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Changelog

Source: NEWS.md

iTALK 0.1.1

Bug Fixes

  • Fixed critical loop bug in DEG() function where for(i in ncol(combination)) only iterated once instead of all combinations
  • Fixed deprecated ggplot2 parameters in TimePlot(): fun.y → fun, fun.ymin → fun.min, fun.ymax → fun.max
  • Fixed deprecated igraph function in NetView(): graph.data.frame → graph_from_data_frame
  • Added .groups='drop' to dplyr summarize() to avoid warnings

Performance Improvements

  • Optimized WilcoxTest() logFC calculation using rowMeans() with proper pseudocount handling
  • Improved rawParse() performance by replacing loop rbind with lapply + do.call(rbind, ...)
  • Optimized storage mode conversion using direct matrix operation instead of apply

Code Quality

  • Cleaned up code comments and improved code style consistency
  • Improved cross-platform SSL handling in BioMart utilities

iTALK 0.1.0.9000

New Features

Cross-Species Analysis Support

Added automatic species conversion for seamless mouse data analysis:

  • Automatic detection: Identifies mouse vs human from gene names
  • BioMart integration: Accurate ortholog mapping via Ensembl
  • Smart caching: ~15s first query, instant subsequent
  • Zero-touch operation: Works automatically

New Functions: - detect_species() - Species identification - convert_species_biomart() - Ortholog mapping - convert_expression_matrix() - Matrix conversion - convert_data_species() - Data frame conversion

Modified Functions: - FindLR() - Enhanced with automatic species conversion - New parameters: convert_species, ensembl_version, mirror, cache - Fully backward compatible

New Files: - R/utils_biomart.R - BioMart utilities - R/species_conversion.R - Conversion framework

Dependencies: - Added biomaRt, httr, R.cache, digest

All other iTALK functionality unchanged.

Contributors

  • Zaoqu Liu (Maintainer)
  • Yuanxin Wang (Original author)