Update dependencies

What's Changed

• bug fix to address #55 by @nicolerg in #56

Full Changelog: v1.6.5...v1.6.6

It depends

What's Changed

• Update dependencies by @nicolerg in #54

Full Changelog: v1.6.4...v1.6.5

Summer bug

What's Changed

• #52 vena cava bug fix by @nicolerg in #53

Full Changelog: v1.6.2...v1.6.4

Ready for the World

This package provides functions to fetch, explore, and reproduce the processed data and downstream analysis results presented in the main paper for the first large-scale multi-omic multi-tissue endurance exercise training study conducted in young adult rats by the Molecular Transducers of Physical Activity Consortium (MoTrPAC).
The goal of this release is to generate a citation in Zenodo

ATAC the bug

Summary:

• Bug fix in atac_timewise_da() and atac_training_da() when n_features = Inf.

What's Changed

• Bug fix in atac da fx by @nicolerg in #51

Full Changelog: v1.6.1...v1.6.2

Refmenable

Summary

• Accommodate RefMet IDs as feature IDs in plot_feature_normalized_data() and plot_feature_logfc().
• Pass the user-supplied version of the feature identifier when plot_feature_logfc() is called within plot_feature_normalized_data().

What's Changed

• allow refmet IDs by @nicolerg in #50

Full Changelog: v1.6.0...v1.6.1

Enriching

Summary

• Add functions for GSEA and PTM-SEA: ssGSEA2_wrapper(), prepare_gsea_input(),
  prepare_ptmsea_input(), find_flanks(), load_uniprot_human_fasta()
• Add extract_top_trajectories() function.

What's Changed

• add ssGSEA fx by @nicolerg in #48
• add gsea fx by @nicolerg in #49

Full Changelog: v1.5.2...v1.6.0

He sed she sed

Summary

• For enrichment_network_vis() with argument return_html=TRUE, don't require GNU sed.

What's Changed

• don't require GNU sed by @nicolerg in #47

Full Changelog: v1.5.1...v1.5.2

Vizzy whiz

Summary

• In enrichment_network_vis(), include pathway names in determination of node labels.
• In enrichment_network_vis(), use MotrpacRatTraining6moData::FEATURE_TO_GENE_FILT as
  feature_to_gene default instead of the unfiltered version.
• Add more details to enrichment_network_vis() docs.

What's Changed

• improve network vis by @nicolerg in #46

Full Changelog: v1.5.0...v1.5.1

Major minor improvements

Summary

• Add load_feature_annotation(). MoTrPAC/MotrpacRatTraining6moData#43
• Add tissues, assays, and cluster arguments to enrichment_network_vis() to
  provide an alternate way for users to specify results from MotrpacRatTraining6moData::GRAPH_PW_ENRICH.
• Add tests for enrichment_network_vis(). #45
• Use signif() instead of round() to display values in plot titles. #41
• Add counts argument to transcript_normalize_counts() and atac_normalize_counts()
  to allow user-supplied data. #43
• Add note about reproducibility issues to documentation for transcript_normalize_counts(). MoTrPAC/MotrpacRatTraining6moData#41
• Move MotrpacRatTraining6moData from Imports to Depends. This means MotrpacRatTraining6moData is also attached (not just loaded) when MotrpacRatTraining6mo is attached. #40
• Replace fetch_object(name_as_string) with get(name_as_string, envir=as.environment("package:MotrpacRatTraining6moData")). #40
• Change URLs for load_methyl_feature_annotation() and load_atac_feature_annotation().
• Fix bug in plot_feature_logfc() that prevented epigenetic features from being plotted.
• Speed up plot_feature_logfc() for differential epigenetic features.
• In get_rdata_from_url(), calculate log fold-change standard errors for METHYL
  differential analysis results: logFC_se = logFC/zscore MoTrPAC/MotrpacRatTraining6moData#44
• Require newest version of MotrpacRatTraining6moData.

What's Changed

• minor improvements by @nicolerg in #44

Full Changelog: v1.4.3...v1.5.0