Changes in version 1.1.15 (2026-03-06) o Replace row-wise apply() overlap counting in .wmeanvec() with vectorized overlap-length computation. o Vectorize transcript-to-window splitting in makewindows() internals (remove cluster-based parallel approach). o Reduce repeated maptrack reads by optionally loading the full track once and filtering per chromosome. o Improve .retrievebgval skipping conversion to data.frame. o Update docs/version/NEWS accordingly. Changes in version 1.1.14 (2026-01-28) o Fix: Add missing expdf argument to plotmulti internal functions. Changes in version 1.1.13 (2025-12-11) o Remove unused variable in genesECDF. o Remove digit in variables. o Fix bug due to row and col names in teprmulti. o Add table of contents to vignette. o Add installation section to vignette with GitHub install instructions. o Standardize all stop() error messages with consistent '[tepr] Error:' prefix. o Standardize all warning() messages with consistent '[tepr] Warning:' prefix. o Fix incorrect warning text in plothistoknee and plotmetagenes (previously said 'auc' when displaying histograms and metagenes). o Refactor the error messages in the tests for consistency and clarity. o Replace deprecated 'size' with 'linewidth' in geom_line (ggplot2 3.4.0+). Changes in version 1.1.12 (2025-11-04) o An error message is now appearing if the user provide a wrong experiment table. o Change the test formula for the direction and strand columns in the checkexptab function that was triggered unexpectedly when an incorrect exptab was provided. o Add a testthat for the checkexptab function. Changes in version 1.1.11 (2025-10-24) o Add indications in the error message of meandifference function if the user has more than two conditions. o In the vignette, the chromosomes are now imported from the package instead of downloading them from the web. Changes in version 1.1.10 (2025-09-03) o Export function from MASS to match ggplot2 update. o Replace SeqinfoForUCSCGenome by retrievechrom in vignette to avoid online resources problems. Changes in version 1.1.9 (2025-08-18) o Unhide and export .retrievechrom function and use it to create chromtabtest in tests to avoid error due to online ressource problems. o Update documentation. Changes in version 1.1.8 (2025-04-22) o Remove acronym in package title. o Remove listing of technology acronyms in Description of DESCRIPTION. o In documentation, replace dontrun by donttest if the example cannot be run or takes more than 5 seconds. o Use tempdir() instead of getwd() by default. o Change package title from "Transcription Elongation Profile" to "Transcription Elongation Profiling". Acronym "tepr" is kept. o Remove the joinfiles function that was used during the bash processing. o kneeallconds can now be run independently of the number of conditions. o \dontrun is used in the examples of functions handling more than two conditions: plotmulti and teprmulti. o package is now available on CRAN. Changes in version 1.1.7 o Replace all identical tests by equal in testthat. o Remove the use of BiocStyle for the vignette. o Move pictures to inst/extdata. o Replace markdown image integration with knitr. o Add check on the type of chromtab at beginning of preprocessing function. o Remove all uppercase in package name in all files. o Remove redundant 'in R' when mentionning package name. o Version submited to CRAN waiting for approval. Changes in version 1.1.6 o Create release to obtain doi on Zenodo. Changes in version 1.1.5 o Update URL to black list repository. o In vignette, add missing url to cugusi.tsv. Changes in version 1.1.3 o In the subfunction .divideannoinwindows of makewindows, replace hardcoded 200 by nbwindows. o Add filter chromtab in quickstart of the vignette. o In vignette, limit chromtabtest to chr13. o Add verifications on chromosome names in preprocessing and blacklisthighmap functions. o Add forcechrom param to the preprocessing and blacklisthighmap functions and modify documentation. o In preprocessing.R, add forcechrom = TRUE in .createbedgraphlistwmean because the verification is done at the start of the preprocessing function. o Set showtime default to FALSE in createtablescores. o Add test on genome name and chromtab at beginning of preprocessing. o Set genomename to NA and saveobjectpath to getwd() by default in preprocessing function. o Add countna to the error message of .extractstr in utils.R. o Add information to the error messages in .extractstr (utils.R), .condcolidx (meandifference.R), averageandfilterexprs and .expressedtrans subfunction, createtablescores, .checkempty (allauc.R), .computeupdown (attenuation.R). o Add tests in the tests/testthat folder for each function. o Add zenodo download commands in the vignette. Data are under doi 10.5281/zenodo.15050723. o Add code to avoid triggering warnings in blacklisthighmap, .removeblackandlowmap, .retrievemaptrack. o Remove tidyselect deprecated message in universegroup.R (lines 119, 127, 143, 153). o Add in testthat condition for macos: Evaluate equality instead of identity. o Add doi after merging with main branch. o Modifications upon suggestions by "R CMD check --as-cran": Set title in case and remove the first sentence of description in DESCRIPTION, change black list url in vignette. Changes in version 1.1.2 o Modifications and corrections to pass R CMD check. o Creation of .returnexpcolnames in utils.R. o Simplification of averageandfilterexprs and create subfunction .expressedtrans. o In .computeecdf, under the comment "Shrink the results back to the transtable keeping ecdf columns", change code to remove the 'dot' usage which throws an error by R CMD check. o In .computeecdf, also change the way column names are modified under the comment "Removing strand from column names" for the same reason. o In .normalizeandsummarize, replace code for "Selecting coord and mean values" to remove the use of dot. o Add a .github/workflows that test the package on windows, macos, and ubuntu o Add a .Rbuildignore to exclude the .github folder and manual.pdf during package creation o Correct bug about direction in loop if dfstrandlist of the function .expressedtrans in averageandfilterexprs. o Folder inst/extdata reduced from 111 Mb to 504K o Add error if no transcript is identified as expressed in averageandfilterexprs. This case prevents the rest of the code to be executed. o Add a README.md o Change outfold = "." parameter to outfold = getwd() in plotauc, plotecdf, plothistoknee, plotmetagenes, and plotmulti to avoid potential errors with windows. o Change tmpfold = "./tmp" to tmpfold = "tmp" in blacklisthighmap and preprocessing to avoid potential errors with windows. o Change finaltabpath = "./" to finaltabpath = getwd() in createtablescores and preprocessing to avoid potential errors with windows. o Change workingdir = "." to workingdir = getwd() in joinfiles. o Rename the default 'tmp' folder by 'tmptepr' to avoid issues of pre-allocated space. Define the default path with file.path(getwd(), "tmptepr"). o In .mergefiles of createtablescores, add specific code when OS is windows. It uses a power-shell syntax and system2. o add file encoding utf8 for windows check in createtablescores. -- vignette o With the reduced data of the package, the preprocesssing in the "quick start" section of the vignette now takes 38 seconds instead of 7 minutes. o Use two different exptab in the package. One for preprocessing and one for the downstream analysis. The code of the quick start section is modified accordingly. o The downstream part is now done on 6 transcripts instead of a 100. This aims at reducing the size of the package. o Display the results of the quick start code o Improve preprocessing description o Reduce code in different sections since quickstart is now executed in background o Add '?' before function names o add figure of the global structure of the package o remove explicit path to current directory and use getwd where appropriate o remove outfold from plot functions in annex o add optional line in quickstart to get chromtab o remove preprocessing in bash section Changes in version 1.1.1 o Optimize the vignette text with Gemini. o Update output of the full tepr analysis in annex of the vignette. o Add allauc and update doc of kneeallconds. o Updated pictures in vignette. Changes in version 1.1.0 o Create a showallcomp function to choose what to exclude in teprmulti dontcompare parameter. o Create a kneeallconds function that enables to calculate knees for each condition separately. o Create section 5.4 "More than two conditions" in the vignette with the "teprmulti analysis", "plotmulti", and "Calculating knee for each condition" subsections. Changes in version 1.0.4 o Remove dontcompare parameter from allauc and tepr. o Add code to remove conditions with a dontcompare vector in teprmulti. Changes in version 1.0.3 o tepr can now handle a single condition. See section 5.6 of the vignette. Changes in version 1.0.2 o Add functions teprmulti and plotmulti to use when more than two conditions are present. New sections 5.4 and 5.5 of the vignette. Changes in version 1.0.1 o Solve bug due to chromtab parameter. o Chromtab is now a parameter in case of connection hickups. o Manual has been updated. o Add code to vignette to use the data provided with the package. Changes in version 1.0.0 o Preprocessing is now done in R. Changes in version 0.0.99 o Pre-processing with bash.