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echoverse: Break up echolocatoR into sub-packages #62

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15 of 17 tasks
bschilder opened this issue Aug 28, 2021 · 0 comments
Open
15 of 17 tasks

echoverse: Break up echolocatoR into sub-packages #62

bschilder opened this issue Aug 28, 2021 · 0 comments
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enhancement New feature or request

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@bschilder
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bschilder commented Aug 28, 2021

This will make it more modular and easier to debug.

Proposed modules:

  • echolocatoR (echoverse branch): Core functions such as workflow and utilities.
  • echofinemap: Fine-mapping functions.
  • echoLD: LD downloading and processing (UKB, 1KG).
  • echoAI: API access to variant-level AI predictions (IMPACT, DeepSEA, SpliceAI).
  • echoannot: API access to variant-level epigenomic/genomic annotations (XGR, Roadmap, ENCODE).
  • echotabix: Tabix-indexing of tabular and vcf files.
  • echopeaks: Peak calling (MACS2). Now integrated into echoannot, with additional functionality available via PeakyFinders
  • echovalidate: Validation functions such as annotation enrichment with bootstrapping.
  • echoconda: Conda env utility functions.
  • catalogueR: eQTL Catalogue API and colocalization.
  • downloadR: Single- or multi-threaded downloading functions.
  • ggLocusZoom: Locus plotting. Replaced by echoplot.
  • echoplot: Locus plotting (replacement for ggLocusZoom).
  • echodata: Fine-mapping results, echolocatoR Fine-mapping Portal API, and related datasets.
  • echogithub: Extract data and metadata from GitHub

Extra modules

@bschilder bschilder added the enhancement New feature or request label Aug 28, 2021
@bschilder bschilder self-assigned this Aug 28, 2021
@bschilder bschilder changed the title **echoverse**: Break up echolocatoR into sub-packages echoverse: Break up echolocatoR into sub-packages Mar 4, 2022
@bschilder bschilder moved this from Todo to In Progress in 🦇🦇 echoverse 🦇🦇 Aug 27, 2022
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