NEWS

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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

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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.

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Contributors

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