{"id":21015690,"url":"https://github.com/gersteinlab/bay2ctrls","last_synced_at":"2025-10-18T00:01:59.721Z","repository":{"id":273351760,"uuid":"908869967","full_name":"gersteinlab/Bay2Ctrls","owner":"gersteinlab","description":null,"archived":false,"fork":false,"pushed_at":"2024-12-27T07:01:08.000Z","size":16,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":10,"default_branch":"main","last_synced_at":"2025-01-20T12:08:00.642Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"R","has_issues":true,"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/gersteinlab.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":"2024-12-27T07:00:33.000Z","updated_at":"2024-12-27T07:01:11.000Z","dependencies_parsed_at":"2025-01-20T12:08:02.783Z","dependency_job_id":"f050dc4a-967b-4e14-8c22-7dacc869ade5","html_url":"https://github.com/gersteinlab/Bay2Ctrls","commit_stats":null,"previous_names":["gersteinlab/bay2ctrls"],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/gersteinlab%2FBay2Ctrls","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/gersteinlab%2FBay2Ctrls/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/gersteinlab%2FBay2Ctrls/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/gersteinlab%2FBay2Ctrls/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/gersteinlab","download_url":"https://codeload.github.com/gersteinlab/Bay2Ctrls/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":243446925,"owners_count":20292446,"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":"2024-11-19T10:10:57.647Z","updated_at":"2025-10-18T00:01:59.686Z","avatar_url":"https://github.com/gersteinlab.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"## Bay2Ctrls: Bayesian model to integrate two types of ChIP-seq controls for binding site detection\nTwo types of controls were widely used for ChIP-seq: DNA input controls and mock IP controls. This software was developed to combine both for better binding site detection.\n\nThis R package is based on SPP, and the wrapper script (run_Bay2Ctrls.R) for the R package is adapted from the ENCODE ChIP-seq pipeline. \n\n### DATA INPUT\nThe software accecpt four files as input:  \nThe first set is the DNA input controlled IP experiment. This DNA control (di) and the IP (i) are the results from conventional ChIP-seq.  \nThe second set is the mock IP experiment. This includes the mock IP (m) and its corresponding DNA input (dm).\n\n### DATA OUTPUT\nBinding peaks are in the narrow peak file format\n\n### DATA DOWNLOAD\nDownload the test data [here](http://archive2.gersteinlab.org/proj/MockOrNot/Bay2Ctrls/test_data/)  \nAll raw and processed data are available [here](http://archive2.gersteinlab.org/proj/MockOrNot/Data/)\n\n### DEPENDENCE\n- [SPP](https://cran.r-project.org/web/packages/spp/index.html)\n- [caTools](https://cran.r-project.org/web/packages/caTools/index.html)\n\nTested with\n- R 3.6.1\n- SPP 1.16.0\n- caTools 1.18.0\n\nPlease note that you might encounter a lot of issues if you want to install SPP from source. We recommend you install it via R `install.package(\"spp\")`.\n\n### INSTALLATION\n`devtools::install_github(\"gersteinlab/Bay2Ctrls\")`\n\n### USAGE\nRun the wrapper script **run_Bay2Ctrls.R** as the following:  \n`Rscript run_Bay2Ctrls.R -ip=\u003cIP_file\u003e -mock=\u003cmockIP_control_file\u003e -input4ip=\u003cDNA_input_control_file\u003e -input4mock=\u003cDNA_input_control_for_mockIP_file\u003e [Bay2Ctrls_parameters, ...] [SPP_parameters, ...]`\n\n##### Example  \n`Rscript run_Bay2Ctrls.R -ip=test_data/a.rep0.tagAlign.gz -mock=test_data/EMb1.rep0.tagAlign.gz -input4ip=test_data/ap.rep0.tagAlign.gz -input4mock=test_data/EMb1p.rep0.tagAlign.gz -npeak=30000 -x=-500:85 -s=0:5:1200 -odir=./ -filtchr='.*_[CD].*' -savr -savp -rf -out=test.cc -npeak=30000 -totReads=10000000 -mcstep=1000000`\n\nYou might also use the R package Bay2Ctrls in your scripts. See man pages for individual functions(TODO).  \n\n##### Paramters specific for Bay2Ctrls\n\u003cpre\u003e\n-ip            a *.tagAlign.gz file containing mapped reads from the IP experiment (i)  \n-mock          a *.tagAlign.gz file containing mapped reads from the mock IP experiment (m)  \n-input4ip      a *.tagAlign.gz file containing mapped reads from the DNA input control for the IP experiment (di)  \n-input4mock    a *.tagAlign.gz file containing mapped reads from the DNA input control for the mock IP experiment (dm)  \n-totReads      scaling the numbers of reads of the four experiments to the same level, e.g. -totReads=10000000\n-mcstep        simulation steps for the Bayesian model, e.g. -mcstep=1000000\n\u003c/pre\u003e\n\n##### Intrinsic parameters of SPP\n\u003cpre\u003e\n-npeak         the number of total narrow peaks to be output, e.g. -npeak=30000  \n-x             avoid phantom peaks, e.g. -x=-500:85  \n-s             genomic distance for signal correlation, e.g. -s=0:5:1200  \n-out           output log file  \n-rf            remove previous results  \n-odir          output directory  \n-p             number of processors to be used\n\u003c/pre\u003e\nMore options for output format please refer to the spp R package [github](https://github.com/hms-dbmi/spp) or [CRAN](https://cran.r-project.org/web/packages/spp/index.html)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgersteinlab%2Fbay2ctrls","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fgersteinlab%2Fbay2ctrls","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgersteinlab%2Fbay2ctrls/lists"}