{"id":19434431,"url":"https://github.com/likelet/datools","last_synced_at":"2025-04-24T20:32:03.709Z","repository":{"id":86650723,"uuid":"67436439","full_name":"likelet/DAtools","owner":"likelet","description":"Java based bioinformatics data analysis tool kits ","archived":false,"fork":false,"pushed_at":"2019-04-12T13:06:39.000Z","size":3238,"stargazers_count":9,"open_issues_count":0,"forks_count":2,"subscribers_count":3,"default_branch":"master","last_synced_at":"2025-04-22T00:18:48.757Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"https://likelet.github.io/DAtools/","language":"Java","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/likelet.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":"2016-09-05T16:40:09.000Z","updated_at":"2023-05-18T12:08:20.000Z","dependencies_parsed_at":null,"dependency_job_id":"3092fe62-01fa-4025-9c12-dad525addbf6","html_url":"https://github.com/likelet/DAtools","commit_stats":null,"previous_names":[],"tags_count":2,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/likelet%2FDAtools","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/likelet%2FDAtools/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/likelet%2FDAtools/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/likelet%2FDAtools/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/likelet","download_url":"https://codeload.github.com/likelet/DAtools/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":250704794,"owners_count":21473764,"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":[],"created_at":"2024-11-10T14:46:23.907Z","updated_at":"2025-04-24T20:32:03.704Z","avatar_url":"https://github.com/likelet.png","language":"Java","readme":"# DAtools\n[DAtools](https://likelet.github.io/DAtools/) is a collection of  common data analysis comand in java language, which was mainly developed and used by myself. This project provided series of analysis functions as well as pipelines applying for daily data analysis tasks incuding NGSdata processing.\n\n## Screen shoot of DAtools\n\u003cimg src=\"DAtools/image/screenshoot.png\"\u003e\n\n## Function gallary\n\n* 0.\tBED Process :\u003cbr/\u003e\n\t\t```\tjava -jar DAtools.jar -bed```\u003cbr/\u003e\n* 1.\tDevided fastq into two file by length :\u003cbr/\u003e\n\t\t```\tjava -jar DAtools.jar -devidedFastQbylength length all.fq out1.fq out2.fq```\u003cbr/\u003e\n* 2.\tDose ComposationFunctions :\u003cbr/\u003e\n\t\t```\tjava -jar DAtools.jar -dose```\u003cbr/\u003e\n* 3.\tDraw genelength Distribution :\u003cbr/\u003e\n\t\t```\tjava -jar DAtools.jar -genelengthDis```\u003cbr/\u003e\n* 4.\tExome-seq function* \u003cbr\u003e \n\t\t```\tjava -jar DAtools.jar -exome```\u003cbr/\u003e\n* 5.\tExtract expression data from cufflinks outputfile :* \u003cbr\u003e \n\t\t```\tjava -jar DAtools.jar -getcufflinksExpress cuffout_dir```\u003cbr/\u003e\n* 6.\tExtract fastaSequence by idfile :\u003cbr/\u003e\n\t\t```\tjava -jar DAtools.jar -extractFastabyID fastafile idfile(one id in one line) outfile)```\u003cbr/\u003e\n* 7.\tFunctions to convert file format :\u003cbr/\u003e\n\t\t```\tjava -jar DAtools.jar -convertFormat ```\u003cbr/\u003e\n* 8.\tGenerate a Ven plot by certain data input:\u003cbr/\u003e\n\t\t```\tjava -jar DAtools.jar -venplot datafile maintext plotType```\u003cbr/\u003e\n* 9.\tGetovelap of two list with unique output:\u003cbr/\u003e\n\t\t```\tjava -jar DAtools.jar -getoverlap filelist1 filelist2 outputfile uniqueA uniqueB```\u003cbr/\u003e\n* 10.\tGetovelap of two list:\u003cbr/\u003e\n\t\t```\tjava -jar DAtools.jar -getoverlap filelist1 filelist2 outputfile```\u003cbr/\u003e\n* 11.\tKegg Analysis :\u003cbr/\u003e\n\t\t```\tjava -jar DAtools.jar -kegg ```\u003cbr/\u003e\n* 12.\tLocal GO mapping of gene list :\u003cbr/\u003e\n\t\t```\tjava -jar DAtools.jar -gomap obofile annotation nametype(1 for uniprotID(new);2 for geneSympol) genelistfile output```\u003cbr/\u003e\n* 13.\tMetaGenome analysis :\u003cbr/\u003e\n\t\t```\tjava -jar DAtools.jar -meta```\u003cbr/\u003e\n* 14.\tMulti mapfile merged to matrix\u003cbr/\u003e\n\t\t```\tjava -jar DAtools.jar -multi2matrix  dir suffix outputfile  ```\u003cbr/\u003e\n* 15.\tProcesing FastQ files :\u003cbr/\u003e\n\t\t```\tjava -jar DAtools.jar -fastqP```\u003cbr/\u003e\n* 16.\tProcess Fasta files\u003cbr/\u003e\n\t\t```\tjava -jar DAtools.jar -Fasta```\u003cbr/\u003e\n* 17.\tProcessing Excel format :\u003cbr/\u003e\n\t\t```\tjava -jar DAtools.jar -excel ```\u003cbr/\u003e\n* 18.\tRNAseq Differential Expression Analysis(M):\u003cbr/\u003e\n\t\t```\tjava -jar DAtools.jar -RNAseqDE -mode WR(orSC) condition1 condition2 outputfile ```\u003cbr/\u003e\n* 19.\tRNAseq Mappng/quantitifaction(M):\u003cbr/\u003e\n\t\t```\tjava -jar DAtools.jar -RNAseqpipe \u003cfastq1\u003e \u003cfastq2\u003e \u003clibrary\u003e \u003cgtf\u003e```\u003cbr/\u003e\n* 20.\tRemove SUMO-FC adaptors :\u003cbr/\u003e\n\t\t```\tjava -jar DAtools.jar -removeAdapter fastafile adapter(TATA,CACA,GAGA) type(N/C)```\u003cbr/\u003e\n* 21.\tSeperate fastq File by index :\u003cbr/\u003e\n\t\t```\tjava -jar DAtools.jar -sepFastq fastaqfile indexmapfile```\u003cbr/\u003e\n* 22.\tSepfastaFilebyIndex :\u003cbr/\u003e\n\t\t```\tjava -jar DAtools.jar -sepFastabyIndex fastafile indexlist(TATA,CACA,GAGA)```\u003cbr/\u003e\n* 23.\tShorter sequencename of genome seq to parse gtg files :\u003cbr/\u003e\n\t\t```\tjava -jar DAtools.jar -genomenamecut genome.fa out.fa ```\u003cbr/\u003e\n* 24.\tSplit the xml file generated by blast :\u003cbr/\u003e\n\t\t```\tjava -jar DAtools.jar -BlastXMLsplit fileinputxml seqnumber```\u003cbr/\u003e\n* 25.\tSummary the unigenes distribution with trinity's output(Decreased) :\u003cbr/\u003e\n\t\t```\tjava -jar DAtools.jar -unigenedistribution isunigene trinity.fasta```\u003cbr/\u003e\n\n\n## Designers:\nQi Zhao, zhaoqi699@sina.com\u003cbr/\u003e\n\n## Developers:\nQi Zhao, zhaoqi699@sina.com\u003cbr/\u003e\n\n## Copyright\n\n\n## Citation \nNot implemented yet \n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flikelet%2Fdatools","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Flikelet%2Fdatools","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flikelet%2Fdatools/lists"}