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
iscream_1.3.0.zip(r-4.7)iscream_1.3.0.zip(r-4.6)iscream_1.3.0.zip(r-4.5)
iscream_1.3.0.tgz(r-4.6-x86_64)iscream_1.3.0.tgz(r-4.6-arm64)iscream_1.3.0.tgz(r-4.5-x86_64)iscream_1.3.0.tgz(r-4.5-arm64)
iscream_1.3.0.tar.gz(r-4.7-arm64)iscream_1.3.0.tar.gz(r-4.7-x86_64)iscream_1.3.0.tar.gz(r-4.6-arm64)iscream_1.3.0.tar.gz(r-4.6-x86_64)
manual.pdf |manual.html✨
card.svg |card.png
iscream/json (API)
NEWS

# 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

6.29 score 12 scripts 212 downloads 17 exports 12 dependencies

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

TargetResultTimeFilesSyslog
bioc-checksWARNING248
linux-devel-arm64OK265
linux-devel-x86_64OK281
source / vignettesOK372
linux-release-arm64OK257
linux-release-x86_64OK339
macos-release-arm64OK185
macos-release-x86_64OK327
macos-oldrel-arm64OK151
macos-oldrel-x86_64OK319
windows-develFAIL191
windows-releaseFAIL125
windows-oldrelOK337
wasm-releaseFAIL156

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

James Eapen

Rendered fromiscream.Rmdusingknitr::rmarkdownon May 30 2026.

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

Getting htslib headers

Rendered fromhtslib.rmdusingknitr::rmarkdownon May 30 2026.

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

Improving iscream performance

Rendered fromperformance.Rmdusingknitr::rmarkdownon May 30 2026.

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

iscream compatible data structures

Rendered fromdata_structures.Rmdusingknitr::rmarkdownon May 30 2026.

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

iscream vs Rsamtools::scanTabix

Rendered fromtabix.Rmdusingknitr::rmarkdownon May 30 2026.

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

Manuscript data availabiliy

Rendered frommanuscript_data.Rmdusingknitr::rmarkdownon May 30 2026.

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

Plotting TSS methylation profiles

Rendered fromTSS.Rmdusingknitr::rmarkdownon May 30 2026.

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