# Inferring clusters of orthologous and paralogous transcripts
``Algorithm to infer clusters of isoorthologous transcripts using gene-level homology relationships and a Reciprocal Best Hits approach``
<!-- ABOUT THE PROJECT -->
<h2 id="about-the-project">About The Project</h2>
<!-- OVERVIEW -->
<h3 id="overview">Overview</h3>
`A graph-based method to infer isoorthology & recent paralogy relations in a set of homologous transcripts`
---
<!-- Requirements -->
<h3 id="requirements"> Requirements</h3>
* __`python3 (at leat python 3.6)`__
* __`NetworkX`__
* __`Pandas`__
* __`Numpy`__
* __`ETE toolkit`__
<!-- Package -->
<h3 id="package">About the package</h3>
``install the package``
<pre><code>pip3 install transcriptorthology</code></pre>
``import package and use the main function``
<pre><code>from transcriptorthology.transcriptOrthology import inferring_transcripts_isoorthology
if __name__ == '__main__':
gtot_path = './execution/mapping_gene_to_transcripts/ENSGT00390000003967.fasta'
gt_path = './execution/NHX_trees/ENSGT00390000003967.nhx'
lower_bound = 0.7
transcripts_msa_path = './execution/transcripts_alignments/ENSGT00390000003967.alg'
tsm_value = 1
constraint = 1
output_folder = './execution/output_folder'
<span style="color:red;">inferring_transcripts_isoorthology</span>(<span style="color:red;">transcripts_msa_path</span>, <span style="color:green;">gtot_path</span>, <span style="color:purple;">gt_path</span>,<span style="color:orange;">tsm_value</span>,<span style="color:yellow;">lower_bound</span>,<span style="color:gray;">constraint</span>,<span style="color:gray;">output_folder</span>)</code></pre>
---
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Copyright © 2023 CoBIUS LAB
Raw data
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"author": "Wend Yam Donald Davy Ouedraogo",
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"description": "\n# Inferring clusters of orthologous and paralogous transcripts\n\n``Algorithm to infer clusters of isoorthologous transcripts using gene-level homology relationships and a Reciprocal Best Hits approach``\n\n\n\n<!-- ABOUT THE PROJECT -->\n<h2 id=\"about-the-project\">About The Project</h2>\n\n\n<!-- OVERVIEW -->\n<h3 id=\"overview\">Overview</h3>\n\n`A graph-based method to infer isoorthology & recent paralogy relations in a set of homologous transcripts`\n\n---\n\n\n<!-- Requirements -->\n<h3 id=\"requirements\"> Requirements</h3>\n\n* __`python3 (at leat python 3.6)`__\n* __`NetworkX`__\n* __`Pandas`__\n* __`Numpy`__\n* __`ETE toolkit`__\n\n\n\n\n<!-- Package -->\n<h3 id=\"package\">About the package</h3>\n\n``install the package``\n<pre><code>pip3 install transcriptorthology</code></pre>\n\n``import package and use the main function``\n<pre><code>from transcriptorthology.transcriptOrthology import inferring_transcripts_isoorthology\n\n\nif __name__ == '__main__':\n gtot_path = './execution/mapping_gene_to_transcripts/ENSGT00390000003967.fasta'\n gt_path = './execution/NHX_trees/ENSGT00390000003967.nhx'\n lower_bound = 0.7\n transcripts_msa_path = './execution/transcripts_alignments/ENSGT00390000003967.alg'\n tsm_value = 1\n constraint = 1\n output_folder = './execution/output_folder'\n \n <span style=\"color:red;\">inferring_transcripts_isoorthology</span>(<span style=\"color:red;\">transcripts_msa_path</span>, <span style=\"color:green;\">gtot_path</span>, <span style=\"color:purple;\">gt_path</span>,<span style=\"color:orange;\">tsm_value</span>,<span style=\"color:yellow;\">lower_bound</span>,<span style=\"color:gray;\">constraint</span>,<span style=\"color:gray;\">output_folder</span>)</code></pre>\n\n\n\n\n---\n<br>\n<br>\n<br>\n<br>\n<br>\n<br>\nCopyright \u00a9 2023 CoBIUS LAB\n\n\n\n\n\n\n",
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