User: boaty

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boaty110
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Posts by boaty

<prev • 36 results • page 1 of 4 • next >
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Better way for speedup of Humann3 metagenomics analysis pipeline?
... Hi guys, This is an open question. While dealing with microbiome metagenomics data by humann3, I found that it is quite time-consuming. With 40-core cups and 240 GB MEM, single sample analysis took 4 hours for nucleotide-searching only and 9 hours for translated-searching included and this is inac ...
humann metagenomics alignment pipeline written 2 days ago by boaty110
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is it possible to get a .jplace file from a phyloseq obj?
... Hello everyone, Someone is familiar with pplacer pipeline? I got this phyloseq obj in R which has otu table, tax table, meta table and tree. This obj is generated by DADA2. Now I want to create a .jplace file from a phyloseq so I made a little research. 1. jplace is made from pplacer software w ...
tree phyloseq phyml taxtastic pplacer written 3 months ago by boaty110
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Answer: A: htseq count error
... it seems that you aligned your reads on some reference other than genome, the RNAME is KB317696.1 not chromosome. And you want to count reads on each exon, your GTF coordinates are coordinate for a gene the pb is HTSeq-count does not work in this way, you need to align reads on genome then feed HTSe ...
written 4 months ago by boaty110
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Comment: C: best R package for tree(data structure) in 2020?
... thanks a lot. I've already used ape in phyloseq objects, how can I miss this packages....... ...
written 4 months ago by boaty110
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Comment: C: htseq coun error
... needs more information for debug. If your bam file is OK, then it is probably something wrong with --idattr locus_tag and your off file ...
written 4 months ago by boaty110
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best R package for tree(data structure) in 2020?
... Hi guys, Just a quick question, is anyone using tree in R analysis? I need to switch my data structure from data.from to tree in order to handle taxonomy data. Any advise for a R package? Thanks in advance ...
pacakge R tree written 4 months ago by boaty110 • updated 4 months ago by Kevin Blighe61k
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Comment: C: is there a method like PLS-DA, but for a quantitative Y value?
... thanks Kevin for your answer, It is exactly what I am looking for! In your package, you are using loadings to classify and calculate correlations between PCs and category names(eg. Size, Grade etc.). In my case, only 1 category : log2(fold-change). I do not know if log2 ratio is linear or maybe n ...
written 4 months ago by boaty110
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Answer: A: How to split sequence in fasta file based on long runs of Ns?
... I suggest you to use SeqIO.par in biopython or read.fasta() in sequinr. Those tools will transform fasta 4 lines format into a list of object which concatenate fasta sequence line into a string. Then just use split method to cut them ...
written 4 months ago by boaty110
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is there a method like PLS-DA, but for a quantitative Y value?
... Hi guys, I'm using PLS-DA to select the most importance genes contributing to group differences. Now, I am looking for a statistical method that fit quantitative Y. For a normal PLS-DA, we have X (n*p) matrix which contains quantity data and Y (n) vector with qualitative information such as treat ...
pls-da pls written 4 months ago by boaty110 • updated 4 months ago by Kevin Blighe61k
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Comment: C: How to make differential expression analysis with normalized data?
... look at this first [tximport][1] tximport will take normalised count and length information to recompute raw count...... you can use tximport to get pseudo raw count then use deseq2 for GDE It works for almost all the modern count quantification tools like kallisto, stringtie. But you need to know w ...
written 10 months ago by boaty110

Latest awards to boaty

Popular Question 8 days ago, created a question with more than 1,000 views. For is it meaningless for comparing averages from data with different sample size?
Popular Question 5 months ago, created a question with more than 1,000 views. For is it meaningless for comparing averages from data with different sample size?
Supporter 12 months ago, voted at least 25 times.
Scholar 19 months ago, created an answer that has been accepted. For A: guidance for communication online seach engine with python or R script?
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: guidance for communication online seach engine with python or R script?

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