{"id":19998761,"url":"https://github.com/quantixed/volcanoplot","last_synced_at":"2026-03-09T14:05:29.633Z","repository":{"id":100276168,"uuid":"107754967","full_name":"quantixed/VolcanoPlot","owner":"quantixed","description":"Making volcano plots from proteomic data in IgorPro","archived":false,"fork":false,"pushed_at":"2024-06-27T12:42:57.000Z","size":2669,"stargazers_count":1,"open_issues_count":0,"forks_count":0,"subscribers_count":3,"default_branch":"master","last_synced_at":"2025-03-01T23:28:24.276Z","etag":null,"topics":["igor-pro","proteomics-data","statistics","volcano"],"latest_commit_sha":null,"homepage":null,"language":"IGOR Pro","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/quantixed.png","metadata":{"files":{"readme":"README.md","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,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2017-10-21T05:50:04.000Z","updated_at":"2025-01-31T06:29:56.000Z","dependencies_parsed_at":"2023-06-05T01:00:38.949Z","dependency_job_id":"d50502ff-9a1c-4fe3-b676-d33c85f57509","html_url":"https://github.com/quantixed/VolcanoPlot","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/quantixed/VolcanoPlot","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/quantixed%2FVolcanoPlot","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/quantixed%2FVolcanoPlot/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/quantixed%2FVolcanoPlot/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/quantixed%2FVolcanoPlot/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/quantixed","download_url":"https://codeload.github.com/quantixed/VolcanoPlot/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/quantixed%2FVolcanoPlot/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":30297880,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-03-09T13:46:43.843Z","status":"ssl_error","status_checked_at":"2026-03-09T13:46:42.821Z","response_time":61,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.5:443 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":["igor-pro","proteomics-data","statistics","volcano"],"created_at":"2024-11-13T05:09:25.370Z","updated_at":"2026-03-09T14:05:29.616Z","avatar_url":"https://github.com/quantixed.png","language":"IGOR Pro","readme":"# VolcanoPlot\n\n[![DOI](https://zenodo.org/badge/107754967.svg)](https://zenodo.org/doi/10.5281/zenodo.12570017)\n\nMaking volcano plots from proteomic data in IgorPro\n\n- [Using data direct from MaxQuant](#from-maxquant)\n- [Doing manual analysis](#manual-analysis)\n- [Volcano Plot outputs](#outputs)\n- [Subcellular analysis](#subcellular-analysis)\n- [Further notes](#further-notes)\n\n## From MaxQuant\n\nYou can load data from a `proteinGroups.txt` file using the *Load MaxQuant Data...* option. This will load the data and do the analysis.\nThis procedure will do a comparison of \"LFQ Intensity\" from proteomics data using two conditions.\n\nTell Igor which two conditions you want to compare (give Igor a wildcard searchstring to specify waves), e.g. `ctrl*` and `test*` will find ctrl_1,ctrl_2 etc. and test_1,test_2 etc.\n\nAlso tell Igor what the basevalue is. This is the intensity assigned to any proteins which were not detected. Default is 0 (for MaxQuant).\n\nIf you have several `proteinGroups.txt` files, it is possible to analyse them together using the *Load Multiple MaxQuant...* option.\nDue to potential differences in LFQ values between files, the default is to display the mean of ratios rather than the ratio of means.\nPaired T-test is the default test, otherwise this option will give equivalent outputs as for a single file.\n\nFor both types of analysis it there is an option to give Perseus style processing.\nWhen this option is checking the difference is calculated by subtraction using log2 transformed LFQ data, rather than a ratio of the linear data.\n\n## Manual analysis\n\nAnalysis can also be started manually from the Proteomics menu.\nIn this case, supply data (intensity, LFQ_Intensty or peptides) for the conditions you want to analyse (with logical naming) and also the protein names. These need to be in TextWaves with names `NAME` and `SHORTNAME`.\n\nMinimum data to run (all in `root:`):\n\n- Three waves of condition1\n- Three waves of condition2 - logical naming advised\n- NAME and SHORTNAME textwaves\n\n## Outputs\n\nIgor will make a Volcano Plot of the comparison. Proteins are coloured according to magnitude of change from control and according to P-value. Proteins can be clicked on to reveal their `SHORTNAME`.\n\nTransforms and imputation are done exactly as described for the default settings in Perseus.\n\n## Secondary analysis\n\n\u003cdetails\u003e\n\t\u003csummary\u003eAn option for using Gene Ontology terms to filter the data is included...\u003c/summary\u003e\n\n\n### Subcellular analysis\n\nOnce the data has been processed, you can do further (subcellular) analysis. For example, you may want to only view the hits that are associated with a certain GO Term or group of GO Terms. This is possible but involves some manual steps.\n\nSelect _Proteomics \u003e Subcellular Analysis \u003e Make List to Retrieve Uniprot Data_\n\nFollow the instructions and paste the data into Uniprot's [ID mapping tool](https://www.uniprot.org/uploadlists). Select the appropriate species as shown, and submit.\n\n![Screen01](img/uniprot01.png?raw=true)\n\nYou will see your results, but we need additional columns. Click here. Select _Gene Ontology (cellular component)_ and _Subcellular location [CC]_ as shown and save. You only need to do this on your browser once and your choice will be remembered for your next visit if you have cookies enabled.\n\n![Screen02](img/uniprot02.png?raw=true)\n\n![Screen03](img/uniprot03.png?raw=true)\n\nYou should see these columns. Click save.\n\n![Screen04](img/uniprot04.png?raw=true)\n\nWe need to filter for Reviewed records, click here.\n\n\u003cimg src=\"img/uniprot05.png\" width=\"300\"\u003e\n\nYou should now have fewer records (only the reviewed ones). Now click download.\n\n\u003cimg src=\"img/uniprot06.png\" width=\"300\"\u003e\n\nSelect tab-separated file and Uncompressed.\n\n\u003cimg src=\"img/uniprot07.png\" width=\"300\"\u003e\n\nNow, back in Igor select _Proteomics \u003e Subcellular Analysis \u003e Load and Match Uniprot Data..._\n\nFind the file that you downloaded from Uniprot. Igor will now present you with a list of all the GO Terms that Uniprot found from your hits. Select using cmd-click (on a Mac) and then click _Filter_. Shift-click will select contiguous rows. You can reset the selection by clicking the button or by simply click-selecting one new row.\n\nAfter clicking _Filter_, a new Volcano Plot will be generated together with a table to show you the hits that matched the GO terms you selected. If you want to change your selection, there is no need to reload just select _Proteomics \u003e Subcellular Analysis \u003e Filter for GO Term(s)_ \n\n\u003c/details\u003e\n\n## Further notes\n\nIt is possible to do pairwise comparisons for the volcano plot by clicking the checkbox.\n\nThe default is to look at a 2-fold change, but this can be changed in the dialog box.\n\nA PCA is generated for the selected data.\nThis works by comparing intensities of each detected protein per replicate, in the datasets.\nThe PCA is designed to be equivalent to SIMCA-P+.\n\nNote that on loading of MaxQuant data, any rows that indicate contaminants are filtered out during the load procedure.","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fquantixed%2Fvolcanoplot","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fquantixed%2Fvolcanoplot","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fquantixed%2Fvolcanoplot/lists"}