{"id":33898314,"url":"https://github.com/huishenlab/iscream","last_synced_at":"2025-12-30T08:51:35.574Z","repository":{"id":248920063,"uuid":"564384859","full_name":"huishenlab/iscream","owner":"huishenlab","description":"Make fast and memory efficient BED file queries, summaries, and matrices.","archived":false,"fork":false,"pushed_at":"2025-12-04T17:59:11.000Z","size":11111,"stargazers_count":0,"open_issues_count":0,"forks_count":1,"subscribers_count":4,"default_branch":"main","last_synced_at":"2025-12-08T01:41:44.352Z","etag":null,"topics":["bed","rcpp","tabix","wgbs"],"latest_commit_sha":null,"homepage":"https://huishenlab.github.io/iscream/","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/huishenlab.png","metadata":{"files":{"readme":"README.md","changelog":"NEWS.md","contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2022-11-10T15:50:23.000Z","updated_at":"2025-11-12T14:53:48.000Z","dependencies_parsed_at":"2024-09-16T20:14:07.689Z","dependency_job_id":"5b5b4ad8-5c66-4c02-9e6e-3df5131185f7","html_url":"https://github.com/huishenlab/iscream","commit_stats":null,"previous_names":["huishenlab/iscream"],"tags_count":1,"template":false,"template_full_name":null,"purl":"pkg:github/huishenlab/iscream","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/huishenlab%2Fiscream","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/huishenlab%2Fiscream/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/huishenlab%2Fiscream/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/huishenlab%2Fiscream/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/huishenlab","download_url":"https://codeload.github.com/huishenlab/iscream/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/huishenlab%2Fiscream/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":27669853,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","status":"online","status_checked_at":"2025-12-11T02:00:11.302Z","response_time":56,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["bed","rcpp","tabix","wgbs"],"created_at":"2025-12-11T20:47:21.487Z","updated_at":"2025-12-11T20:47:26.065Z","avatar_url":"https://github.com/huishenlab.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"## iscream \u003ca href=\"https://huishenlab.github.io/iscream/\"\u003e\u003cimg src=\"man/figures/logo.png\" align=\"right\" height=\"138\" style=\"float:right; height:138px;\"/\u003e\u003c/a\u003e\n\n\u003c!-- badges: start --\u003e\n[![R-CMD-check-bioc](https://github.com/huishenlab/iscream/actions/workflows/check-bioc.yml/badge.svg)](https://github.com/huishenlab/iscream/actions/workflows/check-bioc.yml)\n[![Codecov test coverage](https://codecov.io/gh/huishenlab/iscream/graph/badge.svg)](https://app.codecov.io/gh/huishenlab/iscream)\n\u003c!-- badges: end --\u003e\n\niscream aims to efficiently read data from any BED file into formats usable by\nother packages. Using [htslib](https://www.htslib.org/), iscream can query\ngenomic regions like [tabix](https://en.wikipedia.org/wiki/Tabix), summarize the\nqueried data and make matrices, with specific support for WGBS BED files aligned\nby [BISCUIT](https://huishenlab.github.io/biscuit/),\n[Bismark](https://www.bioinformatics.babraham.ac.uk/projects/bismark/) and\n[BSBolt](https://bsbolt.readthedocs.io/en/latest/).\n\nAnalysis and visualization of Whole Genome Bisulfite Sequencing (WGBS)[^1] data\nrequires reading aligned sequencing data into formats that existing packages\nlike [BSseq](https://bioconductor.org/packages/devel/bioc/html/bsseq.html) and\n[scMET](https://github.com/andreaskapou/scMET) can analyze. Getting the data\nfrom on-disk BED files to a matrix of methylation values can be difficult\nbecause, with nearly 30 million CpGs, WGBS data can be quite large. iscream\nmakes importing WGBS data for targeted exploration and analysis faster and more\nmemory efficient.\n\n[^1]: The name iscream comes from \"*Integrating Single-Cell Results for\nExploring and Analyzing Methylation*\" as it was originally developed to read BED\nfiles from WGBS. It was then generalized to work with any BED file.\n\n\n## Dependencies\n\n### *htslib* \u003e= 1.17\n\n*iscream* depends on the *htslib* header files. These may be installed with\nyour package manager:\n\n- ubuntu/debian: `libhts-dev`  \n- fedora/RHEL: `htslib-devel`  \n- brew: `htslib`  \n- nixpkgs: `htslib`\n- conda: `bioconda::htslib`\n\nor built manually: \u003chttps://www.htslib.org/download/\u003e. *iscream* can use\n*Rhtslib* as the htslib source but we recommend installing htslib with\nlibdeflate support for optimal performance - see\n[`vignette(\"htslib\")`](https://huishenlab.github.io/iscream/articles/htslib.html)\nfor more information.\n\n\nThe header files may also be found among your HPC modules - make sure the\n`PKG_CONFIG_PATH` environment variable includes the `pkgconfig` location for\nyour installation of *htslib*. You can verify that the *htslib* development\nlibraries are installed with `pkg-config`:\n\n```bash\n# set path if necessary\nexport PKG_CONFIG_PATH=[path to htslib installation]\n# verify that htslib can be found\npkg-config --cflags --libs htslib\n```\n\n#### *tabix*\n\nSome *htslib* installations do not include the *tabix* executable (on Ubuntu you\nneed to install both *libhts-dev* and *tabix*). *iscream* will work without\n*tabix*, but the `tabix()` function will be faster if the executable is\ninstalled.\n\n### GCC \u003e= 9.4.0\n\nGNU GCC must be installed for OpenMP support. This is usually installed by\ndefault on Linux systems, but may need to be manually installed on MacOS to use\niscream with multiple threads[^2].\n\n[^2]: Using OpenMP is also possible with Clang on MacOS\n(\u003chttps://mac.r-project.org/openmp/\u003e) but installing GCC with Homebrew may be\neasier (\u003chttps://formulae.brew.sh/formula/gcc\u003e).\n\n## Installation\n\n### Bioconductor\n\n```r\nif (!requireNamespace(\"BiocManager\", quietly = TRUE))\n    install.packages(\"BiocManager\")\nBiocManager::install(\"iscream\")\n```\n\n### GitHub\n\nYou can install the development version from Github by cloning the repo and\nrunning\n\n```bash\ngit clone https://github.com/huishenlab/iscream\nR CMD INSTALL iscream\n```\n\nYou can also use the R [`devtools`](https://devtools.r-lib.org/) package:\n\n```r\ndevtools::install_github(\"huishenlab/iscream\")\n```\n\nor [`pak`](https://pak.r-lib.org/):\n\n```r\npak::pkg_install(\"huishenlab/iscream\")\n```\n\n### Usage\n\nSee the [quick start guide](https://huishenlab.github.io/iscream/articles/iscream.html)\nfor an overview of iscream's functionality and the [function reference](https://huishenlab.github.io/iscream/reference/)\nfor all available functions. Bug reports may be submitted through [GitHub issues](https://github.com/huishenlab/iscream/issues).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fhuishenlab%2Fiscream","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fhuishenlab%2Fiscream","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fhuishenlab%2Fiscream/lists"}