iscream
This package is for version 3.22 of Bioconductor; for the stable, up-to-date release version, see iscream.
Make fast and memory efficient BED file queries, summaries and matrices
Bioconductor version: 3.22
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")):
Installation
To install this package, start R (version "4.5") 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")| An introduction to iscream | HTML | R Script |
| htslib.html | HTML | R Script |
| Improving iscream performance | HTML | |
| iscream compatible data structures | HTML | R Script |
| iscream vs Rsamtools::scanTabix | HTML | |
| Manuscript data availabiliy | HTML | |
| Plotting TSS methylation profiles | HTML | |
| Reference Manual | ||
| NEWS | Text | |
| INSTALL | Text | |
| LICENSE | Text |
Details
| biocViews | DNAMethylation, DataImport, Sequencing, SingleCell, Software |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.22 (R-4.5) (< 6 months) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.5) |
| 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 |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | iscream_1.0.0.tar.gz |
| Windows Binary (x86_64) | iscream_1.0.0.zip (64-bit only) |
| macOS Binary (x86_64) | iscream_1.0.0.tgz |
| macOS Binary (arm64) | iscream_1.0.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/iscream |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/iscream |
| Bioc Package Browser | https://code.bioconductor.org/browse/iscream/ |
| Package Short Url | https://bioconductor.org/packages/iscream/ |
| Package Downloads Report | Download Stats |