seqpac

DOI: 10.18129/B9.bioc.seqpac  

Seqpac: A Framework for smallRNA analysis in R using Sequence-Based Counts

Bioconductor version: Release (3.17)

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).

Author: Daniel Natt [aut, cre, fnd], Lovisa Örkenby [ctb], Signe Skog [ctb], Anita Öst [aut, fnd]

Maintainer: Daniel Natt <daniel.natt at liu.se>

Installation

To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("seqpac")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("seqpac")

 

HTML	R Script	A guide to small RNA analysis using Seqpac
Text		NEWS

Details

biocViews	AnnotationWorkflow, BasicWorkflow, EpigeneticsWorkflow, GeneExpressionWorkflow, Workflow
Version	1.0.0
License	GPL-3
Depends	R (>= 4.2.0)
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
LinkingTo
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, readr, vroom
SystemRequirements
Enhances
URL	https://github.com/Danis102/seqpac
BugReports	https://github.com/Danis102/seqpac/issues
Depends On Me
Imports Me
Suggests Me
Links To Me

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	seqpac_1.0.0.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/seqpac
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/seqpac
Package Short Url	https://bioconductor.org/packages/seqpac/
Package Downloads Report	Download Stats