User: cpad0112

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cpad01127.7k
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Posts by cpad0112

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Comment: C: Need help with R script to edit x-axis of snp density plot
... some example data would help @OP ...
written 20 hours ago by cpad01127.7k
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Comment: C: Reference is deletion and negative genomic position label
... querying b151 dbsnp vcf didn't yield any results. $ tabix ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606_b151_GRCh38p7/VCF/All_20180418.vcf.gz 1:45194429-45194431 ...
written 20 hours ago by cpad01127.7k
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Comment: C: multiple fasta conversion using java
... All OP's fasta files seem to start with `xa` (from the description in OP). To be safe, it may be better for OP to restrict the code either with `x` or `xa` (some thing like `ls x*.txt` or `ls xa*.txt`) ...
written 1 day ago by cpad01127.7k
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Comment: C: How to fix the error in meshes package?
... https://www.biostars.org/u/45426/ 39 entry in geneID1 seems to be problematic and try removing it, Try running for 39 and it will fail: geneSim(geneID1=geneID1[39], geneID2 = geneID2, measure ="Resnik", combine = "BMA",semData=meshdata) and geneSim(geneID1=geneID1[40], geneID2 = geneID2, ...
written 1 day ago by cpad01127.7k
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Comment: C: How can I implement RY-coding to every third nucleotide in an alignment using co
... https://gist.github.com/cpad0112/22e551eaa6a6508fc9b6345e9aac8162 Fasta files must be flattened (`seqkit seq -w 0 input fasta` for flattening fasta) ...
written 1 day ago by cpad01127.7k
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Comment: C: Convert GDCResults object (nested lists) to a human readable data frame
... GenomicDataCommons v1.2.0 has `as.data.frame.GDCResults` function. Try `help(package = GenomicDataCommons)` to see the functions. I think there is basic functionality issue. Try `GenomicDataCommons::status()` ...
written 1 day ago by cpad01127.7k
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Comment: C: Convert GDCResults object (nested lists) to a human readable data frame
... @OP: Try this. tagging the author: https://www.biostars.org/u/287/ library("GenomicDataCommons") test = cases() %>% filter(~ project.project_id=='TCGA-CHOL') %>% results(n=10) %>% as.data.frame()) Unfortunately, I am not able to connect to gdc server. ...
written 1 day ago by cpad01127.7k
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Comment: C: Convert GDCResults object (nested lists) to a human readable data frame
... https://www.rdocumentation.org/packages/GenomicDataCommons/versions/1.3.1/topics/as.data.frame.GDCResults copy/pasted from webpage: expands = c("diagnoses","diagnoses.treatments","annotations", "demographic","exposures") head(cases() %>% expand(expands) %>% results() %>% as.da ...
written 1 day ago by cpad01127.7k
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Answer: A: If a string appears twice in column 1, select the higher value in column 2
... with [datamash][1]. Added an extra row to check for sorting. $ sed 's/%//g' test.txt | datamash -sfg 1 max 4| cut --complement -f5 | sed 's/$/%/g' sample1 200000 120000 90% sample2 200000 190000 95% $ cat test.txt sample1 200000 120000 60% sample1 200000 115000 57.5% ...
written 2 days ago by cpad01127.7k
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Answer: C: a problem with read ped file in plink?
... echo "AA GG TG CC" | sed 's/\s//g;s/./& /g' or echo "AA GG TG CC" | sed 's/./& /g' | tr -s " " A A G G T G C C ...
written 3 days ago by cpad01127.7k

Latest awards to cpad0112

Scholar 1 day ago, created an answer that has been accepted. For A: .fai file generation for a vcf file containing snps
Teacher 3 days ago, created an answer with at least 3 up-votes. For A: convert SNP calls to amino acid change
Commentator 3 days ago, created a comment with at least 3 up-votes. For C: Problem installing Rgraphviz in R
Good Answer 4 days ago, created an answer that was upvoted at least 5 times. For A: How to make a clear box plot or whatever beautiful for showing the ratio of two
Commentator 6 days ago, created a comment with at least 3 up-votes. For C: Problem installing Rgraphviz in R
Voter 7 days ago, voted more than 100 times.
Scholar 11 days ago, created an answer that has been accepted. For A: .fai file generation for a vcf file containing snps
Teacher 11 days ago, created an answer with at least 3 up-votes. For A: convert SNP calls to amino acid change
Teacher 13 days ago, created an answer with at least 3 up-votes. For A: convert SNP calls to amino acid change
Appreciated 13 days ago, created a post with more than 5 votes. For C: can someone read this result to me
Scholar 13 days ago, created an answer that has been accepted. For A: .fai file generation for a vcf file containing snps
Scholar 15 days ago, created an answer that has been accepted. For A: .fai file generation for a vcf file containing snps
Teacher 16 days ago, created an answer with at least 3 up-votes. For A: convert SNP calls to amino acid change
Scholar 16 days ago, created an answer that has been accepted. For A: .fai file generation for a vcf file containing snps
Teacher 19 days ago, created an answer with at least 3 up-votes. For A: convert SNP calls to amino acid change
Scholar 20 days ago, created an answer that has been accepted. For A: .fai file generation for a vcf file containing snps
Scholar 22 days ago, created an answer that has been accepted. For A: .fai file generation for a vcf file containing snps
Scholar 25 days ago, created an answer that has been accepted. For A: .fai file generation for a vcf file containing snps
Teacher 25 days ago, created an answer with at least 3 up-votes. For A: convert SNP calls to amino acid change
Scholar 25 days ago, created an answer that has been accepted. For A: .fai file generation for a vcf file containing snps
Commentator 25 days ago, created a comment with at least 3 up-votes. For C: Problem installing Rgraphviz in R
Scholar 25 days ago, created an answer that has been accepted. For A: .fai file generation for a vcf file containing snps
Scholar 5 weeks ago, created an answer that has been accepted. For A: .fai file generation for a vcf file containing snps
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: convert SNP calls to amino acid change
Scholar 5 weeks ago, created an answer that has been accepted. For A: .fai file generation for a vcf file containing snps

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