User: cara78

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cara7810
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EU
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2 years, 2 months ago
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Posts by cara78

<prev • 25 results • page 1 of 3 • next >
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Comment: C: WGCNA on gene abundance data
... It was sequenced ribosomes Dna and the counts were determined from researching papers where the copy number was determined. I have 473 genes and 48 samples. I originally had 50 sa,pleas but they were removed after the quality control step. Sorry about the code and thanks for the tip to fix it. ...
written 2.4 years ago by cara7810
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WGCNA on gene abundance data
... I am trying to do co-occurrence analysis using WGCNA. My data is foreach species I have the abundance counts. Before I began WGCNA me data was log transformed and missing data is NA. I do have a lot of NAs in the dataset but they are consistently spread out across the samples. I have been using t ...
wgcna soft threshold gene abundance written 2.4 years ago by cara7810
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(Closed) Perl to calculate average in csv based on information at end of file
... I have a CSV file with three columns in order called Mb_size, tax_id, and parent_id. There is a relationship between tax_id and parent_id, for example, in the csv file at the end where you have 22.2220658537 for the mb size, 5820 is the tax id and 5819 is the parent id. As move up the file 5819 the ...
perl csv average written 3.0 years ago by cara7810
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Problem using Krona Phylogeny to make xml file tree, get blank page
... I have recently installed Krona as per the instructions on there website, taxonomy files and install them with updateTaxonomy and then install. I then used ImportXML for my file which created the html file. It didnt work at first, so  I had to use deployResources with the command "./deployResources. ...
phylogeny xml krona blank written 3.3 years ago by cara7810
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software advise: visualise the phylogenetic tree that uses bubbles on the branches to indicate abundance.
... I have a phyloxml(.xml) which was made after pplacer analysis. I need to visualise the phylogenetic tree with software that uses bubbles on the branches to indicate abundance. Would anyone know any software that will take the xml file and uses bubbles on the branches to indicate abundance?   ...
advise xml tree phylogenetic abundance written 3.3 years ago by cara7810 • updated 3.3 years ago by jhc2.8k
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guide tree convert multfurcating to difurcating
... I need to convert a guide tree I got off NCBI. NCBI common taxonomy tree will only give out multifurcating guide tree such as below. Clustalw, where I need to use it will only accept difurcating guide trees. ( 'synthetic construct':4, 'unclassified sequences':4, 'Paramecium bursaria Chlorella virus ...
guide tree multifurcating difurcating convert written 3.4 years ago by cara7810 • updated 3.4 years ago by Brice Sarver2.5k
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Comment: C: Use NCBI guide tree in Clustalw
... Yes I checked the names, they are the same. The guide tree contains the same names as in the input sequence file. I used their taxa IDs to get the guide tree off NCBI. ...
written 3.4 years ago by cara7810
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Use NCBI guide tree in Clustalw
... I want to use a guide tree I got in NCBI common taxonomy tree to use with my MSA in clustalw to produce an alternative arrangement of the MSA based on the NCBI guide tree. The guide tree from NCBI  I got looks like this, ( 'synthetic construct':4, 'unclassified sequences':4, 'Paramecium bursaria C ...
ncbi clustalw msa guide tree written 3.4 years ago by cara7810 • updated 3.4 years ago by blackgore60
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Comment: C: DNA multiple sequence alignment quality check software advise
... I want to do phylogeny and they are all eukariotes. I made the MSA with clustal omega. ...
written 3.4 years ago by cara7810
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DNA multiple sequence alignment quality check software advise
... Hello, I want to do quality check on my multiple sequence alignment which is in DNA. There are a number of these software for protein but hard to find a good one for DNA. I want to see if the alignment is good and if bad then tell me so I can remove it. That sort of thing.   Does anyone know of a ...
quality check quality control msa dna written 3.4 years ago by cara7810 • updated 3.4 years ago by Brice Sarver2.5k

Latest awards to cara78

Great Question 2.3 years ago, created a question with more than 5,000 views. For determine if a number is greater than elements in a row matrix in R
Popular Question 3.8 years ago, created a question with more than 1,000 views. For determine if a number is greater than elements in a row matrix in R

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