CHANGES IN VERSION 1.31.1 ------------------------ o Fix bugs in genes_kept to deal with NA in data CHANGES IN VERSION 1.27.4 ------------------------ o Fix bugs in vignette o Improvements for notes and warnings in R cmd check CHANGES IN VERSION 1.27.3 ------------------------ o Improvement for plot_pathway_overall function CHANGES IN VERSION 1.27.2 ------------------------ o Fix bugs in convertId function, which was caused by the updates of biomaRt package CHANGES IN VERSION 1.27.1 ------------------------ o Fix bugs in download_KEGGfile function, which was caused by the updates of KEGG web site. o New function: plot_pathway_overall function to plot gene expression in pathway level. o Improvement for documents and examples. CHANGES IN VERSION 1.25.1 ------------------------ o Fix bugs in download_KEGGfile function. CHANGES IN VERSION 1.19.3 ------------------------ o Fix bugs in download_KEGGfile function, which was caused by the updates of KEGG web site. CHANGES IN VERSION 1.19.1 ------------------------ o Fix a bug in download_KEGGfile function, which was caused by the updates of KEGG web site. CHANGES IN VERSION 1.9.3 ------------------------ o Fix a bug in example of convertId function, which was caused by update of BioMart database. Thanks Dan. CHANGES IN VERSION 1.9.1 ------------------------ o Fix a bug when pathway_min is set to 1. Thanks Norbert Auer. CHANGES IN VERSION 1.7.7 ------------------------ NEW FEATURES o New function: The pathway map without species information can be used as reference map with parameter speciesRefMap. CHANGES IN VERSION 1.7.6 ------------------------ NEW FEATURES o New function: Downloading the latest pathway/gene link from KEGG website. CHANGES IN VERSION 1.7.5 NEW FEATURES o Changes in examples. CHANGES IN VERSION 1.7.4 ------------------------ NEW FEATURES o Improvement for documents and examples. CHANGES IN VERSION 1.7.3 ------------------------ NEW FEATURES o Improvement for the web interface. CHANGES IN VERSION 1.7.2 ------------------------ NEW FEATURES o New function plot_pathway_cor: Caculating correlations between groups in each pathway and comparing with the correlations for other genes. CHANGES IN VERSION 1.7.1 ------------------------ NEW FEATURES o Compound data was also supported; The parameters were modified for web interface. CHANGES IN VERSION 0.99.2 ------------------------- NEW FEATURES o Improvement in processing expression matrix with only one time point CHANGES IN VERSION 0.99.1 ------------------------- NEW FEATURES o Add the parameter lwd when type='lines' CHANGES IN VERSION 0.99.0 ------------------------- NEW FEATURES o Improvement in the description of this package. Add notes for users in plot_profile function CHANGES IN VERSION 0.1.2 ------------------------ o Improvement in the codes of vignette file and re-submit to bioconductor as the final version CHANGES IN VERSION 0.1.0 ------------------------ NEW FEATURES o Submit to bioconductor CHANGES IN VERSION 0.0.7 ------------------------ NEW FEATURES o Finish the vignette file CHANGES IN VERSION 0.0.6 ------------------------ NEW FEATURES o Improvement in help file and example source CHANGES IN VERSION 0.0.5 ------------------------ NEW FEATURES o Add return value for plot_pathway function; Release to my colleague CHANGES IN VERSION 0.0.4 ------------------------- NEW FEATURES o Finish help files and example source CHANGES IN VERSION 0.0.3 ------------------------ NEW FEATURES o Add example data files CHANGES IN VERSION 0.0.2 ------------------------ NEW FEATURES o Improvement in figure details CHANGES IN VERSION 0.0.1 ------------------------ NEW FEATURES o Build 'CHANGES IN VERSION' package by CMD Install and CMD check