{"id":13717107,"url":"https://github.com/vrrenske/BactMAP","last_synced_at":"2025-05-07T06:31:56.390Z","repository":{"id":162023208,"uuid":"69977992","full_name":"vrrenske/BactMAP","owner":"vrrenske","description":"gateway for segmentation data to Rstats \u0026 visualization with ggplot2 - in development","archived":false,"fork":false,"pushed_at":"2023-10-24T14:31:41.000Z","size":126667,"stargazers_count":4,"open_issues_count":5,"forks_count":4,"subscribers_count":1,"default_branch":"master","last_synced_at":"2024-11-14T05:33:50.261Z","etag":null,"topics":["fluorescence-data","ggplot","visualization"],"latest_commit_sha":null,"homepage":"http://veeninglab.com/","language":"R","has_issues":false,"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/vrrenske.png","metadata":{"files":{"readme":"README.Rmd","changelog":null,"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}},"created_at":"2016-10-04T15:18:16.000Z","updated_at":"2023-12-22T05:41:38.000Z","dependencies_parsed_at":null,"dependency_job_id":"61ec7b43-f1cd-4a09-9b2e-94ca3fa6b3f6","html_url":"https://github.com/vrrenske/BactMAP","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/vrrenske%2FBactMAP","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/vrrenske%2FBactMAP/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/vrrenske%2FBactMAP/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/vrrenske%2FBactMAP/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/vrrenske","download_url":"https://codeload.github.com/vrrenske/BactMAP/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":252826899,"owners_count":21810201,"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":["fluorescence-data","ggplot","visualization"],"created_at":"2024-08-03T00:01:18.031Z","updated_at":"2025-05-07T06:31:54.990Z","avatar_url":"https://github.com/vrrenske.png","language":"R","funding_links":[],"categories":["Microbiology"],"sub_categories":[],"readme":"---\ntitle: \"BacTMAP\"\noutput:\n  github_document:\n    fig_width: 2\n    fig_height: 2\n    \n---\n\n```{r setup, include=FALSE}\nknitr::opts_chunk$set(echo = TRUE, warning = FALSE, message = FALSE)\nlibrary(bactMAP)\n```\n\n## BacTMAP - Bacteria Tool for Microscopy Analysis \u0026 Plotting\n\n\u003cimg src=\"man//figures//logo_bactmap_pink.png\" width=\"200\" height=\"200\" /\u003e\n\nThis package is meant to make it easier for microbiologists to combine and analyse segmentation \u0026 fluorescence data derived from custom software like Oufti, Morphometrics, MicrobeJ or Supersegger. There are standard functions for importing several popular programs, but also options for importing CSVs or Matlab files with a specific structure. If your favorite segmentation or spot detection program is missing, don't hesitate to ask!\n\nI use ggplot and many ggplot-extensions to make visual summaries of the segmentation \u0026 fluorescence data, show the cell genealogy, plot protein trajectories in the cell and many other things. This can give you a quick overview of your data to make a decision on further analysis and custom visualization.\n\nIn the [wiki](https://github.com/vrrenske/BactMAP/wiki) you will find a manual and some examples on how to use BactMAP as a gateway between your segmentation \u0026 fluorescence data.\n\n**BactMAP is still in development. Not all functions listed below are fully tested \u0026 documented yet. If you have any comments, requests, please let me know!**\n\n## Download and install package\n\n```\n#install devtools if not done yet\ninstall.packages(\"devtools\")\n\n#install bactmap from my github repository\ndevtools::install_github(\"vrrenske/bactMAP\")\n\n#or install it with all dependencies\ndevtools::instal_github(\"vrrenske/bactMAP\", dependencies=TRUE)\n\n#load package\nlibrary(bactMAP)\n```\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fvrrenske%2FBactMAP","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fvrrenske%2FBactMAP","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fvrrenske%2FBactMAP/lists"}