{"id":16956538,"url":"https://github.com/bgamari/hphoton","last_synced_at":"2026-07-16T19:33:17.457Z","repository":{"id":6499473,"uuid":"7739972","full_name":"bgamari/hphoton","owner":"bgamari","description":"Tools for analysis of data from single-molecule fluorescence experiments in Haskell","archived":false,"fork":false,"pushed_at":"2018-03-30T23:54:36.000Z","size":517,"stargazers_count":3,"open_issues_count":0,"forks_count":1,"subscribers_count":1,"default_branch":"master","last_synced_at":"2026-05-27T14:41:52.669Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"Haskell","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/bgamari.png","metadata":{"files":{"readme":"README.mkd","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2013-01-21T20:40:52.000Z","updated_at":"2019-12-31T11:56:40.000Z","dependencies_parsed_at":"2022-09-07T16:13:40.348Z","dependency_job_id":null,"html_url":"https://github.com/bgamari/hphoton","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/bgamari/hphoton","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bgamari%2Fhphoton","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bgamari%2Fhphoton/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bgamari%2Fhphoton/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bgamari%2Fhphoton/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/bgamari","download_url":"https://codeload.github.com/bgamari/hphoton/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bgamari%2Fhphoton/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":35557060,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-05-26T15:22:16.424Z","status":"online","status_checked_at":"2026-07-16T02:00:06.687Z","response_time":83,"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":[],"created_at":"2024-10-13T22:15:18.486Z","updated_at":"2026-07-16T19:33:17.440Z","avatar_url":"https://github.com/bgamari.png","language":"Haskell","funding_links":[],"categories":[],"sub_categories":[],"readme":"# HPhoton: Tools for data analysis for fluorescence experiments\n\nHPhoton is a library and suite of tools written in [Haskell][haskell]\nfor working with time-stamped photon arrival data from fluorescence\nexperiments, namely fluorescence correlation spectroscopy (FCS) and\nFörster resonance energy transfer (FRET).\n\nThe repository contains a number of subtrees,\n * `hphoton` contains the core of the library, implementing much of\n   basis on which the other components are built\n * `hphoton-fpga-timetagger` is a library for reading data produced by\n   the Goldner lab [FPGA timetagger][]\n * `hphoton-tools` provides a set of user-friendly analysis tools\n\n[FPGA timetagger]: http://goldnerlab.physics.umass.edu/wiki/FpgaTimeTagger\n\n## Tools\n\nA number of tools are provided,\n\n * `fret-analysis` provides an end-to-end analysis pipeline for FRET data,\n   including semi-automatic correction for background, crosstalk, and gamma\n   artifacts\n * `alex-analysis` is similar to `fret-analysis` but targets FRET experiments\n   performed with alternating laser excitation (ALEX)\n * `bayes-burst-find` implemenst a Bayesian photon-by-photon\n   fluorescence burst detection scheme\n\n[haskell]: http://www.haskell.org/\n\n## Installation\n\nBeing written in Haskell, HPhoton requires a modern version of the\n[Glasgow Haskell Compiler][ghc] and [cabal][]. These are most\neasily obtained as part of the [Haskell Platform][hp], which is\navailable for most Linux distributions, Mac OS X, and Windows.\nIt is recommended that the `.cabal/bin` directory in your home\ndirectory is in your environment's `PATH`.\n\nInstallation is quite simple,\n\n    $ cabal update\n    $ cabal install cabal-meta\n    $ git clone --recursive https://github.com/bgamari/hphoton.git\n    $ cd hphoton\n    $ cabal-meta install\n\n[ghc]: http://www.haskell.org/ghc/\n[cabal]: http://www.haskell.org/cabal/\n[hp]: http://www.haskell.org/platform/\n\n## Why Haskell?\n\nFor data analysis tasks correctness, reproducibility, and ease of\ncomprehension are paramount. Being a [purely][pure] [functional][]\nlanguage, Haskell is a natural choice for this work. Its rich type\nsystem allows for strong invariants to be checked at compile time and\ncommon patterns to be effectively captured. The strong ecosystem of\nlibraries makes even sophisticated techniques easy to implement and\nthe high performance of the Glasgow Haskell Compiler enables\nimplementation of algorithms which would be prohibitively slow in more\ntraditional choices like Python.\n\n[pure]: http://en.wikipedia.org/wiki/Purely_functional\n[functional]: http://en.wikipedia.org/wiki/Functional_programming\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbgamari%2Fhphoton","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbgamari%2Fhphoton","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbgamari%2Fhphoton/lists"}