{"id":19860959,"url":"https://github.com/razielar/r-scripts","last_synced_at":"2025-07-16T11:35:04.848Z","repository":{"id":128735941,"uuid":"133490789","full_name":"razielar/R-scripts","owner":"razielar","description":null,"archived":false,"fork":false,"pushed_at":"2020-11-06T12:24:54.000Z","size":1586,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-03-01T00:12:44.800Z","etag":null,"topics":["bioinformatics","gene-ontology","ggplot2"],"latest_commit_sha":null,"homepage":null,"language":"Jupyter Notebook","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/razielar.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":"2018-05-15T09:12:09.000Z","updated_at":"2020-11-06T12:24:57.000Z","dependencies_parsed_at":"2023-04-14T23:32:30.771Z","dependency_job_id":null,"html_url":"https://github.com/razielar/R-scripts","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/razielar/R-scripts","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/razielar%2FR-scripts","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/razielar%2FR-scripts/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/razielar%2FR-scripts/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/razielar%2FR-scripts/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/razielar","download_url":"https://codeload.github.com/razielar/R-scripts/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/razielar%2FR-scripts/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":260629629,"owners_count":23038962,"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":["bioinformatics","gene-ontology","ggplot2"],"created_at":"2024-11-12T15:07:40.481Z","updated_at":"2025-06-18T20:34:39.202Z","avatar_url":"https://github.com/razielar.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# R scripts:\n\n### Content:\n\n1. [Obtaining.metadata.R](#Obtaining)\n2. [Pie plot](#pie)\n3. [Count Bar plot](#bar)\n4. [Shannon's entropy and Isoform ratio](#entropy)\n5. [Venn Diagram](#venn)\n6. [Boxplots Area Pixels](#image_pixels)\n7. [GO enrichment](#go)\n\n## 1) \u003ca id='Obtaining'\u003e\u003c/a\u003e Obtaining.metadata.R\n\nAS: *Alternative splicing*\n\nList_of_AS_events.txt:\n\n| AS event   |     Sample 1     |  Sample 2 |  dPSI  |\n|----------|:-------------:|------:| ------:|\n| DmeINT0025681 | 14.9588 | 0.5367 | 14.9409 |\n| DmeINT0006388 | 8.3756 | 1.1523 | 7.0302|\n| DmeALTD0001672-1/2 | 11.6038 | 4.3211 | 6.1084 |\n\nUsage:\n\n```{r}\n\n./Obtaining.metadata.R  List_of_AS_events.txt\n\n```\n\n## 2) \u003ca id='pie'\u003e\u003c/a\u003e Pie.plot.R\n\nThere are three types of usage:\n\n**a)** Default usage: the input file is the standard input:\n\n```{r}\n\nawk -F \"\\t\" '{print $2}' Input.file.txt | ./Pie.plot.R\n\n```\n\n**b)** Specifying some features:\n\n```{r}\n\n./Pie.plot.R --input=Input.file.txt --header=TRUE --output=\"trial.pdf\" --title=\"Example\"\n\n```\n**c)** Specifying a specific color palette:\n\n```{r}\n\nawk -F \"\\t\" '{print $2}' Input.file.txt |\\\n./Pie.plot.R --selectColor=TRUE --palette=/nfs/users2/rg/ramador/R/palettes/example.palette.txt\n\n```\n\n## 3) \u003ca id='bar'\u003e\u003c/a\u003e Bar.ggplot.R\n\nSame features as *Pie.plot.R*\n\nUsage:\n\n```{r}\n\ncat list_of_elements | ./Bar.ggplot.R --title=\"Desired title\" --x_axis_rotation=TRUE\n\n```\n\n## 4) \u003ca id='entropy'\u003e\u003c/a\u003e Shannons.entropy.and.isoform.ratio.R\n\nDescription:\n\nThis script needs **two input** files, a transcript expression matrix in TPM/RPKM/FPMK and a GTF file with the **specific order**: *Gene_ID, Transcript_ID, Gene_Name and Transcript_name* the rest of information within the GTF will be ignored.  \n\nExample of GTF file:\n\n| Gene ID   |     Transcript ID     |  Gene Name |  Transcript Name  |\n|----------|:-------------:|------:| ------:|\n| FBgn0031208 | FBtr0300689 | CG11023 | CG11023-RB |\n| FBgn0031208 | FBtr0300690 | CG11023 | CG11023-RC|\n| FBgn0031208 | FBtr0330654 | CG11023 | CG11023-RD |\n\nFeatures:\n* Handling command-flags: *available*\n* Handling standard input: *not available*\n\n```{r}\n\n./Shannons.entropy.and.isoform.ratio.R  --input_matrix=/Folder/Transcription.matrix.TPM.tsv  --annotation=/Folder/GTF.file.txt\n\n```\n\n## 5) \u003ca id='venn'\u003e\u003c/a\u003e Venn.Diagram.R\n\nDescription:\n\nReceives a tsv file and returns a Venn Diagram and a file with the intersections of the items of input file.\n\nFeatures:\n\n* Handling command-flags: *available*\n* Handling standard input: *available*\n\n## 6) \u003ca id='image_pixels'\u003e\u003c/a\u003e Boxplots Area Pixels\n\nDescription:\n\nReceives a *csv file* and returns Boxplots (ggplot2) in pdf, in x-axis the different phenotypes and y-axis relative wing area in pixels.  \n\n```{r}\n\ncat file.csv | ./Bar.ggplot.R\n\n```\n\n## 7) \u003ca id='go'\u003e\u003c/a\u003e GO enrichment \n\n*Requires R \u003e 3.6* for the Bioconductor libraries: GO.db, GOstats and biomart\n\n\n\n\n\n\n\n\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Frazielar%2Fr-scripts","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Frazielar%2Fr-scripts","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Frazielar%2Fr-scripts/lists"}