{"id":20723965,"url":"https://github.com/mouzkolit/mirfetch","last_synced_at":"2026-05-05T15:40:02.202Z","repository":{"id":175278016,"uuid":"575337222","full_name":"mouzkolit/miRFetch","owner":"mouzkolit","description":"miRNA WebScraper that allows for TargetSpectrum Search","archived":false,"fork":false,"pushed_at":"2023-03-16T10:18:00.000Z","size":3420,"stargazers_count":1,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-01-17T23:19:48.378Z","etag":null,"topics":["multithreading","python","selenium"],"latest_commit_sha":null,"homepage":"","language":"Jupyter Notebook","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/mouzkolit.png","metadata":{"files":{"readme":"README.md","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,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2022-12-07T09:33:19.000Z","updated_at":"2024-09-02T11:42:20.000Z","dependencies_parsed_at":null,"dependency_job_id":"bdfc24ee-c6da-4210-98f9-93143d7e89a4","html_url":"https://github.com/mouzkolit/miRFetch","commit_stats":null,"previous_names":["mouzkolit/mirfetch"],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mouzkolit%2FmiRFetch","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mouzkolit%2FmiRFetch/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mouzkolit%2FmiRFetch/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mouzkolit%2FmiRFetch/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/mouzkolit","download_url":"https://codeload.github.com/mouzkolit/miRFetch/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":242998545,"owners_count":20219371,"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":["multithreading","python","selenium"],"created_at":"2024-11-17T04:11:19.550Z","updated_at":"2026-05-05T15:39:57.179Z","avatar_url":"https://github.com/mouzkolit.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"\u003ch1\u003e miRFetch Package to provide easy access to the DIANA microT and microCDS Webserver \u003c/h1\u003e\n\u003cp\u003e This package allows to submit RNA sequences provided from tRNA fragments ect and determine the Target Spaces using Selenium WebScraping and\nAutomatisation using an easy accessible API\u003c/p\u003e\n\u003cp\u003e Data will be fetched from https://mrmicrot.imsi.athenarc.gr/?r=mrmicrot/index and from\nhttps://dianalab.e-ce.uth.gr/html/dianauniverse/index.php?r=microT_CDS\u003c/p\u003e\n\n\u003ch2\u003e miRT Fetching Segment: \u003c/h2\u003e\n\n\u003cp\u003e To start analysis first a dictionary of sequences must generated, consisting of a key (the name of the RNA sequence) and a list harboring the individual RNA\nsequences like shown below. In Future we will provide also support of pd.DataFrame as well as output from MintMap a Pipeline to annotate \ntRNA fragments\u003c/p\u003e\n\n\n```\nfrom rnaFetch.mirTFetch import mirTFetch \nfrom rnaFetch.mirCDSFetch import microTCDS\n\nRNA = {\"GlyCCC\": [\"GCATTGGTGGTTCAGTGGTAGAATTCTC\", \n                  \"GCATTGGTGGTTCAGTGGTAGAATTCTCGCC\", \n                  \"GCATTGGTGGTTCAGTGGTAGAATTCT\"],\n       \"LysTTT\": [\"GGGAGCGCCCGGATAGCTCAGTCGGTAGAGCATCAGACTTTT\",\n                  \"TCGGGCGGGAGTGGTGGCTTTT\",\n                  \"TCGGGCGGGAGTGGTGGCTTT\"],\n       \"ThrAGT\": [\"TCGAATCCCAGCGGTGCCTCCA\",\n                  \"ATCCCAGCGGTGCCTCCA\",\n                  \"ATCCCAGCGGTGCCTCCG\"]\n      }\n```\n\n\u003cp\u003e Then you can initialize the using \"Chrome\", \"Firefox\" or \"Edge\" \u003c/p\u003e\n\n```\n# Change to Firefox or Edge if you prefer\n# Selenium Driver is initialized in headless mode but you can ask for Browser Window setting headless = None\nfetcht = mirTFetch(\"Chrome\")\n```\n\n\u003cp\u003e We can then set the threshold to consider a target; Can also be added manually via pandas when table is generated\nAnd then we can run the Pipeline to let the miRWebserver determine the Target Spaces, which also includes the BioMart\nMapping using multithreading to convert Ensembl Transcript ID to Ensembl Gene ID and the external gene name, \nwhich can be better used for downstream analysis like GProfiler Analysis or Diana microT CDS analysis\u003c/p\u003e\n\n```\nfetcht.threshold = 0.95\n# this will return a table or save a table in self.prediction_data\n# In addition UTR sequence Table will be provided in self.utr_table\n# data table will be also returned\nfinal_table = fetcht.run_miRNA_analysis(dictionary)\n```\n\n\u003ch2\u003e Get RNA miRNA overlap \u003c/h2\u003e\n\n\u003cp\u003e We also provided overlapping target spaces between miRNAs and queried sequences using the mirCDSFetch module \u003c/p\u003e\n\u003cp\u003e Input the final_table generate after biomart annotation into the following code snippet.\nThe ouptut is a table of miRNA:sequence prediction partner shared in the grouped table. We further allow for specific visualizations of target\nspace overlaps between the queried RNA and miRNAs using Sankey Plots\n\u003c/p\u003e\n\n```\n# This will connect to the microTCDS webpage via a Selenium Driver\n# 500 Genes per run will be supplied in chunks\n# Threshold can be set to a float between 0-1 and will be automatically set \nfetchcds = microTCDS(final_table)\nnew_table = fetchcds.run_miRNA_analysis(threshold = 0.95)\noverlap, grouped = fetchcds.get_mt_cds_overlap(final_table, new_table)\n```\n\n\u003ch2\u003e A second Tutorial how to got directly from list having miRNA detections is shown in the Tutorial Folder \u003c/h2\u003e\n\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmouzkolit%2Fmirfetch","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmouzkolit%2Fmirfetch","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmouzkolit%2Fmirfetch/lists"}