Update README.md

README.md

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 ---
 license: mit
+task_categories:
+- tabular-regression
+tags:
+- biology
+pretty_name: Cryptococcus Coexpression Network
+size_categories:
+- 10M<n<100M
 ---
+# CryptoCEN: A Co-expression network for *Cryptococcus neoformans*
+Elucidating gene function is a major goal in biology, especially among non-model organisms.
+However, doing so is complicated by the fact that molecular conservation does not always
+mirror functional conservation, and that complex relationships among genes are responsible
+for encoding pathways and higher-order biological processes. Co-expression, a promising
+approach for predicting gene function, relies on the general principal that genes with
+similar expression patterns across multiple conditions will likely be involved in the
+same biological process. For Cryptococcus neoformans, a prevalent human fungal pathogen
+greatly diverged from model yeasts, approximately 60% of the predicted genes in the genome
+lack functional annotations. Here, we leveraged a large amount of publicly available
+transcriptomic data to generate a C. neoformans Co-Expression Network (CryptoCEN),
+successfully recapitulating known protein networks, predicting gene function, and
+enabling insights into the principles influencing co-expression. With 100% predictive
+accuracy, we used CryptoCEN to identify 13 new DNA damage response genes, underscoring
+the utility of guilt-by-association for determining gene function. Overall, co-expression
+is a powerful tool for uncovering gene function, and decreases the experimental tests
+needed to identify functions for currently under-annotated genes.
+
+MJ O'Meara, JR Rapala, CB Nichols, C Alexandre, B Billmyre, JL Steenwyk, A Alspaugh, TR O'Meara
+CryptoCEN: A Co-Expression Network for Cryptococcus neoformans reveals novel proteins involved in DNA damage repair
+Code available at https://github.com/maomlab/CalCEN/tree/master/vignettes/CryptoCEN
+
+**h99_transcript_annotations.tsv**
+* Cryptococcus neoforman H99 (NCBI Taxon:235443) annotated protein features collected from FungiDB Release 49
+
+**top_coexp_hits.tsv**
+* top 50 CrypoCEN associations for each gene
+
+**top_coexp_hits_0.05.tsv**
+* top CrypoCEN associations for each gene filtered by score > 0.95 and at most 50 per gene
+
+**Data/estimated_expression_meta.tsv**
+* Metadata for RNAseq estimated expression runs
+
+**Data/estimated_expression.tsv**
+* gene by RNA-seq run estimated expression
+
+**Data/sac_complex_interactions.tsv**
+* C. neoformans genes that are orthologous to S. cerevisiae genes who's proteins are involved in a protein complex
+
+**Networks/CryptoCEN_network.tsv**
+* Co-expression network
+
+**Networks/BlastP_network.tsv**
+* Protein sequence similarity network
+
+**Network/CoEvo_network.tsv**
+* Co-evolution network