Package: seqpac
Type: Package
Title: Seqpac: A Framework for smallRNA analysis in R using
        Sequence-Based Counts
Version: 1.12.0
Authors@R: c(
    person("Signe", "Isacson", email="signe.skog@liu.se", role= c("aut", "ctb")),
    person("Daniel", "Natt", email="daniel.natt@liu.se", role= c("aut", "fnd")),
    person("Lovisa", "Örkenby", email="lovisa.orkenby@liu.se", role= c("aut", "ctb")),
    person("Alessandro", "Gozzo", email="alessandro.gozzo@liu.se", role= c("aut","ctb", "cre"),
    comment=c(ORCID="0000-0002-6466-627X")),
    person("Anna", "Asratian", email="anna.asratian@liu.se", role= c("aut", "ctb")),
    person("Anita", "Öst", email="anita.ost@liu.se", role= c("aut", "fnd"))
    )
Description: Seqpac provides functions and workflows for analysis of
        short sequenced reads. It was originally developed for small
        RNA analysis, but can be implemented on any sequencing raw data
        (provided as a fastq-file), where the unit of measurement is
        counts of unique sequences. The core of the seqpac workflow is
        the generation and subsequence analysis/visualization of a
        standardized object called PAC. Using an innovative targeting
        system, Seqpac process, analyze and visualize sample or
        sequence group differences using the PAC object. A PAC object
        in its most basic form is a list containing three types of data
        frames. - Phenotype table (P): Sample names (rows) with
        associated metadata (columns) e.g. treatment. - Annotation
        table (A): Unique sequences (rows) with annotation (columns),
        eg. reference alignments. - Counts table (C): Counts of unique
        sequences (rows) for each sample (columns). The PAC-object
        follows the rule: - Row names in P must be identical with
        column names in C. - Row names in A must be identical with row
        names in C. Thus P and A describes the columns and rows in C,
        respectively. The targeting system, will either target specific
        samples in P (pheno_target) or sequences in A (anno_target) and
        group them according to a target column in P and A,
        respectively (see vignettes for more details).
License: GPL-3
Encoding: UTF-8
RoxygenNote: 7.3.3
URL: https://github.com/Oestlab/seqpac
BugReports: https://github.com/OestLab/seqpac/issues
biocViews: Workflow, BasicWorkflow, GeneExpressionWorkflow,
        EpigeneticsWorkflow, AnnotationWorkflow
Depends: R (>= 4.5.0)
Imports: Biostrings (>= 2.46.0), foreach (>= 1.5.1), GenomicRanges (>=
        1.30.3), Rbowtie (>= 1.18.0), ShortRead (>= 1.36.1), tibble (>=
        3.1.2), BiocParallel (>= 1.12.0), cowplot (>= 0.9.4),
        data.table (>= 1.14.0), digest (>= 0.6.27), doParallel (>=
        1.0.16), dplyr (>= 1.0.6), factoextra (>= 1.0.7), FactoMineR
        (>= 1.41), ggplot2 (>= 4.0.2), IRanges (>= 2.12.0), parallel
        (>= 3.4.4), reshape2 (>= 1.4.4), rtracklayer (>= 1.38.3),
        stringr (>= 1.4.0), stats (>= 3.4.4), methods, S4Vectors, readr
Suggests: benchmarkme (>= 0.6.0), DESeq2 (>= 1.18.1), GenomeInfoDb (>=
        1.14.0), gginnards (>= 0.0.2), qqman (>= 0.1.8), rmarkdown,
        BiocStyle, knitr, testthat, UpSetR (>= 1.4.0), venneuler,
        R.utils, bigreadr, vroom
VignetteBuilder: knitr
Config/pak/sysreqs: cmake libfreetype6-dev make libbz2-dev libicu-dev
        libjpeg-dev liblzma-dev libpng-dev libuv1-dev libxml2-dev
        libssl-dev libx11-dev xz-utils zlib1g-dev
Repository: Bioconductor 3.23
Date/Publication: 2026-04-28 12:44:54 UTC
RemoteUrl: https://github.com/bioc/seqpac
RemoteRef: RELEASE_3_23
RemoteSha: 32327358db6b9bfba00447e145fd26309278e7ba
NeedsCompilation: no
Packaged: 2026-10-04 17:16:39 UTC; root
Author: Signe Isacson [aut, ctb],
  Daniel Natt [aut, fnd],
  Lovisa Örkenby [aut, ctb],
  Alessandro Gozzo [aut, ctb, cre] (ORCID:
    <https://orcid.org/0000-0002-6466-627X>),
  Anna Asratian [aut, ctb],
  Anita Öst [aut, fnd]
Maintainer: Alessandro Gozzo <alessandro.gozzo@liu.se>