User: Jimbou

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Jimbou820
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820
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Location:
Germany
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2 weeks, 1 day ago
Joined:
7 years ago
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Posts by Jimbou

<prev • 82 results • page 1 of 9 • next >
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Answer: A: Finding overlaps between GRanges objects
... No need for GenomicRanges objects. Try package `valr` which depends a lot on `tidyverse` library(tidyverse) library(valr) # transform example data from above to data.frame and add required column `"chrom"` gr1 <- as.data.frame(gr1) %>% mutate(chrom = "chr1") %> ...
written 10 weeks ago by Jimbou820
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Answer: A: manhattan plot for different color in R
... You can try my R package which is based on ggplot2 [here](https://github.com/roman-tremmel/ggfastman) Then, try facets: library(ggfastman) library(tidyverse) data("gwas_data") gwas_data %>% mutate(pvalue = runif(n(),min = 0, max = 1), ...
written 12 weeks ago by Jimbou820
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Comment: C: Plot GWAS p value distribution for multiple traits
... why do you think a qq plot is not good enough? You can try a manhattan plot as well. ...
written 3 months ago by Jimbou820
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Answer: A: updating SNP names in VCF file
... you can also use SnpSift from the SnpEff package http://snpeff.sourceforge.net/SnpSift.html#annotate java -jar SnpSift.jar annotate dbSnp132.vcf input.vcf > output_annotated.vcf check ftp://ftp.ncbi.nih.gov/snp/organisms/ for other dbSNP builds ...
written 7 months ago by Jimbou820
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Comment: C: Partial or complete overlap of two genomic ranges
... check the `valr` package ...
written 8 months ago by Jimbou820
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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 8 months ago by Jimbou820
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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 10 months ago by Jimbou820
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Comment: C: how to find haplotype of SNPs
... try haplo.stat in R? ...
written 11 months ago by Jimbou820
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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 11 months ago by Jimbou820 • updated 11 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 15 months ago by Jimbou820

Latest awards to Jimbou

Appreciated 5 weeks ago, created a post with more than 5 votes. For A: Aggregate multiple rows based on common values in given columns in R
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For C: merge two data frame with different length
Scholar 7 weeks ago, created an answer that has been accepted. For A: R programming: genotype concordance
Popular Question 7 months ago, created a question with more than 1,000 views. For Comparison of sequence homolgy of two genes
Scholar 7 months ago, created an answer that has been accepted. For A: R programming: genotype concordance
Scholar 7 months ago, created an answer that has been accepted. For A: R programming: genotype concordance
Popular Question 8 months ago, created a question with more than 1,000 views. For Comparison of sequence homolgy of two genes
Teacher 10 months ago, created an answer with at least 3 up-votes. For C: merge two data frame with different length
Teacher 14 months ago, created an answer with at least 3 up-votes. For C: merge two data frame with different length
Scholar 20 months ago, created an answer that has been accepted. For A: Gviz (Bioconductor/R) ordering of groups in AnnotationTrack
Epic Question 24 months ago, created a question with more than 10,000 views. For TCGA Segement Mean, GISTIC and CNVs
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Comparison of sequence homolgy of two genes
Great Question 2.7 years ago, created a question with more than 5,000 views. For TCGA Segement Mean, GISTIC and CNVs
Good Answer 2.9 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 3.1 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 3.1 years ago, asked a question that was upvoted at least 5 times. For TCGA Segement Mean, GISTIC and CNVs
Teacher 3.4 years ago, created an answer with at least 3 up-votes. For C: merge two data frame with different length
Great Question 3.5 years ago, created a question with more than 5,000 views. For TCGA Segement Mean, GISTIC and CNVs
Supporter 3.5 years ago, voted at least 25 times.
Good Question 4.4 years ago, asked a question that was upvoted at least 5 times. For Genome Coordinates Between Assemblies: Liftover A Snp Array
Great Question 4.4 years ago, created a question with more than 5,000 views. For TCGA Segement Mean, GISTIC and CNVs
Popular Question 4.4 years ago, created a question with more than 1,000 views. For TCGA Segement Mean, GISTIC and CNVs
Student 4.4 years ago, asked a question with at least 3 up-votes. For TCGA Segement Mean, GISTIC and CNVs
Popular Question 4.7 years ago, created a question with more than 1,000 views. For TCGA Segement Mean, GISTIC and CNVs
Appreciated 5.0 years ago, created a post with more than 5 votes. For A: Aggregate multiple rows based on common values in given columns in R

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