sequencing
Introduction to Bioconductor for Sequence Data
Bioconductor version: 3.23 · Package version: 1.36.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("sequencing")Details
| Maintainer | Bioconductor Package Maintainer <maintainer@bioconductor.org> |
| Author | Sonali Arora [aut], Martin Morgan [aut], Bioconductor Package Maintainer [cre] |
| License | Artistic-2.0 |
| URL | https://www.bioconductor.org/help/workflows/sequencing/ |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | BasicWorkflow, ImmunoOncologyWorkflow, Workflow |
| Package Short Url | https://bioconductor.org/packages/sequencing/ |
Citation
From within R, enter citation("sequencing"):
Sonali Arora, Martin Morgan. sequencing: Introduction to Bioconductor for Sequence Data. doi:10.18129/B9.bioc.sequencing, R package version 1.36.0, https://bioconductor.org/packages/sequencing.
Generated from the package metadata; it may differ from the package's own citation.
Download
Follow the installation instructions to use this package in your R session.
| Source package | sequencing_1.36.0.tar.gz |
Dependencies
Depends: R (>= 3.3.0), GenomicRanges, GenomicAlignments, Biostrings, Rsamtools, ShortRead, BiocParallel, rtracklayer, VariantAnnotation, AnnotationHub, BSgenome.Hsapiens.UCSC.hg19, RNAseqData.HNRNPC.bam.chr14