User: paolo002

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paolo002100
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Posts by paolo002

<prev • 31 results • page 1 of 4 • next >
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Comment: C: Subset top 5% values of data frames stored in list
... https://stackoverflow.com/questions/53724885/subset-multiple-data-frames-stored-inside-a-list in any case...this was the link but maybe there I did not explain my problem so well... ...
written 1 day ago by paolo002100
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Subset top 5% values of data frames stored in list
... Hi This is probably a question for stack overflow but I am posting it here because there I am not getting much replies, apologies for this. I have a 24 data frames with different number of rows and with various columns (for instance column SNPs ID and other columns with corresponding values for ea ...
R subset written 1 day ago by paolo002100 • updated 1 day ago by zx87546.1k
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Answer: A: calculating allele frequency difference or Fst value ?
... Hi Seta Personally I would recommend ANGSD (http://www.popgen.dk/angsd/index.php/ANGSD). It can calculate Fst in a straightforward way. ...
written 6 days ago by paolo002100
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Answer: A: Assigning SNPs to gene names based on genomic coordinates
... Hi, I have found a nice solution for doing that in R, I post it so maybe it might be useful to other people: Let' say you have a data frame (df) with list of SNPs ID (rs IDs and not annotated IDs) with chromosome number and location in Base Pairs (BP) on the genome ( I show the first 10 rows but th ...
written 7 days ago by paolo002100
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Comment: C: Assigning SNPs to gene names based on genomic coordinates
... ok thanks a lot for all the links. I am taking a look. ...
written 8 days ago by paolo002100
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Assigning SNPs to gene names based on genomic coordinates
... Hi all, I am not sure if this was asked before but I would like to assign a list of SNPs to the corresponding gene names: I have a df such as the following: SNP std.XPEHH CHR BP rank 1 rs376121383 5.86403 2 97868880 1 2 rs9324211 5.86122 2 9786787 ...
R written 8 days ago by paolo002100
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Answer: A: Extracting sample ID and their genotypes
... Is you data a vcf file? If you want to extract individuals from vcf file you can use bcftools and provide a txt file with IDs of those individuals ...
written 18 days ago by paolo002100
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Answer: A: GO network analysis
... Yeah, ClueGO is a very nice CYTOSCAPE plugin to build GO network and it is reliable because the GO terms I got from my RNA-seq data were correct. If I remember correctly you need to send them an email to get the activation code and then you can use ClueGO freely but not sure how does it work now bec ...
written 19 days ago by paolo002100
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Answer: A: Bcftools merge sample order
... If you merge various vcf files into a single large vcf, the merged file will show the sample IDs names in the header in increasing order. The information in the hearder will follow the same order as in the separated files you provided as input. However, I guess be careful if there are not unique ind ...
written 23 days ago by paolo002100
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Answer: A: GO network analysis
... if your question is how to build a GO network, first of all there are various good tools you can use for GO analysis such as DAVID, PANTHER, GOrilla and see what are the GO terms you get from your gene list. I would also suggest ClueGO package in CYTOSCAPE, you can build a nice network there. ...
written 23 days ago by paolo002100

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Student 11 weeks ago, asked a question with at least 3 up-votes. For Subsetting large list of SNPs with R

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