Package: iscream 1.3.0

James Eapen

iscream: Make fast and memory efficient BED file queries, summaries and matrices

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.

Authors:James Eapen [aut, cre], Jacob Morrison [aut], Nathan Spix [ctb], Hui Shen [aut, ths, fnd]

iscream_1.3.0.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
iscream/json (API)

# Install 'iscream' in R:
install.packages('iscream', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/huishenlab/iscream/issues

Pkgdown/docs site:https://huishenlab.github.io

Uses libs:
  • curl– Easy-to-use client-side URL transfer library
  • bzip2– High-quality block-sorting file compressor library
  • xz-utils– XZ-format compression library
  • zlib– Compression library
  • c++– GNU Standard C++ Library v3
  • openmp– GCC OpenMP (GOMP) support library

On BioConductor:iscream-1.3.0(bioc 3.24)iscream-1.2.0(bioc 3.23)

dataimportsoftwaresequencingsinglecelldnamethylationbedrcpptabixwgbscurlbzip2xz-utilszlibcppopenmp

6.27 score 12 scripts 17 exports 12 dependencies

Last updated from:a142d5418b. Checks:1 WARNING, 10 OK, 3 FAIL. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING265
linux-devel-arm64OK251
linux-devel-x86_64OK345
source / vignettesOK367
linux-release-arm64OK282
linux-release-x86_64OK363
macos-release-arm64OK235
macos-release-x86_64OK451
macos-oldrel-arm64OK153
macos-oldrel-x86_64OK481
windows-develFAIL144
windows-releaseFAIL145
windows-oldrelOK313
wasm-releaseFAIL209

Exports:get_df_stringget_granges_stringget_log_levelget_threadshtslib_versionmake_matmake_mat_bsseqmake_mat_grmake_mat_sequery_chromsset_log_levelset_threadssummarize_meth_regionssummarize_regionstabixtabix_grtabix_raw

Dependencies:data.tablelatticeMatrixparallellypbapplyRcppRcppArmadilloRcppParallelRcppProgressRcppSpdlogRhtslibstringfish

An introduction to iscream
Introduction | Installation | Loading iscream | tabix() | Setup | Making queries | Using r Biocpkg("GenomicRanges") | Setting column names | Rsamtools-style output | WGBS BED files | summarize_regions() | make_mat() | Further reading | Session info | References
Rendered fromiscream.Rmdusingknitr::rmarkdown

Last update: 2026-04-21
Started: 2025-01-15

iscream vs Rsamtools::scanTabix
One file | Multiple files | Parsing records into a data frame | Multiple files as data frame | All benchmarks | Runtime | Session info
Rendered fromtabix.Rmdusingknitr::rmarkdown

Last update: 2025-12-29
Started: 2025-06-24

Improving iscream performance
Setup | Input BED files | Regions | Multithreading | tabix() | summarize_regions | make_mat | Session info | References
Rendered fromperformance.Rmdusingknitr::rmarkdown

Last update: 2025-12-29
Started: 2025-07-15

Plotting TSS methylation profiles
Setup | Download the data | Using tabix() | Get the Transcription start sites and flanking regions | Make a tabix query of the TSS flanking regions | Summarize average methylation profile around TSS | Plot average methylation profiles around the TSS | Using summarize_regions | Session info
Rendered fromTSS.Rmdusingknitr::rmarkdown

Last update: 2025-12-29
Started: 2025-01-15

iscream compatible data structures
r Biocpkg("GenomicRanges") | From tabix queries | From summarize_regions() | From make_mat | r Biocpkg("SummarizedExperiment") | Making BSseq objects | Session info
Rendered fromdata_structures.Rmdusingknitr::rmarkdown

Last update: 2025-12-29
Started: 2025-01-15

Getting htslib headers
Conda/miniconda/mamba/micromamba | Pixi | Session info
Rendered fromhtslib.rmdusingknitr::rmarkdown

Last update: 2025-10-21
Started: 2025-04-22

Manuscript data availabiliy
Datasets | References
Rendered frommanuscript_data.Rmdusingknitr::rmarkdown

Last update: 2025-02-12
Started: 2025-02-12