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protr 1.7-3
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
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
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
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
Bug fixes
- Fixed a minor bug in
extractProtFP()
and
extractProtFPGap()
when index = NULL
(thanks,
@fcampelo,
#30).
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
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
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
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
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
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
Bug fixes
- Resolved a critical bug due to improper
ifelse
conditioning (3f6e106)
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
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
Improvements
- Converted table images to Markdown tables in the vignette.
- Updated the screenshot of protrweb in the vignette.
protr 1.4-0
Improvements
- Migrated from Sweave-based PDF vignette to knitr-based HTML
vignette.
protr 1.3-0
Improvements
- Fix obsolete URLs.
- Better R code formatting.
- Better function documentation and vignette formatting.
protr 1.2-1
Improvements
- New documentation website: https://nanx.me/protr/.
- Added Windows continuous integration support using AppVeyor.
- Better R file naming scheme.
protr 1.2-0
Improvements
- Added continuous integration.
- Code code style improvements.
protr 1.1-1
Bug fixes
- Fix URLs that cannot be accessed by
curl -I -L
:
- Use http://protr.org.
- Remove all inaccessible URLs.
protr 1.1-0
2015-12-28
Bug fixes
- Bug fix in
extractCTDD()
.
protr 1.0-1
Bug fixes
- Improvements for dealing with boundary cases in several functions
(thanks for @koefoed’s patches).
Improvements
- Added citation information.
protr 0.5-1
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
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
Improvements
- Added a
LICENSE
file according to CRAN policies.
protr 0.2-0
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
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()
.
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.