{"id":20591745,"url":"https://github.com/rformassspectrometry/spectra","last_synced_at":"2025-04-04T12:07:57.423Z","repository":{"id":34503048,"uuid":"179644188","full_name":"rformassspectrometry/Spectra","owner":"rformassspectrometry","description":"Low level infrastructure to handle MS spectra","archived":false,"fork":false,"pushed_at":"2024-10-17T13:46:02.000Z","size":22201,"stargazers_count":37,"open_issues_count":36,"forks_count":25,"subscribers_count":10,"default_branch":"main","last_synced_at":"2024-10-19T19:33:55.703Z","etag":null,"topics":["bioconductor","mass-spectrometry","metabolomics","proteomics","rstats"],"latest_commit_sha":null,"homepage":"https://rformassspectrometry.github.io/Spectra/","language":"R","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/rformassspectrometry.png","metadata":{"files":{"readme":"README.md","changelog":"NEWS.md","contributing":null,"funding":null,"license":null,"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}},"created_at":"2019-04-05T08:22:17.000Z","updated_at":"2024-10-15T20:15:27.000Z","dependencies_parsed_at":"2024-01-30T10:25:57.329Z","dependency_job_id":"1b8cd67b-5808-4f2f-ae94-a6301c78c822","html_url":"https://github.com/rformassspectrometry/Spectra","commit_stats":{"total_commits":841,"total_committers":10,"mean_commits":84.1,"dds":"0.31747919143876335","last_synced_commit":"6d16816bad6d3e0d545cbb7d9b037649a914923b"},"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/rformassspectrometry%2FSpectra","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/rformassspectrometry%2FSpectra/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/rformassspectrometry%2FSpectra/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/rformassspectrometry%2FSpectra/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/rformassspectrometry","download_url":"https://codeload.github.com/rformassspectrometry/Spectra/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":247174418,"owners_count":20896078,"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","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":["bioconductor","mass-spectrometry","metabolomics","proteomics","rstats"],"created_at":"2024-11-16T07:41:31.289Z","updated_at":"2025-04-04T12:07:57.405Z","avatar_url":"https://github.com/rformassspectrometry.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Low level infrastructure to handle MS spectra\n\n[![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)\n[![R-CMD-check-bioc](https://github.com/RforMassSpectrometry/Spectra/workflows/R-CMD-check-bioc/badge.svg)](https://github.com/RforMassSpectrometry/Spectra/actions?query=workflow%3AR-CMD-check-bioc)\n[![codecov](https://codecov.io/gh/rformassspectrometry/Spectra/branch/main/graph/badge.svg?token=jy0Mid9gKn)](https://codecov.io/gh/rformassspectrometry/Spectra)\n[![license](https://img.shields.io/badge/license-Artistic--2.0-brightgreen.svg)](https://opensource.org/licenses/Artistic-2.0)\n[![years in bioc](http://bioconductor.org/shields/years-in-bioc/Spectra.svg)](https://bioconductor.org/packages/release/bioc/html/Spectra.html)\n[![Ranking by downloads](http://bioconductor.org/shields/downloads/release/Spectra.svg)](https://bioconductor.org/packages/stats/bioc/Spectra/)\n[![build release](http://bioconductor.org/shields/build/release/bioc/Spectra.svg)](https://bioconductor.org/checkResults/release/bioc-LATEST/Spectra/)\n[![build devel](http://bioconductor.org/shields/build/devel/bioc/Spectra.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/Spectra/)\n\nThe Spectra package defines an efficient infrastructure for storing and handling\nmass spectrometry spectra and functionality to subset, process, visualize and\ncompare spectra data. It provides different implementations (backends) to store\nmass spectrometry data. These comprise backends tuned for fast data access and\nprocessing and backends for very large data sets ensuring a small memory\nfootprint.\n\nA (possibly incomplete) list of available backends (along with a link to the R\npackage providing it) is shown below:\n\n- `MsBackendCompDb` (package\n  [*CompoundDb*](https://github.com/rformassspectrometry/CompoundDb): provides\n  access to spectra data (spectra and peaks variables) from a *CompDb*\n  database. Has a small memory footprint because all data (except precursor m/z\n  values) are retrieved on-the-fly from the database.\n\n- `MsBackendDataFrame` (package: *Spectra*): alternative to the\n  `MsBackendMemory` also keeping all data in memory, but supporting `S4` objects\n  as spectra variables because the data is stored internally in a `DataFrame`.\n\n- `MsBackendHdf5Peaks` (package: *Spectra*): on-disk backend similar to\n  `MsBackendMzR`, but the peaks data is stored in HDF5 files (general spectra\n  variables are kept in memory).\n\n- `MsBackendHmdbXml` (package\n  [*MsbackendHmdb*](https://github.com/rformassspectrometry/MsBackendHmdb)):\n  allows import of MS data from xml files of the Human Metabolome Database\n  (HMDB). Extends the `MsBackendDataFrame` and keeps thus all data, after\n  import, in memory.\n\n- `MsBackendMassbank` (package\n  [*MsBackendMassbank*](https://github.com/rformassspectrometry/MsBackendMassbank)):\n  allows to import/export data in MassBank text file format. Extends the\n  `MsBackendDataFrame` and keeps thus all data, after import, in memory.\n\n- `MsBackendMassbankSql` (package\n  [*MsBackendMassbank*](https://github.com/rformassspectrometry/MsBackendMassbank)):\n  allows to directly connect to a MassBank SQL database to retrieve all MS data\n  and variables. Has a minimal memory footprint because all data is retrieved\n  on-the-fly from the SQL database.\n\n- `MsBackendMemory` (package: *Spectra*): *default* backend which keeps all data\n  in memory. Optimized for fast processing.\n\n- `MsBackendMetaboLights` (package\n  [*MsBackendMetaboLights*](https://github.com/rformassspectrometry/MsBackendMetaboLights)):\n  retrieves and caches MS data files from MetaboLights.\n\n- `MsBackendMgf` (package\n  [*MsBackendMgf*](https://github.com/rformassspectrometry/MsBackendMgf)): allows\n  to import/export data in mascot generic format (MGF). Extends the\n  `MsBackendDataFrame` and keeps thus all data, after import, in memory.\n\n- `MsBackendMsp` (package\n  [*MsbackendMsp*](https://github.com/rformassspectrometry/MsBackendMsp)): allows\n  to import/export data in NIST MSP format. Extends the `MsBackendDataFrame` and\n  keeps thus all data, after import, in memory.\n\n- `MsBackendMzR` (package: *Spectra*): by using the `mzR` package it supports\n  import of MS data from mzML, mzXML and CDF files. This backend keeps only\n  general spectra variables in memory and retrieves the peaks data (m/z and\n  intensity values) on-the-fly from the original data files. The backend has\n  thus a smaller memory footprint compared to in-memory backends.\n\n- `MsBackendOfflineSql` (package\n  [*MsBackendSql*](https://github.com/rformassspectrometry/MsBackendSql)):\n  stores all MS data in a SQL database and has thus a minimal memory footprint.\n  Does, in contrast to `MsBackendSql`, not keep an active SQL database\n  connection and can thus support parallel processing.\n\n- `MsBackendRawFileReader` (package\n  [*MsBackendRawFileReader*](https://github.com/fgcz/MsBackendRawFileReader)):\n  implements a backend for reading MS data from Thermo Fisher Scientific's raw\n  data files using the manufacturer's NewRawFileReader .Net libraries. The\n  package generalizes the functionality introduced by the `rawrr` package.\n\n- `MsBackendSql` (package\n  [*MsBackendSql*](https://github.com/rformassspectrometry/MsBackendSql)):\n  stores all MS data in a SQL database and has thus a minimal memory footprint.\n\n- `MsBackendTimsTof` (package\n  [*MsBackendTimsTof*](https://github.com/rformassspectrometry/MsBackendTimsTof):\n  allows import of data from Bruker TimsTOF raw data files (using the\n  `opentimsr` R package).\n\n- `MsBackendWeizMass` (package\n  [*MsBackendWeizMass*](https://github.com/rformassspectrometry/MsBackendWeizMass):\n  allows to access MS data from WeizMass MS/MS spectral databases.\n\n\nFor more information see the package\n[homepage](https://rformassspectrometry.github.io/Spectra).\n\n\n# Installation\n\nThe package can be installed with\n\n```r\ninstall.packages(\"BiocManager\")\nBiocManager::install(\"Spectra\")\n```\n\n\n# Contributions\n\nContributions are highly welcome and should follow the [contribution\nguidelines](https://rformassspectrometry.github.io/RforMassSpectrometry/articles/RforMassSpectrometry.html#contributions).\nAlso, please check the coding style guidelines in the [RforMassSpectrometry\nvignette](https://rformassspectrometry.github.io/RforMassSpectrometry/articles/RforMassSpectrometry.html)\nand importantly, follow our [code of\nconduct](https://rformassspectrometry.github.io/RforMassSpectrometry/articles/RforMassSpectrometry.html#code-of-conduct).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Frformassspectrometry%2Fspectra","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Frformassspectrometry%2Fspectra","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Frformassspectrometry%2Fspectra/lists"}