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baseq

INFRA · APIS
Velocity0.0

Basic Sequence Processing Tool for Biological Data

github.com/ambuvjyn/baseq ↗

A basic DNA and RNA sequence toolkit that went quiet for three years, then jumped to 2.0.

bioinformaticssequence-processingfasta-fastqdormant-projectr-package
◆Current state
baseq provides elementary sequence processing for biological data in R: cleaning DNA and RNA strings, counting bases and patterns, GC content, translation and reverse complement, and readers and writers for FASTA and FASTQ. The 0.1.x releases all landed in a two-week window in 2023, several of them backfilled within seconds of each other and in an order that does not match their version numbers. A 2.0 tag then appeared in March 2026 after three years of silence, with release notes naming only a development pull request and a CI workflow.
◆Where it's heading
The visible history is a package assembled quickly and then left alone. Across the 0.1.x tags the notes are a printed inventory of exported functions rather than a changelog, with consecutive versions restating the same list unchanged, so the actual increments have to be inferred by diffing those inventories: file-level cleaning and GC content arrived at 0.1.3, and the FASTA and FASTQ readers, writers and converters at 0.1.1. What the 2.0 release contains is not stated anywhere in the feed, which makes the most significant-looking tag here also the least legible.
◆Prediction
Nothing in these entries supports a confident prediction. The reappearance of activity after three years and the addition of a CI workflow suggest maintenance has resumed, but until a release describes its own contents there is no basis for saying in what direction.

◆Recent moves

  1. 5mo ago

    Version 2.0 arrives after three years, contents undisclosed

    A jump from 0.1.4 to 2.0 following three years without a release, with notes listing only a development pull request and the addition of a GitHub Actions workflow. The version jump implies substantial change but the entry does not describe any, so what users get from upgrading cannot be determined from this feed.

    View source ↗
  2. 3y ago

    baseq Version 0.1.4

    The release notes restate the previous version's function inventory without change, so nothing in this entry identifies what 0.1.4 altered. Two weeks separate it from 0.1.3, the last release to show a genuinely different list.

    View source ↗
  3. 3y ago

    Separate DNA and RNA cleaning, plus file-level helpers

    The inventory grows here for the first time since the initial burst: dedicated DNA and RNA cleaning functions, file variants of both, and a file-level GC content function. Since these notes are inventories rather than changelogs, comparing successive lists is the only way to locate the change.

    View source ↗
  4. 3y ago

    baseq Version 0.1.2

    Restates the same function inventory as the version tagged a minute earlier, with no additions or removals. One of several tags pushed in rapid succession whose stamps do not follow their version numbers.

    View source ↗
  5. 3y ago

    First CRAN release: eleven core sequence operations

    ⚡ SPARK

    The original release, carrying a flat list of eleven functions covering sequence cleaning, base and pattern counting, GC content, DNA and RNA interconversion, translation, reverse complement and FASTA reading. Everything later in the 0.1.x line extends this base with file handling and FASTQ support.

    View source ↗
  6. 3y ago

    FASTA and FASTQ readers, writers and converters added

    Reorganises the inventory into categories and adds the file input and output layer: FASTA and FASTQ readers returning data frames or lists, matching writers, and a FASTQ to FASTA converter. Despite carrying a stamp thirty seconds earlier than the initial release, the larger function list places this after it.

    View source ↗