User: jolespin

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jolespin110
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Posts by jolespin

<prev • 66 results • page 1 of 7 • next >
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Comment: C: How to run Maple-2.3.0 (genome.jp) on the command-line?
... "We are sorry, but the stand-alone version of MAPLE is not provided." :( Copy and paste life . I might try to make an apple script tool. Do you know of anything else that can achieve this type of module completion ratio? I have been using genome properties but the kegg ids are so nice to work with ...
written 18 months ago by jolespin110
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How to run Maple-2.3.0 (genome.jp) on the command-line?
... I would like to use: http://www.genome.jp/tools/maple/ I have 33 draft genomes and I want to calculate the module completeness ratios for all of the draft genomes. I've been doing them individually through the browser but it's taking a long time. It also crashed when I ran too many at the same ti ...
fasta maple kegg modules functional written 18 months ago by jolespin110
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What are some robust correlation measures for network analysis?
... **What are the most reputable and robust correlation measures for compositional data like gene expression profiles?** To my knowledge there are`biweight midcorrelation` which is implemented in `WGCNA` and `SparCC`. `Biweight midcorrelation` is relatively easy to code up to use outside of `R`'s en ...
network correlation gene-expression robust written 2.0 years ago by jolespin110
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Can someone describe how the SparCC corrected correlation measure works?
... I've been reading this paper. The first part of the algorithm makes perfect sense but I'm not sure how the Dirchlet Process plays a role and why the iterative steps are needed? ![enter image description here][1] http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002687 This i ...
genome microbiome metagenomics chip-seq rna-seq written 2.1 years ago by jolespin110
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Download NCBI genome sequences from Python
... I have data that looks like: 1. Cronobacter phage Dev2 Characterization of lytic Cronobacter turicensis phage Dev2 isolated from wastewater treatment Kingdom: Viruses Chromosome: 1 Genome ID: 36224 2. Pseudomonas phage vB_Pae-TbilisiM32 Modified complete genome sequ ...
genome python sequences genomics ncbi written 2.1 years ago by jolespin110 • updated 2.1 years ago by Jenez510
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Find potential biological significance of a k-mer?
... I have a list of K-mers ranging from 5 - 10mers. I tried looking in http://meme-suite.org/tools/tomtom but I'm not sure if this is my best option. The k-mers are in diatoms and many of the databases are geared towards human and mouse. I looked at the output of `tomtom` and the sequence logos were ...
genome domain sequence kmer dna written 2.2 years ago by jolespin110
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How to make ortholog table with Reciprocal Best Hit blast (Python?) ?
... I have 2 fasta files containing all of the proteins from 2 distance organisms (A `Spirochaetes` and a `Firmicutes`). I want to map the genes from the `Firmicutes` to it's best hit in the `Spirochaetes`. **What is the best way to do this and the most accepted way?** I'm very familiar with `Pyth ...
genome gene ortholog protein blast written 2.2 years ago by jolespin110 • updated 2.2 years ago by Christophe Dessimoz500
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How to interpret the SeqIO.parse record for GenBank features?
... I'm calling these attributes of the feature class: `feature.location, feature.type, feature.strand` from the `record.features` in `SeqIO.parse(gbk_file,"genbank")` **Output:** [0:6183918](+) source 1 join{[1871:2015](-), [1776:1872](-), [1751:1775](-), [1419:1752](-), [1304:1418](-), ...
genome sequence biopython genbank parse written 2.6 years ago by jolespin110
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Where to download complete Genbank file?
... I want to download the **Genbank** file of `Anabaena variabilis`. It's on NCBI http://www.ncbi.nlm.nih.gov/assembly/276508 This organism has: (i) a chromosome; (ii) 3 plasmids; and (iii) a non-nuclear incision element. I can download all of these individually but **is there a place where A ...
genome genes genbank file download written 2.6 years ago by jolespin110 • updated 2.6 years ago by genomax59k
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How does WGCNA decide which genes are connected?
... I'm using the **Weighted Gene Coexpression Network Analysis** package (**WGCNA**) in **R** and I am trying to figure out how the **adjacency matrix** is defined. **I understand how the correlation matrix is created along with why the power is used but adjacency matrices should be either 1 or 0.** ...
gene wgcna network analysis coexpression written 2.6 years ago by jolespin110 • updated 20 months ago by sina.nassiri20

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Great Question 23 months ago, created a question with more than 5,000 views. For Any Way To Ncbi Blast Multiple Protein Sequences?
Popular Question 23 months ago, created a question with more than 1,000 views. For C. Elegans Genome Browser ?
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Any Way To Ncbi Blast Multiple Protein Sequences?
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Help creating .sqn file using tbl2asn to submit multiple sequences to Genbank
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Masters vs. PhD in Bioinformatics
Popular Question 2.6 years ago, created a question with more than 1,000 views. For C. Elegans Genome Browser ?
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Help creating .sqn file using tbl2asn to submit multiple sequences to Genbank
Popular Question 2.8 years ago, created a question with more than 1,000 views. For Masters vs. PhD in Bioinformatics
Popular Question 3.1 years ago, created a question with more than 1,000 views. For Help creating .sqn file using tbl2asn to submit multiple sequences to Genbank
Scholar 3.3 years ago, created an answer that has been accepted. For A: Python package similar to METATOOL 5.0 ?
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Scholar 3.6 years ago, created an answer that has been accepted. For A: Python package similar to METATOOL 5.0 ?
Scholar 3.7 years ago, created an answer that has been accepted. For A: Python package similar to METATOOL 5.0 ?
Scholar 3.7 years ago, created an answer that has been accepted. For A: Python package similar to METATOOL 5.0 ?
Popular Question 3.8 years ago, created a question with more than 1,000 views. For Help creating .sqn file using tbl2asn to submit multiple sequences to Genbank
Popular Question 4.6 years ago, created a question with more than 1,000 views. For Any Way To Ncbi Blast Multiple Protein Sequences?

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