seqpac/DESCRIPTION at master · OestLab/seqpac · GitHub

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Package: seqpac
Type: Package
Title: Seqpac: A Framework for smallRNA analysis in R using Sequence-Based Counts
Version: 1.8.2
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
LazyData: false
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