Package: seqpac
Type: Package
Title: Seqpac: A Framework for smallRNA analysis in R using
        Sequence-Based Counts
Version: 1.11.0
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: 7.3.2
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 (>= 3.3.3), 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
git_url: https://git.bioconductor.org/packages/seqpac
git_branch: devel
git_last_commit: 094789d
git_last_commit_date: 2025-10-29
Repository: Bioconductor 3.23
Date/Publication: 2025-11-07
NeedsCompilation: no
Packaged: 2025-11-07 18:12:36 UTC; biocbuild
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>
