iscream
This is thereleased version of iscream; for the devel version, seeiscream.
Make fast and memory efficient BED file queries, summaries and matrices
Bioconductor version: Release (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]
ORCID: 0000-0001-6016-3598, Jacob Morrison [aut] ORCID: 0000-0001-8592-4744, Nathan Spix [ctb], Hui Shen [aut, ths, fnd] ORCID: 0000-0001-9767-4084
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 appropriateBioconductor 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 + fileLICENSE |
| 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
FollowInstallation 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 |