NEWS

---

tepr 1.1.15 (2026-03-06)

• Replace row-wise apply() overlap counting in .wmeanvec() with vectorized overlap-length computation.
• Vectorize transcript-to-window splitting in makewindows() internals (remove cluster-based parallel approach).
• Reduce repeated maptrack reads by optionally loading the full track once and filtering per chromosome.
• Improve .retrievebgval skipping conversion to data.frame.
• Update docs/version/NEWS accordingly.

tepr 1.1.14 (2026-01-28)

• Fix: Add missing expdf argument to plotmulti internal functions.

tepr 1.1.13 (2025-12-11)

• Remove unused variable in genesECDF.
• Remove digit in variables.
• Fix bug due to row and col names in teprmulti.
• Add table of contents to vignette.
• Add installation section to vignette with GitHub install instructions.
• Standardize all stop() error messages with consistent '[tepr] Error:' prefix.
• Standardize all warning() messages with consistent '[tepr] Warning:' prefix.
• Fix incorrect warning text in plothistoknee and plotmetagenes (previously said 'auc' when displaying histograms and metagenes).
• Refactor the error messages in the tests for consistency and clarity.
• Replace deprecated 'size' with 'linewidth' in geom_line (ggplot2 3.4.0+).

tepr 1.1.12 (2025-11-04)

• An error message is now appearing if the user provide a wrong experiment table.
• Change the test formula for the direction and strand columns in the checkexptab function that was triggered unexpectedly when an incorrect exptab was provided.
• Add a testthat for the checkexptab function.

tepr 1.1.11 (2025-10-24)

• Add indications in the error message of meandifference function if the user has more than two conditions.
• In the vignette, the chromosomes are now imported from the package instead of downloading them from the web.

tepr 1.1.10 (2025-09-03)

• Export function from MASS to match ggplot2 update.
• Replace SeqinfoForUCSCGenome by retrievechrom in vignette to avoid online resources problems.

tepr 1.1.9 (2025-08-18)

• Unhide and export .retrievechrom function and use it to create chromtabtest in tests to avoid error due to online ressource problems.
• Update documentation.

tepr 1.1.8 (2025-04-22)

• Remove acronym in package title.
• Remove listing of technology acronyms in Description of DESCRIPTION.
• In documentation, replace dontrun by donttest if the example cannot be run or takes more than 5 seconds.
• Use tempdir() instead of getwd() by default.
• Change package title from "Transcription Elongation Profile" to "Transcription Elongation Profiling". Acronym "tepr" is kept.
• Remove the joinfiles function that was used during the bash processing.
• kneeallconds can now be run independently of the number of conditions.
• \dontrun is used in the examples of functions handling more than two conditions: plotmulti and teprmulti.
• package is now available on CRAN.

tepr 1.1.7

• Replace all identical tests by equal in testthat.
• Remove the use of BiocStyle for the vignette.
• Move pictures to inst/extdata.
• Replace markdown image integration with knitr.
• Add check on the type of chromtab at beginning of preprocessing function.
• Remove all uppercase in package name in all files.
• Remove redundant 'in R' when mentionning package name.
• Version submited to CRAN waiting for approval.

tepr 1.1.6

• Create release to obtain doi on Zenodo.

tepr 1.1.5

• Update URL to black list repository.
• In vignette, add missing url to cugusi.tsv.

tepr 1.1.3

• In the subfunction .divideannoinwindows of makewindows, replace hardcoded 200 by nbwindows.
• Add filter chromtab in quickstart of the vignette.
• In vignette, limit chromtabtest to chr13.
• Add verifications on chromosome names in preprocessing and blacklisthighmap functions.
• Add forcechrom param to the preprocessing and blacklisthighmap functions and modify documentation.
• In preprocessing.R, add forcechrom = TRUE in .createbedgraphlistwmean because the verification is done at the start of the preprocessing function.
• Set showtime default to FALSE in createtablescores.
• Add test on genome name and chromtab at beginning of preprocessing.
• Set genomename to NA and saveobjectpath to getwd() by default in preprocessing function.
• Add countna to the error message of .extractstr in utils.R.
• Add information to the error messages in .extractstr (utils.R), .condcolidx (meandifference.R), averageandfilterexprs and .expressedtrans subfunction, createtablescores, .checkempty (allauc.R), .computeupdown (attenuation.R).
• Add tests in the tests/testthat folder for each function.
• Add zenodo download commands in the vignette. Data are under doi 10.5281/zenodo.15050723.
• Add code to avoid triggering warnings in blacklisthighmap, .removeblackandlowmap, .retrievemaptrack.
• Remove tidyselect deprecated message in universegroup.R (lines 119, 127, 143, 153).
• Add in testthat condition for macos: Evaluate equality instead of identity.
• Add doi after merging with main branch.
• 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.

tepr 1.1.2

• Modifications and corrections to pass R CMD check.
• Creation of .returnexpcolnames in utils.R.
• Simplification of averageandfilterexprs and create subfunction .expressedtrans.
• 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.
• In .computeecdf, also change the way column names are modified under the comment "Removing strand from column names" for the same reason.
• In .normalizeandsummarize, replace code for "Selecting coord and mean values" to remove the use of dot.
• Add a .github/workflows that test the package on windows, macos, and ubuntu
• Add a .Rbuildignore to exclude the .github folder and manual.pdf during package creation
• Correct bug about direction in loop if dfstrandlist of the function .expressedtrans in averageandfilterexprs.
• Folder inst/extdata reduced from 111 Mb to 504K
• Add error if no transcript is identified as expressed in averageandfilterexprs. This case prevents the rest of the code to be executed.
• Add a README.md
• Change outfold = "." parameter to outfold = getwd() in plotauc, plotecdf, plothistoknee, plotmetagenes, and plotmulti to avoid potential errors with windows.
• Change tmpfold = "./tmp" to tmpfold = "tmp" in blacklisthighmap and preprocessing to avoid potential errors with windows.
• Change finaltabpath = "./" to finaltabpath = getwd() in createtablescores and preprocessing to avoid potential errors with windows.
• Change workingdir = "." to workingdir = getwd() in joinfiles.
• Rename the default 'tmp' folder by 'tmptepr' to avoid issues of pre-allocated space. Define the default path with file.path(getwd(), "tmptepr").
• In .mergefiles of createtablescores, add specific code when OS is windows. It uses a power-shell syntax and system2.
• add file encoding utf8 for windows check in createtablescores. -- vignette
• 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.
• 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.
• The downstream part is now done on 6 transcripts instead of a 100. This aims at reducing the size of the package.
• Display the results of the quick start code
• Improve preprocessing description
• Reduce code in different sections since quickstart is now executed in background
• Add '?' before function names
• add figure of the global structure of the package
• remove explicit path to current directory and use getwd where appropriate
• remove outfold from plot functions in annex
• add optional line in quickstart to get chromtab
• remove preprocessing in bash section

tepr 1.1.1

• Optimize the vignette text with Gemini.
• Update output of the full tepr analysis in annex of the vignette.
• Add allauc and update doc of kneeallconds.
• Updated pictures in vignette.

tepr 1.1.0

• Create a showallcomp function to choose what to exclude in teprmulti dontcompare parameter.
• Create a kneeallconds function that enables to calculate knees for each condition separately.
• Create section 5.4 "More than two conditions" in the vignette with the "teprmulti analysis", "plotmulti", and "Calculating knee for each condition" subsections.

tepr 1.0.4

• Remove dontcompare parameter from allauc and tepr.
• Add code to remove conditions with a dontcompare vector in teprmulti.

tepr 1.0.3

• tepr can now handle a single condition. See section 5.6 of the vignette.

tepr 1.0.2

• Add functions teprmulti and plotmulti to use when more than two conditions are present. New sections 5.4 and 5.5 of the vignette.

tepr 1.0.1

• Solve bug due to chromtab parameter.
• Chromtab is now a parameter in case of connection hickups.
• Manual has been updated.
• Add code to vignette to use the data provided with the package.

tepr 1.0.0

• Preprocessing is now done in R.

tepr 0.0.99

• Pre-processing with bash.