFCs are only used to provide a direction of the expression change e.g. separate upregulated and down-regulated genes? I'm asking since I used spearman rhos instead of the fold changes which works very well by the way ;) ...
written 7 months ago by Jimbou730
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Comment: C: Annotate genomic positions with dbSNP rsIds
... Thanks a lot. Started as you recommended, but switched to bcftools in the end. ...
written 13 months ago by Jimbou730
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Answer: A: Annotate genomic positions with dbSNP rsIds
... I will write down my solution as an answer for documentation purposes. I started as Pirerre recommended, but then I used bcftools instead of GATK. First, I created a header .txt file for the custom vcf file ##fileformat=VCFv4.0 ##fileDate=09052019 ##source=allchr_allvsall_sex_adjuste ...
written 13 months ago by Jimbou730
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Annotate genomic positions with dbSNP rsIds
... Although I already found some ways to annotate genomic positions with rsIDs using e.g. UCSC table browser, I'm not happy with that since I want a one-in-all linux script taking also strand issues (flipped alleles A-T vs- T-A or switched reference alleles) into account. What I have: chr posit ...
dbsnp position rsid chr tool written 13 months ago by Jimbou730
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Difference of CN probes and SNP probes on genotyping microchip arrays
... Is there a difference between copy number (CN) probes compared to SNP probes on SNP arrays such as the Affymetrix 6.0 SNP array? Physically there could be longer oligos for the CN probes? Do you have to analyse both probes differently, e.g. do tools such as PennCNV use both probes for CNV detectio ...
array affymetrix snp cnv written 2.9 years ago by Jimbou730 • updated 2.9 years ago by Biostar ♦♦ 20

Latest awards to Jimbou

Popular Question 16 days ago, created a question with more than 1,000 views. For Comparison of sequence homolgy of two genes
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For C: merge two data frame with different length
Teacher 7 months ago, created an answer with at least 3 up-votes. For C: merge two data frame with different length
Scholar 13 months ago, created an answer that has been accepted. For A: Gviz (Bioconductor/R) ordering of groups in AnnotationTrack
Epic Question 16 months ago, created a question with more than 10,000 views. For TCGA Segement Mean, GISTIC and CNVs
Popular Question 21 months ago, created a question with more than 1,000 views. For Comparison of sequence homolgy of two genes
Great Question 2.1 years ago, created a question with more than 5,000 views. For TCGA Segement Mean, GISTIC and CNVs
Good Answer 2.2 years ago, created an answer that was upvoted at least 5 times. For A: Aggregate multiple rows based on common values in given columns in R
Appreciated 2.5 years ago, created a post with more than 5 votes. For A: Aggregate multiple rows based on common values in given columns in R
Good Question 2.5 years ago, asked a question that was upvoted at least 5 times. For TCGA Segement Mean, GISTIC and CNVs
Teacher 2.7 years ago, created an answer with at least 3 up-votes. For C: merge two data frame with different length
Great Question 2.8 years ago, created a question with more than 5,000 views. For TCGA Segement Mean, GISTIC and CNVs
Supporter 2.9 years ago, voted at least 25 times.
Great Question 3.7 years ago, created a question with more than 5,000 views. For TCGA Segement Mean, GISTIC and CNVs
Good Question 3.7 years ago, asked a question that was upvoted at least 5 times. For Genome Coordinates Between Assemblies: Liftover A Snp Array
Popular Question 3.7 years ago, created a question with more than 1,000 views. For TCGA Segement Mean, GISTIC and CNVs
Student 3.7 years ago, asked a question with at least 3 up-votes. For TCGA Segement Mean, GISTIC and CNVs
Popular Question 4.0 years ago, created a question with more than 1,000 views. For TCGA Segement Mean, GISTIC and CNVs
Appreciated 4.3 years ago, created a post with more than 5 votes. For A: Aggregate multiple rows based on common values in given columns in R
Popular Question 4.5 years ago, created a question with more than 1,000 views. For TCGA Segement Mean, GISTIC and CNVs
Scholar 4.5 years ago, created an answer that has been accepted. For A: R programming: genotype concordance
Appreciated 4.5 years ago, created a post with more than 5 votes. For A: Aggregate multiple rows based on common values in given columns in R
Scholar 4.5 years ago, created an answer that has been accepted. For A: R programming: genotype concordance
Scholar 4.5 years ago, created an answer that has been accepted. For A: R programming: genotype concordance
Teacher 4.5 years ago, created an answer with at least 3 up-votes. For C: merge two data frame with different length

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