seqpac

DOI: 10.18129/B9.bioc.seqpac    

This is the development version of seqpac; to use it, please install the devel version of Bioconductor.

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

Bioconductor version: Development (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>

Citation (from within R, enter citation("seqpac")):

Installation

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

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 0.99.18
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
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Package Archives

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

Source Package seqpac_0.99.18.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/
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