User: haneenih7

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haneenih780
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haneenih7
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PhD student

Posts by haneenih7

<prev • 56 results • page 1 of 6 • next >
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Comment: C: segmentation fault in Bayenv2
... the same problem here, no answer found! ...
written 8 weeks ago by haneenih780
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Comment: C: GO and KEGG from DESeq2 counts
... topGO R package is very good and it will work very well for your DESeq2 if you have the GO labels for your genes/proteins sequences: https://bioconductor.org/packages/release/bioc/html/topGO.html https://bioconductor.org/packages/release/bioc/vignettes/topGO/inst/doc/topGO.pdf ...
written 3 months ago by haneenih780
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Comment: C: How do I calculate Jaccard distance between pair-wise OTUs species
... I do analyze the bacterial community with mothur. https://mothur.org/wiki/miseq_sop/ And you could calculate the dissimilarity indices or the distance between two communities. Using different methods that are implemented in mothur pipeline Example Jaccard: https://mothur.org/wiki/jclass/ ...
written 3 months ago by haneenih780
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Comment: C: Can we compare two LD decay curves by statistical test to say they are different
... Very good. Now I understand your point. Thanks a lot! And with vcftools http://vcftools.sourceforge.net/man_latest.html I can define the physical window Example: `--ld-window-bp 100000` compute the LD between SNPs being maximum 100 kb apart ...
written 4 months ago by haneenih780
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Comment: C: Can we compare two LD decay curves by statistical test to say they are different
... You are right! The sample size of the two groups are very different, the cultivated group with 157 individuals, while the wild group is only 14 individuals. What do you mean by comparing the distance R^2=0.2? Just by saying: > Genome-wide linkage disequilibrium (LD) analyses revealed a faster ...
written 4 months ago by haneenih780
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Comment: C: Can we compare two LD decay curves by statistical test to say they are different
... This was my initial plan, but using paired t-test you compare the means between two related groups. Does it make sense to compare the two means of curves? ...
written 4 months ago by haneenih780
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Can we compare two LD decay curves by statistical test to say they are different?
... Hello, Is it possible to compare two curves and say they are different not just by eyes, but providing statistical test? Here is LD decay plot of two plant species. And by eyes, I see the difference in which the blue one decay faster at the beginning. The Genome-wide LD decay was calculated by P ...
R snp statistics written 4 months ago by haneenih780
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Comment: C: How to remove characters after specific symbol from all columns, and make all ch
... Yes, I managed to do it with awk and sed; To remove the last 6 characters from a file in each column ` awk '{for(i=1;i<=NF;i++) sub(/......$/,X,$i)}1' ` ...
written 5 months ago by haneenih780
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How to remove characters after specific symbol from all columns, and make all charachters sperated by space and comma except the first column
... Hi all, I am trying to modify the formate of a big file: The file is tab-delimited Here how the file looks like: AB11.1 CB:0078_0.53 CB:0044464_0.42 CB:0005623_0.466 AB10.1 AB01.2 CB:0036_0.4 CB:0003824_0.4 CB:0005575_0.7 CB:0005622_0.2 CB:0005623_0.6 AB01.2 CB:0036_0.3 ...
bash written 5 months ago by haneenih780 • updated 5 months ago by RamRS30k
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Comment: C: For each row retain the cell with maximum value in R
... The code is perfectly working. It was something to do with the input file. Thank you very much! I really appreciate your help :) ...
written 5 months ago by haneenih780

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Popular Question 5 weeks ago, created a question with more than 1,000 views. For mantel test in vegan r package

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