CHANGES IN VERSION 1.99.2 2020-10-22 ------------------------------------ BUG FIXES o Change codes to make the package pass all Rcmd check with R 4.0.3 CHANGES IN VERSION 1.19.2 2020-10-02 ------------------------------------ BUG FIXES o Change codes to make the package pass all Rcmd check with R 4.0 CHANGES IN VERSION 1.19.1 2020-09-30 ------------------------------------ BUG FIXES o Fix a bug in est_power_distribution, which make results incorrect when power is very large. CHANGES IN VERSION 1.15.1 2018-11-12 ------------------------------------ BUG FIXES o Fix a bug in power estiamtion (cumsumBorder.cpp), which make results incorrect when k not equal to one. CHANGES IN VERSION 1.9.1 2017-08-03 ------------------------------------ BUG FIXES o Fix a bug about estimating genes in pathway power in est_power_distribution function, which was caused by update of KEGG web site. CHANGES IN VERSION 0.99.8 2015-04-12 ------------------------------------ BUG FIXES o Fix a bug in example of optimize_parameter function, which was caused by update of heatmap3 package. Thanks Dan. CHANGES IN VERSION 0.99.7 2015-04-06 ------------------------------------ BUG FIXES o Fix a bug in example of convertId function, which was caused by update of BioMart database. Thanks Dan. CHANGES IN VERSION 0.99.5 2015-04-06 ------------------------------------ SIGNIFICANT USER-VISIBLE CHANGES o Minor changes for genes with less than 1 read count; CHANGES IN VERSION 0.99.4 ------------------------- NEW FEATURES o The user friendly web interface was improved BUG FIXES o Bug fixed: Max sample size for distribution based sample size estimation; o Bug fixed: Keep consistent for all function names; SIGNIFICANT USER-VISIBLE CHANGES o Other improvement based on the comments from Bioconductor reviewer; CHANGES IN VERSION 0.99.3 2014-11-23 ------------------------------------ SIGNIFICANT USER-VISIBLE CHANGES o New parameter: countFilterInRawDistribution, selectedGeneFilterByCount; o Other improvement based on the comments from Bioconductor reviewer; CHANGES IN VERSION 0.99.2 ------------------------- SIGNIFICANT USER-VISIBLE CHANGES o The vignette was switched to a BiocStyle; o Other improvement based on the comments from Bioconductor reviewer; CHANGES IN VERSION 0.99.1 2014-10-19 ------------------------------------ SIGNIFICANT USER-VISIBLE CHANGES o Parameter was used to determine the power of genes below minAveCount; o Some recommendations from BiocCheck were improved; CHANGES IN VERSION 0.99.0 2014-10-16 ------------------------------------ SIGNIFICANT USER-VISIBLE CHANGES o Submit to Bioconductor. CHANGES IN VERSION 0.5.0 2014-10-15 ----------------------------------- NEW FEATURES o The datasets from TCGA were moved to RnaSeqSampleSizeData package; o The examples were improved; o The vignette was generated; CHANGES IN VERSION 0.4.0 2014-10-10 ----------------------------------- NEW FEATURES o Rcpp package was used to make some functions faster; o The package structure was improved; o The web interface was improved; CHANGES IN VERSION 0.3.0 2014-08-01 ----------------------------------- NEW FEATURES o Beta approximate method was improved and used in most of the cases; o Read count and dispersion distribution estimation function was improved; o Estimation power or sample size by read count and dispersion distribution was improved. RnaSeqSampleSize 0.2.0 2014-06-01 --------------------------------- NEW FEATURES o The function of estimation power or sample size by read count and dispersion distribution was imported and improved. CHANGES IN VERSION 0.1.7 2014-03-30 ----------------------------------- SIGNIFICANT USER-VISIBLE CHANGES o An approximate estimation method was used to decrease the running time when average read count (lambda0) was larger than 20; NEW FEATURES o A plotting power curve function plot_power_curve was provided; CHANGES IN VERSION 0.1.6 2014-03-19 ----------------------------------- SIGNIFICANT USER-VISIBLE CHANGES o The code was improved to fit the web interface; NEW FEATURES o The function est_power was provided for power estimation; BUG FIXES o A bug was fixed; CHANGES IN VERSION 0.1.5 2014-03-16 ----------------------------------- SIGNIFICANT USER-VISIBLE CHANGES o The C code for R function dnbinom was improved to decrease the running time greatly; o The powers for different N in estimating sample size were returned to prepare power curve; CHANGES IN VERSION 0.1.4 2014-03-01 ------------------------------------ NEW FEATURES o A user friendly web interface was provided at http://cqs.mc.vanderbilt.edu/shiny/RnaSeqSampleSize/; CHANGES IN VERSION 0.1.3 2014-02-17 ----------------------------------- SIGNIFICANT USER-VISIBLE CHANGES o The algorithm was improved to decrease the memory usage; CHANGES IN VERSION 0.1.2 2014-02-04 ----------------------------------- SIGNIFICANT USER-VISIBLE CHANGES o A more detail parameter to sample size table was provided; o The algorithm was improved to decrease the running time and memory usage; CHANGES IN VERSION 0.1.1 2014-02-04 ----------------------------------- SIGNIFICANT USER-VISIBLE CHANGES o The algorithm was improved to decrease the running time greatly; CHANGES IN VERSION 0.1.0 2014-01-24 ----------------------------------- SIGNIFICANT USER-VISIBLE CHANGES o A more detail parameter to sample size table was provided to make sample size estimation faster; o An estimated time to perform sample size estimation will be displayed; BUG FIXES o A bug fixed when sample size N equals to 1; CHANGES IN VERSION 0.0.1 2014-01-10 ----------------------------------- SIGNIFICANT USER-VISIBLE CHANGES o First version.