User: newbiebio

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newbiebio80
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Posts by newbiebio

<prev • 32 results • page 1 of 4 • next >
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Comment: C: How to convert xml file to txt file
... Thank you for your suggestion. I will be aware of that. Since I just joined for a few months, I tried to learn. ...
written 20 months ago by newbiebio80
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How to convert xml file to txt file
... I downloaded some clinical data from gdc, which is xml file. I would like to know how to convert xml file to txt file. Thanks in advance. ...
table xml written 20 months ago by newbiebio80
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Answer: A: How to extract snp names?
... I tried a very stupid way, but it works. If you have NotePat++, just press "Ctrl+H", use replace function. In the 'find what', type in (\w+)-(\w+)-(\w+) (\d+) (\d+) (\w+) ([\+\-]) (\d) (\d) (\d) (\d) 'replace with',type in \1-\2 Hope it helps.. ...
written 20 months ago by newbiebio80
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Answer: A: genes that map to hg38 coordinates
... Maybe you could try bedtools. First, go to ensembl and download refgenome's gtf file. Then use 'bedtools intersect -wo -a ref.gtf -b you_input.bed" ...
written 20 months ago by newbiebio80
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Answer: A: access the phenotype information
... head function only shows the first six rows in the variable ...
written 20 months ago by newbiebio80
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Comment: C: differential expression and meta analysis of microarray
... You could try these two http://homer.salk.edu/homer/basicTutorial/affymetrix.html https://www.biostars.org/p/196330/ Hope it will help. ...
written 20 months ago by newbiebio80
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Answer: A: NCBI Gene(Nucleotide sequence) to chromosome location
... Maybe you can try UCSC MySQL. This is a tutorial http://crazyhottommy.blogspot.com/2013/11/mysql-rocks.html Then type as bellow select chrom, name,txStart,txEnd from refGene where name=''NMxxx"; ...
written 21 months ago by newbiebio80
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Comment: C: Known a gene sequence to find it's homology to yeast gene
... Thank you so much natasha. Actually, the gene is a lncRNA. ...
written 21 months ago by newbiebio80
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Known a gene sequence to find it's homology to yeast gene
... Known one gene sequence, how to find if it's homology to any yeast gene? I used blast and under 'choose search set", there is organism, I chose yeast. Is that a right way? And What database should I choose? ...
blast written 21 months ago by newbiebio80
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Answer: A: Analysing microarray data
... You could read the link that Venu recommanded or click this link(http://jura.wi.mit.edu/bio/education/bioinfo2007/arrays/array_exercises_1R.html) Usually, we use affy and limma package from Bioconductor to analysis microarray data. source("https://bioconductor.org/biocLite.R") #download these two ...
written 21 months ago by newbiebio80

Latest awards to newbiebio

Scholar 21 months ago, created an answer that has been accepted. For A: Delete rows in dataframe in R
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: Delete rows in dataframe in R

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