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Changelog

Source: NEWS.md

protr 1.7-4

CRAN release: 2024-09-11

Improvements

  • Improved dependency error handling for similarity calculation functions that use pairwise sequence alignment (#56):
    • Added upfront checks for Biostrings and pwalign dependencies.
    • Now they throw clear errors early if dependency conditions are not met.
    • The new behavior prevents error messages from appearing in results.

protr 1.7-3

CRAN release: 2024-08-30

Improvements

  • For sequence similarity calculations using pairwise sequence alignment, the Biostrings version is now detected at runtime to determine if the pwalign package is needed. This is because the relevant components have been moved from Biostrings to pwalign since Bioconductor 3.19 and Biostrings 2.72.0. This enhancement ensures that protr works properly regardless of the versions of R, Bioconductor, and Biostrings installed (thanks, @ecrespoSSF, #52).

protr 1.7-2

CRAN release: 2024-07-21

Improvements

  • Running citation("protr") now gives better output with the BibTeX citation key. This is improved by adding the key argument to the bibentry() call in inst/CITATION (#49).
  • Revised vignette("protr") to fix typos and grammar issues. Updated images to use knitr::include_graphics() chunks, resolving pkgdown 2.1.0 accessibility hints for missing alt text (#50).

protr 1.7-1

CRAN release: 2024-04-20

New features

  • crossSetSim() now gains two new arguments batches and verbose.

    The batches argument allows users to split the similarity computations into multiple batches, which is useful when dealing with a large number of sequences and limited RAM. The verbose argument enables progress updates during the computation. This brings crossSetSim() to feature parity with parSeqSim(). (thanks, @ofleitas, #41)

  • A new function crossSetSimDisk() has been implemented as a disk-based version of crossSetSim().

    This function follows a similar approach to parSeqSimDisk(), where partial results from each batch are cached on the hard drive and merged at the end. This allows for processing larger protein sequence sets that may not fit into RAM (#41).

protr 1.7-0

CRAN release: 2023-10-30

New features

  • crossSetSim() is added for calculating pairwise similarity between two sets of protein sequence based on sequence alignment (thanks, @seb-mueller, #34).

protr 1.6-3

CRAN release: 2023-03-05

Bug fixes

Improvements

  • Added a comment about system.file() usage to avoid confusion (thanks, @jonalv, #31).
  • Replaced previous CI/CD solutions with GitHub Actions workflows.
  • Fixed broken or moved links in function documentation and vignettes.
  • Replaced the original logo with a new hex sticker logo.

protr 1.6-2

CRAN release: 2019-05-18

Improvements

  • Switched to the tidyverse code style.
  • Updated GitHub repository links to reflect the handle change.
  • Removed AppVeyor CI due to the frequent Bioconductor dependency installation issues.

protr 1.6-1

CRAN release: 2019-02-24

Improvements

  • Added a new argument batches to parSeqSim(). The new argument supports breaking down the pairwise similarity computation into smaller batches. This is useful when you have a large number of protein sequences, enough number of CPU cores, but not enough RAM to compute and hold all the pairwise similarities in a single batch. Also, use the other new argument verbose to track the computation progress.

New features

  • Added a new function parSeqSimDisk(). Compared to the in-memory version parSeqSim(), this new function caches the partial results in each batch to the hard drive and merges the results together in the end. This could further reduce the memory usage for parallel similarity computations involving a large number of protein sequences.

Bug fixes

  • Fixed an issue in parGOSim() that will create minor numerical inconsistencies in results due to argument matching.

protr 1.6-0

CRAN release: 2019-02-11

Bug fixes

  • Updated twoGOSim() and parGOSim() to use the latest GOSemSim API for computing GO based semantic similarity. Issues in the code examples are also fixed. We thank Denisa Duma for the feedback.

protr 1.5-2

CRAN release: 2018-11-22

Bug fixes

  • Fixed the API endpoint issue (from HTTP to HTTPS) in getUniProt().

Improvements

  • Added two new parameters gap.opening and gap.extension to parSeqSim(), allowing more flexible tuning of the sequence alignment for more types of amino acid sequence data. We thank Dr. Maisa Pinheiro for the feedback.
  • Added floating TOC and new CSS style in the vignette to improve navigation and readability.

protr 1.5-1

CRAN release: 2018-07-13

New features

  • Added a new function removeGaps() for removing/replacing gaps (-) or any irregular characters from protein sequences, to make them suitable for feature extraction or sequence alignment based similarity computation. We thank Dr. Maisa Pinheiro for the feedback.

protr 1.5-0

CRAN release: 2017-11-18

Bug fixes

  • Resolved a critical bug due to improper ifelse conditioning () for the distribution descriptor in CTD. We thank Jielu Yan from the University of Macau for kindly reporting this issue.

Improvements

  • General fixes and improvements for the package vignette.

protr 1.4-2

CRAN release: 2017-09-29

Improvements

  • Functions are now organized into sections on the documentation website (https://nanx.me/protr/reference/).
  • Use system font stack instead of Google Fonts in vignettes to avoid pandoc SSL issue.

protr 1.4-1

CRAN release: 2017-07-09

Improvements

  • Converted table images to Markdown tables in the vignette.
  • Updated the screenshot of protrweb in the vignette.

protr 1.4-0

CRAN release: 2017-06-06

Improvements

  • Migrated from Sweave-based PDF vignette to knitr-based HTML vignette.

protr 1.3-0

CRAN release: 2017-05-08

Improvements

  • Fix obsolete URLs.
  • Better R code formatting.
  • Better function documentation and vignette formatting.

protr 1.2-1

CRAN release: 2016-12-30

Improvements

  • New documentation website: https://nanx.me/protr/.
  • Added Windows continuous integration support using AppVeyor.
  • Better R file naming scheme.

protr 1.2-0

CRAN release: 2016-11-12

Improvements

  • Added continuous integration.
  • Code code style improvements.

protr 1.1-1

CRAN release: 2015-12-29

Bug fixes

  • Fix URLs that cannot be accessed by curl -I -L:
    1. Use http://protr.org.
    2. Remove all inaccessible URLs.

protr 1.1-0

2015-12-28

Bug fixes

protr 1.0-1

CRAN release: 2015-11-27

Bug fixes

  • Improvements for dealing with boundary cases in several functions (thanks for @koefoed’s patches).

Improvements

  • Added citation information.

protr 0.5-1

CRAN release: 2014-12-24

Improvements

  • Minor improvements and fixes for documentation.

protr 0.5-0

2014-12-18

Improvements

  • Added functions allowing users to specify their own classification of the amino acid.
  • Documentation improvements.
  • Other minor improvements.

protr 0.4-1

CRAN release: 2014-10-10

Improvements

  • General documentation improvements.

protr 0.4-0

2014-09-20

New features

  • Added profile-based descriptors derived by PSSM.

protr 0.3-0

2014-06-20

Improvements

  • Added an example workflow using protr in the vignette.

protr 0.2-1

CRAN release: 2014-01-25

Improvements

  • Added a LICENSE file according to CRAN policies.

protr 0.2-0

CRAN release: 2013-12-19

New features

  • Second release.
  • Added Proteochemometric (PCM) Modeling descriptors, parallelized similarity computation derived by protein sequence alignment and Gene Ontology (GO) semantic similarity measures between a list of protein sequences / GO terms / Entrez gene IDs.
  • Added miscellaneous tools and datasets.
  • Initial version of scales-based descriptors derived by principal components analysis.
  • Initial version of scales-based descriptors derived by AA-properties (AAindex).
  • Initial version of scales-based descriptors derived by 20+ classes of 2D and 3D molecular descriptors.
  • Initial version of scales-based descriptors derived by factor analysis.
  • Initial version of scales-based descriptors derived by multidimensional scaling.
  • Initial version of BLOSUM and PAM Matrix-Derived Descriptors.
  • Initial version of parallelized pairwise similarity calculation with a list of protein sequences.
  • Initial version of pairwise semantic similarity calculation with a list of GO terms / Entrez gene IDs.
  • Initial version of Auto Cross Covariance (ACC) for generating scales-based descriptors of the same length.
  • Introducing ProtWeb, the web service based on protr: http://protr.org.

protr 0.1-0

CRAN release: 2012-11-18

New features

  • Initial version.
  • First version of Amino Acid Composition descriptor.
  • First version of Dipeptide Composition descriptor.
  • First version of Tripeptide Composition descriptor.
  • First version of Normalized Moreau-Broto Autocorrelation descriptor.
  • First version of Moran Autocorrelation descriptor.
  • First version of Geary Autocorrelation descriptor.
  • First version of CTD - Composition descriptor.
  • First version of CTD - Transition descriptor.
  • First version of CTD - Distribution descriptor.
  • First version of Conjoint Triad descriptor.
  • First version of Sequence Order Coupling Number descriptor.
  • First version of Quasi-Sequence-Order descriptor.
  • First version of Pseudo Amino Acid Composition descriptor.
  • First version of Amphiphilic Pseudo Amino Acid Composition descriptor.
  • First version of readFASTA().
  • First version of getUniProt().
  • First version of protcheck().
  • First version of protseg().