Changes in version 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

                     Changes in version 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)