Add initial README

README.md

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 ---
 license: mit
+task_categories:
+- tabular-regression
+tags:
+- biology
+pretty_name: Toxoplasma gondii Coexpression Network
+size_categories:
+- 10M<n<100M
 ---
+# ToxoCEN: A Co-expression network for *Toxoplasma gondii*
+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 Toxoplasma gondii, a prevalent human eukaryotic pathogen
+greatly diverged from malaria, approximately 47% of the predicted genes in the genome
+lack functional annotations. Here, we leveraged a large amount of publicly available
+transcriptomic data to generate a T. gondii Co-Expression Network (ToxoCEN),
+recapitulating known protein networks, predicting gene function, and
+enabling insights into the principles influencing co-expression. 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
+ToxoCEN: A Co-Expression Network for Toxoplasma gondii
+Code available at https://github.com/maomlab/CalCEN/tree/master/vignettes/ToxoCEN
+
+**TGME49_transcript_annotations.tsv**
+* [Toxoplasma gondii ME49](https://toxodb.org/toxo/app/record/dataset/NCBITAXON_508771) (NCBI Taxon:508771) annotated protein features collected from [ToxoDB](https://toxodb.org/toxo/app) Release 64
+
+**top_coexp_hits.tsv**
+* top 50 ToxoCEN associations for each gene
+
+**top_coexp_hits_0.15.tsv**
+* top ToxoCEN associations for each gene filtered by score > 0.85 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
+
+**Networks/ToxoCEN_network.tsv**
+* ToxoCEN Co-expression network
+
+**Networks/BlastP_network.tsv**
+* Protein sequence similarity network