sequencing
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see sequencing.
Introduction to Bioconductor for Sequence Data
Bioconductor version: 3.9
Bioconductor enables the analysis and comprehension of high- throughput genomic data. We have a vast number of packages that allow rigorous statistical analysis of large data while keeping technological artifacts in mind. Bioconductor helps users place their analytic results into biological context, with rich opportunities for visualization. Reproducibility is an important goal in Bioconductor analyses. Different types of analysis can be carried out using Bioconductor, for example; Sequencing : RNASeq, ChIPSeq, variants, copy number etc.; Microarrays: expression, SNP, etc.; Domain specific analysis : Flow cytometry, Proteomics etc. For these analyses, one typically imports and works with diverse sequence-related file types, including fasta, fastq, BAM, gtf, bed, and wig files, among others. Bioconductor packages support import, common and advanced sequence manipulation operations such as trimming, transformation, and alignment including quality assessment.
Author: Sonali Arora [aut], Martin Morgan [aut], Bioconductor Package Maintainer [cre]
Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org>
citation("sequencing")):
Installation
To install this package, start R (version "3.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("sequencing")
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("sequencing")| Introduction to Bioconductor for Sequence Data | HTML | R Script |
Details
| biocViews | BasicWorkflow, ImmunoOncologyWorkflow, Workflow |
| Version | 1.8.0 |
| License | Artistic-2.0 |
| Depends | R (>= 3.3.0), GenomicRanges, GenomicAlignments, Biostrings, Rsamtools, ShortRead, BiocParallel, rtracklayer, VariantAnnotation, AnnotationHub, BSgenome.Hsapiens.UCSC.hg19, RNAseqData.HNRNPC.bam.chr14 |
| Imports | |
| System Requirements | |
| URL | https://www.bioconductor.org/help/workflows/sequencing/ |
See More
| Suggests | knitr, rmarkdown, BiocStyle |
| Linking To | |
| Enhances | |
| 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 | sequencing_1.8.0.tar.gz |
| Windows Binary | |
| Mac OS X 10.11 (El Capitan) | |
| Source Repository | git clone https://git.bioconductor.org/packages/sequencing |
| Source Repository (Developer Access) | git clone [email protected]:packages/sequencing |
| Package Short Url | https://bioconductor.org/packages/sequencing/ |
| Package Downloads Report | Download Stats |