{"id":28529895,"url":"https://github.com/tanaylab/misha","last_synced_at":"2026-05-25T06:11:09.842Z","repository":{"id":56274305,"uuid":"204272371","full_name":"tanaylab/misha","owner":"tanaylab","description":"Genomic data analysis suite","archived":false,"fork":false,"pushed_at":"2026-04-21T10:13:34.000Z","size":35185,"stargazers_count":4,"open_issues_count":3,"forks_count":1,"subscribers_count":2,"default_branch":"master","last_synced_at":"2026-04-21T10:22:33.691Z","etag":null,"topics":["genomic-data-analysis"],"latest_commit_sha":null,"homepage":"https://tanaylab.github.io/misha/","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/tanaylab.png","metadata":{"files":{"readme":"README.Rmd","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":"2019-08-25T09:20:51.000Z","updated_at":"2026-04-19T10:24:23.000Z","dependencies_parsed_at":"2024-03-12T14:31:56.862Z","dependency_job_id":"dc88943b-8a12-4f72-992d-296bc2b77795","html_url":"https://github.com/tanaylab/misha","commit_stats":null,"previous_names":[],"tags_count":36,"template":false,"template_full_name":null,"purl":"pkg:github/tanaylab/misha","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/tanaylab%2Fmisha","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/tanaylab%2Fmisha/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/tanaylab%2Fmisha/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/tanaylab%2Fmisha/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/tanaylab","download_url":"https://codeload.github.com/tanaylab/misha/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/tanaylab%2Fmisha/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":32307022,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-04-26T17:23:19.671Z","status":"ssl_error","status_checked_at":"2026-04-26T17:23:19.195Z","response_time":129,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.6:443 state=error: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"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":["genomic-data-analysis"],"created_at":"2025-06-09T14:12:36.570Z","updated_at":"2026-05-25T06:11:09.836Z","avatar_url":"https://github.com/tanaylab.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"---\noutput: github_document\n---\n\n\u003c!-- README.md is generated from README.Rmd. Please edit that file --\u003e\n\n```{r, include = FALSE}\nknitr::opts_chunk$set(\n    collapse = TRUE,\n    comment = \"#\u003e\",\n    fig.path = \"man/figures/README-\",\n    out.width = \"100%\"\n)\n```\n\n# misha\n\n\u003c!-- badges: start --\u003e\n[![CRAN status](https://www.r-pkg.org/badges/version/misha)](https://CRAN.R-project.org/package=misha)\n[![R-CMD-check](https://github.com/tanaylab/misha/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/tanaylab/misha/actions/workflows/R-CMD-check.yaml)\n\u003c!-- badges: end --\u003e\n\nThe `misha` package is a toolkit for analysis of genomic data. it implements an efficient data structure for storing genomic data, and provides a set of functions for data extraction, manipulation and analysis.\n\n## Installation\n\nYou can install the released version of misha from [CRAN](https://CRAN.R-project.org) with:\n\n```{r, eval=FALSE}\ninstall.packages(\"misha\")\n```\n\nOr from conda:\n\n```bash\nconda install -c aviezerl r-misha\n```\n\nAnd the development version from GitHub with:\n\n```{r, eval=FALSE}\nremotes::install_github(\"tanaylab/misha\")\n```\n\n## Usage\n\nSee the [Genomes](https://tanaylab.github.io/misha/articles/Genomes.html) vignette for instructions on how to create a misha database for common genomes.\n\nSee the [user manual](https://tanaylab.github.io/misha/articles/Manual.html) for more usage details.\n\n### Using misha with an LLM agent\n\nFor agents (Claude Code, Copilot, Cursor, etc.) writing misha analysis code in a downstream project, point them at the maintained agent guides in this repo:\n\n- [`agent-guides/misha-core.md`](https://github.com/tanaylab/misha/blob/master/agent-guides/misha-core.md) - concepts, bootstrap, and the everyday recipes (intervals, annotation, distance, extract, vtracks, gscreen, gdist, gtrack.create). Start here.\n- [`agent-guides/misha-advanced.md`](https://github.com/tanaylab/misha/blob/master/agent-guides/misha-advanced.md) - 2D / Hi-C pile-ups, insulation, sequence and PWM tracks, bulk import/export, new genomes and cross-species.\n- [`agent-guides/misha-anti-patterns.md`](https://github.com/tanaylab/misha/blob/master/agent-guides/misha-anti-patterns.md) - silent footguns referenced inline from the above.\n\nThe core guide is ~4k words and targets a system-prompt-sized context. For Claude Code-style setups, dropping `misha-core.md` (or all three) into the project's `CLAUDE.md` / `AGENTS.md` is the intended use.\n\n**Drop-in prompt (no clone needed).** Paste the block below into your agent at the start of a misha task. It points the agent at the raw files on GitHub, so it works without a local checkout:\n\n````\nBefore writing any misha code, fetch and read:\n\n- https://raw.githubusercontent.com/tanaylab/misha/master/agent-guides/misha-core.md  (mandatory: concepts + everyday recipes)\n- https://raw.githubusercontent.com/tanaylab/misha/master/agent-guides/misha-anti-patterns.md  (silent footguns; cross-referenced from core)\n- https://raw.githubusercontent.com/tanaylab/misha/master/agent-guides/misha-advanced.md  (consult on demand: 2D / Hi-C, PWM, import/export, new genomes)\n\nFollow the conventions in those files. When you hit a recipe with an \"Avoid:\" block, treat it as a hard rule.\n````\n\nPin to a release tag for stability by replacing `master` with any tag that contains `agent-guides/` (the directory landed in `v5.7.0`, so `v5.7.0` or later).\n\n#### Running scripts from old versions of misha (\u003c 4.2.0)\n\nStarting in `misha` 4.2.0, the package no longer stores global variables such as `ALLGENOME` or `GROOT`. Instead, these variables are stored in a special environment called `.misha`. This means that scripts written for older versions of `misha` will no longer work. To run such scripts, either add a prefix of `.misha$` to all those variables (`.misha$ALLGENOME` instead of `ALLGENOME`), or run the following command before running the script:\n\n```{r, eval=FALSE}\nALLGENOME \u003c\u003c- .misha$ALLGENOME\nGROOT \u003c\u003c- .misha$GROOT\nALLGENOME \u003c\u003c- .misha$ALLGENOME\nGINTERVID \u003c\u003c- .misha$GINTERVID\nGITERATOR.INTERVALS \u003c\u003c- .misha$GITERATOR.INTERVALS\nGROOT \u003c\u003c- .misha$GROOT\nGWD \u003c\u003c- .misha$GWD\nGTRACKS \u003c\u003c- .misha$GTRACKS\n```\n\n\n\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftanaylab%2Fmisha","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Ftanaylab%2Fmisha","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftanaylab%2Fmisha/lists"}