iscream
Make fast and memory efficient BED file queries, summaries and matrices
Bioconductor version: 3.24 · Package version: 1.3.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
BED files store ranged genomic data that can be queried even when the files are compressed. iscream can query data from BED files and return them in muliple formats: parsed records or their summary statistics as data frames or GenomicRanges objects, and matrices as matrix, GenomicRanges, or SummarizedExperiment objects. iscream also provides specialized support for importing methylation data.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("iscream")Details
| Maintainer | James Eapen <james.eapen@vai.org> |
| Author | James Eapen [aut, cre] (ORCID: <https://orcid.org/0000-0001-6016-3598>), Jacob Morrison [aut] (ORCID: <https://orcid.org/0000-0001-8592-4744>), Nathan Spix [ctb], Hui Shen [aut, ths, fnd] (ORCID: <https://orcid.org/0000-0001-9767-4084>) |
| License | MIT + file LICENSE |
| URL | https://huishenlab.github.io/iscream/, https://github.com/huishenlab/iscream/ |
| Bug Reports | https://github.com/huishenlab/iscream/issues/ |
| System Requirements | htslib: htslib-devel (rpm) or libhts-dev (deb) & tabix: htslib-tools (rpm) or tabix (deb) & GNU make |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | DNAMethylation, DataImport, Sequencing, SingleCell, Software |
| Package Short Url | https://bioconductor.org/packages/iscream/ |
Citation
From within R, enter citation("iscream"):
James Eapen, Jacob Morrison, Hui Shen. iscream: Make fast and memory efficient BED file queries, summaries and matrices. doi:10.18129/B9.bioc.iscream, R package version 1.3.0, https://bioconductor.org/packages/iscream.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
- An introduction to iscream
- Getting htslib headers
- Improving iscream performance
- iscream compatible data structures
- iscream vs Rsamtools::scanTabix
- Manuscript data availabiliy
- Plotting TSS methylation profiles
Download
Follow the installation instructions to use this package in your R session.
| Source package | iscream_1.3.0.tar.gz |
| macOS binary (arm64) | iscream_1.3.0.tgz |
| macOS binary (x86_64) | iscream_1.3.0.tgz |
Dependencies
Depends: R (>= 4.4)
Imports: Rcpp, Matrix, data.table, methods, pbapply, parallelly, stringfish
LinkingTo: Rcpp, RcppArmadillo, RcppProgress, RcppSpdlog, Rhtslib, stringfish
Suggests: BiocFileCache, BiocStyle, bsseq, ggplot2, ggridges, knitr, microbenchmark, rmarkdown, GenomicRanges, IRanges, Rsamtools, SummarizedExperiment, S4Vectors, testthat (>= 3.0.0)