iscream
This is the released version of iscream; for the devel version, see iscream.
Make fast and memory efficient BED file queries, summaries and matrices
Bioconductor version: Release (3.23)
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.
Author: James Eapen [aut, cre] 
, Jacob Morrison [aut] , Nathan Spix [ctb], Hui Shen [aut, ths, fnd]
Maintainer: James Eapen <james.eapen at vai.org>
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 1.2.0, https://bioconductor.org/packages/iscream.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("iscream")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("iscream")| iscream compatible data structures | HTML | R Script |
| htslib.html | HTML | R Script |
| An introduction to iscream | HTML | R Script |
| Manuscript data availabiliy | HTML | |
| Improving iscream performance | HTML | |
| iscream vs Rsamtools::scanTabix | HTML | |
| Plotting TSS methylation profiles | HTML | |
| Reference Manual | ||
| NEWS | Text | |
| INSTALL | Text | |
| LICENSE | Text |
Details
| biocViews | DNAMethylation, DataImport, Sequencing, SingleCell, Software |
| Version | 1.2.0 |
| In Bioconductor since | BioC 3.22 (R-4.5) (1 year) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.4) |
| Imports | Rcpp, Matrix, data.table, methods, pbapply, parallelly, stringfish |
| System Requirements | htslib: htslib-devel (rpm) or libhts-dev (deb) & tabix: htslib-tools (rpm) or tabix (deb) & GNU make |
| URL | https://huishenlab.github.io/iscream/ https://github.com/huishenlab/iscream/ |
| Bug Reports | https://github.com/huishenlab/iscream/issues/ |
See More
| Suggests | BiocFileCache, BiocStyle, bsseq, ggplot2, ggridges, knitr, microbenchmark, rmarkdown, GenomicRanges, IRanges, Rsamtools, SummarizedExperiment, S4Vectors, testthat (>= 3.0.0) |
| Linking To | Rcpp, RcppArmadillo, RcppProgress, RcppSpdlog, Rhtslib, stringfish |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | iscream_1.2.0.tar.gz |
| Windows Binary (x86_64) | iscream_1.2.0.zip |
| macOS Binary (big-sur-x86_64) | iscream_1.2.0.tgz |
| macOS Binary (sonoma-arm64) | iscream_1.2.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/iscream |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/iscream |
| Package Short Url | https://bioconductor.org/packages/iscream/ |
| Package Downloads Report | Download Stats |