User: Noushin N

gravatar for Noushin N
Noushin N400
Reputation:
400
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Trusted
Location:
Baltimore, MD
Scholar ID:
Google Scholar Page
Last seen:
1 month ago
Joined:
4 years, 7 months ago
Email:
n**************@gmail.com

Posts by Noushin N

<prev • 78 results • page 1 of 8 • next >
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Answer: A: Remove columns and rows which have only NAs without deleting all the data
... Assuming that you want to remove any rows or columns containing `NA` values, you can try the following approach. x = matrix(seq(49), ncol = 7) x[2,5]= NA x [,1] [,2] [,3] [,4] [,5] [,6] [,7] [1,] 1 8 15 22 29 36 43 [2,] 2 9 16 23 NA 37 ...
written 5 months ago by Noushin N400
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Answer: A: retrieve genomic coordinate on mRNA
... [Transvar webserver][1] can handle this task. As you said, there will likely be multiple hits for each genomic positions. [1]: http://bioinformatics.mdanderson.org/transvarweb/ ...
written 6 months ago by Noushin N400
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Comment: C: B Allele Frequency (VAF) Segmentation Analysis
... If possible, can you show the raw minor allele frequency plot (using scatter plot format of the first figure)? ...
written 10 months ago by Noushin N400
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Comment: C: Where is the BigWig Supplementary Information?
... I checked the supplementary table links on 2 browsers (chrome 56.0 and safari 10.0), and I cannot open them either. ...
written 10 months ago by Noushin N400
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Comment: C: Understanding coverage command
... Probably not the actual reason, but a tempting question here: Can the value of 10 you are reporting possibly be in log2? ...
written 11 months ago by Noushin N400
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Answer: A: is there any R package to measure the efficiency of different exome capture kits
... If you can relax the requirement of being in R, you may want to check out [calculateHsMetrics][1] from Picard. It extracts metrics (including what you mention) from target-capture sequencing experiments and may get the job done. [1]: https://broadinstitute.github.io/picard/picard-metric-definit ...
written 11 months ago by Noushin N400
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Comment: C: How to extract FORMAT information (GT, PG, PI, etc) from each SAMPLE in a vcf fi
... Have you defined your sampleIDs variable before referencing it? Regarding `PG` and `PI` fields, here is a fix that can handle missing values: ``` sample_PG = [record.genotype(sampleID).get('PG') if 'PG' in record.genotype(sampleID) else '.' for sampleID in sampleIDs] sample_PI = [record.genotype( ...
written 12 months ago by Noushin N400
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Comment: C: How to extract FORMAT information (GT, PG, PI, etc) from each SAMPLE in a vcf fi
... Thanks for the tip! I wasn't aware that this syntax is discouraged. ...
written 12 months ago by Noushin N400
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Answer: A: How to extract FORMAT information (GT, PG, PI, etc) from each SAMPLE in a vcf fi
... ### Problem 1 It can be addressed by using python list comprehensions as follows: If you are sure that all samples include `GT` field, you can use: ``` sample_genotypes = [record.genotype(sampleID)['GT'] for sampleID in sampleIDs] ``` ``` print >>output, '\t'.join([contig, pos, ref_allele, ...
written 12 months ago by Noushin N400
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Answer: A: Benjamin Hochberg adjust P-values
... I would like to add a cautionary note about the above answer here, regarding the [nonmonotonocity][1] of q-values (corrected p-values) that would result from the formula. The source code for the p.adjust function in R is here: > BH = { > i <- lp:1L > o <- order( ...
written 13 months ago by Noushin N400

Latest awards to Noushin N

Popular Question 11 weeks ago, created a question with more than 1,000 views. For NGS preprocessing pipleine for ion torrent data
Appreciated 5 months ago, created a post with more than 5 votes. For Somatic mutation calling without matched normal
Scholar 13 months ago, created an answer that has been accepted. For A: Extract allele frequencies from VCF
Scholar 16 months ago, created an answer that has been accepted. For A: Extract allele frequencies from VCF
Popular Question 19 months ago, created a question with more than 1,000 views. For Mutect Allele Counts Vs Mpileup
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Mutect Allele Counts Vs Mpileup
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Somatic mutation calling without matched normal
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Somatic Mutation Phasing
Student 2.6 years ago, asked a question with at least 3 up-votes. For Somatic mutation calling without matched normal
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Parsing Base String From Samtools Mpileup
Popular Question 3.6 years ago, created a question with more than 1,000 views. For Parsing Base String From Samtools Mpileup
Supporter 3.8 years ago, voted at least 25 times.

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