# ------------------------------------------------
# CITATION.cff file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
# ------------------------------------------------
 
cff-version: 1.2.0
message: 'To cite package "seqpac" in publications use:'
type: software
license: GPL-3.0-only
title: 'seqpac: Seqpac: A Framework for smallRNA analysis in R using Sequence-Based
  Counts'
version: 1.12.0
doi: 10.1101/2021.03.19.436151
abstract: '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).'
authors:
- family-names: Isacson
  given-names: Signe
  email: signe.skog@liu.se
- family-names: Natt
  given-names: Daniel
  email: daniel.natt@liu.se
- family-names: Örkenby
  given-names: Lovisa
  email: lovisa.orkenby@liu.se
- family-names: Gozzo
  given-names: Alessandro
  email: alessandro.gozzo@liu.se
  orcid: https://orcid.org/0000-0002-6466-627X
- family-names: Asratian
  given-names: Anna
  email: anna.asratian@liu.se
- family-names: Öst
  given-names: Anita
  email: anita.ost@liu.se
preferred-citation:
  type: article
  title: 'Seqpac: A New Framework for small RNA analysis in R using Sequence-Based
    Counts'
  authors:
  - family-names: Skog
    given-names: Signe
  - family-names: Orkenby
    given-names: Lovisa
  - family-names: Kugelberg
    given-names: Unn
  - family-names: Tariq
    given-names: Kanwal
  - family-names: Farrants
    given-names: Ann-Kristin Ostlund
  - family-names: Ost
    given-names: Anita
  - family-names: Natt
    given-names: Daniel
    email: daniel.natt@liu.se
  journal: bioRxiv
  year: '2021'
  doi: 10.1101/2021.03.19.436151
  volume: _
  issue: _
  start: _
repository: https://bioconductor.org/
repository-code: https://github.com/OestLab/seqpac
commit: 32327358db6b9bfba00447e145fd26309278e7ba
url: https://github.com/Oestlab/seqpac
date-released: '2026-04-28'
contact:
- family-names: Gozzo
  given-names: Alessandro
  email: alessandro.gozzo@liu.se
  orcid: https://orcid.org/0000-0002-6466-627X