maom commited on
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9ce0bc5
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1 Parent(s): e6b3eda

add header and take2 in selecting columns

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  1. app.py +23 -5
app.py CHANGED
@@ -4,6 +4,24 @@ import numpy as np
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  import pandas as pd
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  import altair as alt
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  top_coexp_hits = datasets.load_dataset(
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  path = "maomlab/CryptoCEN",
@@ -17,10 +35,10 @@ gene_id = st.text_input(
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  help = "CNAG Gene ID e.g. CNAG_04365")
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  top_coexp_hits = top_coexp_hits[
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- top_coexp_hits.gene_id_1 == gene_id,
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- ['gene_id_1', 'gene_symbol_1', 'description_1',
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- 'gene_id_2', 'gene_symbol_2', 'description_2',
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- 'coexp_score', 'blastp_EValue']]
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-
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  st.table(top_coexp_hits)
 
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  import pandas as pd
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  import altair as alt
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+ st.markdown("""
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+ # CryptoCEN Top50 co-expressed partners
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+
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+ **CryptoCEN** is a co-expression network for *Cryptococcus neoformans* built on 1,524 RNA-seq runs across 34 studies.
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+ A pair of genes are said to be co-expressed when their expression is correlated across different conditions and
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+ is often a marker for genes to be involved in similar processes.
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+
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+ To Cite:
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+ MJ O'Meara, JR Rapala, CB Nichols, C Alexandre, B Billmyre, JL Steenwyk, A Alspaugh,
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+ TR O'Meara CryptoCEN: A Co-Expression Network for Cryptococcus neoformans reveals
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+ novel proteins involved in DNA damage repair
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+ * Code available at https://github.com/maomlab/CalCEN/tree/master/vignettes/CryptoCEN
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+ * Full network and dataset: https://huggingface.co/datasets/maomlab/CryptoCEN
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+
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+ ## Look up top-coexpressed partners:
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+ Put in the ``CNAG_#######`` gene_id for a gene and expand the table to get the top 50 co-expressed genes.
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+ ``coexp_score`` ranges between ``[0-1]``, where ``1`` is the best and greater than ``0.85`` can be considered significant.
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+ """)
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  top_coexp_hits = datasets.load_dataset(
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  path = "maomlab/CryptoCEN",
 
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  help = "CNAG Gene ID e.g. CNAG_04365")
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  top_coexp_hits = top_coexp_hits[
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+ top_coexp_hits.gene_id_1 == gene_id,]
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+ top_coexp_hits = top_coexp_hits[[
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+ 'gene_id_1', 'gene_symbol_1', 'description_1',
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+ 'gene_id_2', 'gene_symbol_2', 'description_2',
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+ 'coexp_score', 'blastp_EValue']]
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  st.table(top_coexp_hits)