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code
code
 
 
excel
excel
 
 
fasta
fasta
 
 
location
location
 
 
tree
tree
 
 
.Rhistory
.Rhistory
 
 
.gitattributes
.gitattributes
 
 
.gitignore
.gitignore
 
 
PVC.Rproj
PVC.Rproj
 
 
README.md
README.md
 
 
Verrucomicrobia_proteins.fasta
Verrucomicrobia_proteins.fasta
 
 
Verrucomicrobia全球分布数据.xlsx
Verrucomicrobia全球分布数据.xlsx
 
 
analysis.ipynb
analysis.ipynb
 
 
download_16sgene.ipynb
download_16sgene.ipynb
 
 
download_genome.ipynb
download_genome.ipynb
 
 
download_protein.ipynb
download_protein.ipynb
 
 
download_protein_files.ipynb
download_protein_files.ipynb
 
 
draft.py
draft.py
 
 
draft2.py
draft2.py
 
 
f-cell.xlsx
f-cell.xlsx
 
 
f-otu.pdf
f-otu.pdf
 
 
find.ipynb
find.ipynb
 
 
g-cell-heatmap.pdf
g-cell-heatmap.pdf
 
 
g-otu-heatmap.pdf
g-otu-heatmap.pdf
 
 
genome2pathway.ipynb
genome2pathway.ipynb
 
 
get-env-info.ipynb
get-env-info.ipynb
 
 
get-env-info.pdf
get-env-info.pdf
 
 
get-env-info.qmd
get-env-info.qmd
 
 
get_gene.ipynb
get_gene.ipynb
 
 
get_metadata.ipynb
get_metadata.ipynb
 
 
get_protein_name.ipynb
get_protein_name.ipynb
 
 
get_proteinnames_from_GCA.ipynb
get_proteinnames_from_GCA.ipynb
 
 
heatmap.pdf
heatmap.pdf
 
 
machine learning.Rmd
machine learning.Rmd
 
 
machine-learning.html
machine-learning.html
 
 
machine_pathway.ipynb
machine_pathway.ipynb
 
 
map_abundance.Rmd
map_abundance.Rmd
 
 
new_file.txt
new_file.txt
 
 
output.csv
output.csv
 
 
screenshot.png
screenshot.png
 
 
search_PVC_from_single_sample.ipynb
search_PVC_from_single_sample.ipynb
 
 
search_bacteria_from_PMS_single_result.ipynb
search_bacteria_from_PMS_single_result.ipynb
 
 
taxon_from_ncbi.ipynb
taxon_from_ncbi.ipynb
 
 
test.txt
test.txt
 
 
tidy_environment(genome).Rmd
tidy_environment(genome).Rmd
 
 
tidy_environment(genome)_2.Rmd
tidy_environment(genome)_2.Rmd
 
 
true.Rmd
true.Rmd
 
 
true.html
true.html
 
 
verrucomicrobia_samples.csv
verrucomicrobia_samples.csv
 
 
verrucomicrobia_samples.txt
verrucomicrobia_samples.txt
 
 
verrucomicrobia_samples_with_coordinates.csv
verrucomicrobia_samples_with_coordinates.csv
 
 
world.pdf
world.pdf
 
 

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PVC

Get the data from database (NCBI and KEGG)

Find the pathways of every samples and calculate the number of every pathways.

Use the Machine Learning to predict the environment of every samples.

Reseach the key pathways.

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