{"id":16036583,"url":"https://github.com/dgrtwo/barseqg3","last_synced_at":"2025-04-05T05:13:52.871Z","repository":{"id":21425867,"uuid":"24743994","full_name":"dgrtwo/BarSeqG3","owner":"dgrtwo","description":"Reproduction information for \"Design and Analysis of Bar-Seq Experiments\"","archived":false,"fork":false,"pushed_at":"2014-10-03T02:08:59.000Z","size":7604,"stargazers_count":2,"open_issues_count":0,"forks_count":1,"subscribers_count":3,"default_branch":"master","last_synced_at":"2025-02-10T13:12:17.606Z","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":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/dgrtwo.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}},"created_at":"2014-10-03T02:08:21.000Z","updated_at":"2018-09-17T09:44:09.000Z","dependencies_parsed_at":"2022-09-02T01:22:13.445Z","dependency_job_id":null,"html_url":"https://github.com/dgrtwo/BarSeqG3","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dgrtwo%2FBarSeqG3","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dgrtwo%2FBarSeqG3/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dgrtwo%2FBarSeqG3/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dgrtwo%2FBarSeqG3/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/dgrtwo","download_url":"https://codeload.github.com/dgrtwo/BarSeqG3/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":247289431,"owners_count":20914464,"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":"2024-10-08T22:05:51.351Z","updated_at":"2025-04-05T05:13:52.848Z","avatar_url":"https://github.com/dgrtwo.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"Design and Analysis of Bar-seq Experiments\n==========================================\n\nThis repository contains instructions for reproducing the manuscript:\n\n[David G. Robinson, Wei Chen, John D. Storey and David Gresham. \"Design and\nAnalysis of Bar-seq Experiments.\" G3. 10.1534/g3.113.008565](http://www.g3journal.org/content/4/1/11.long)\n\nWe use [knitr](http://yihui.name/knitr/) to generate the manuscript from the\ninput data, and compile the manuscript with LaTeX.\n\nThis was originally provided as [File S1 with the original manuscript](http://www.g3journal.org/content/4/1/11/suppl/DC1)- providing it as a GitHub repository is an attempt to make it easier to keep it working, whether with bugs in the original or with changing R packages.\n\n### SETUP\n\nThis manuscript requires R at least version 2.15 (recommended 3.0) to reproduce,\nas well as pdflatex to compile. You'll also need to install the\nfollowing packages from CRAN and BioConductor:\n\n    install.packages(c(\"plyr\", \"data.table\", \"reshape\", \"ggplot2\", \"gplots\",\n                       \"colorRamps\", \"gridExtra\", \"xtable\"))\n\n    source(\"http://bioconductor.org/biocLite.R\")\n    biocLite(c(\"GSEABase\", \"org.Sc.sgd.db\", \"GO.db\", \"edgeR\", \"DESeq\",\n               \"qvalue\"))\n\nYou also have to install the eigenR2 package from [here](http://www.genomine.org/eigenr2/)\n\n### REPRODUCTION\n\nTo reproduce the manuscript, run the following lines on your terminal:\n\n    Rscript -e \"library(knitr); knit('Robinson_2013.Rnw')\"   # reproduce manuscript\n    pdflatex Robinson_2013.tex                               # compile LaTeX\n\nIn a few minutes it should generate the full PDF of the manuscript, along with\nall figures except 1A and all tables except Tables 1 and 2.\n\n### SESSION\n\nThe manuscript was originally compiled with the following sessionInfo():\n\n    R version 3.0.1 (2013-05-16)\n    Platform: x86_64-apple-darwin10.8.0 (64-bit)\n\n    locale:\n    [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8\n\n    attached base packages:\n    [1] grid      parallel  stats     graphics  grDevices utils     datasets \n    [8] methods   base     \n\n    other attached packages:\n     [1] qvalue_1.34.0        gridExtra_0.9.1      scales_0.2.3        \n     [4] colorRamps_2.3       gplots_2.11.3        MASS_7.3-28         \n     [7] KernSmooth_2.23-10   caTools_1.14         gdata_2.13.2        \n    [10] gtools_3.0.0         eigenR2_1.0          xtable_1.7-1        \n    [13] reshape_0.8.4        plyr_1.8             ggplot2_0.9.3.1.99  \n    [16] GO.db_2.9.0          org.Sc.sgd.db_2.9.1  RSQLite_0.11.4      \n    [19] DBI_0.2-7            GSEABase_1.22.0      graph_1.38.3        \n    [22] annotate_1.38.0      AnnotationDbi_1.22.6 DESeq_1.12.1        \n    [25] lattice_0.20-23      locfit_1.5-9.1       Biobase_2.20.1      \n    [28] BiocGenerics_0.6.0   edgeR_3.2.4          limma_3.16.7        \n    [31] data.table_1.8.8     knitr_1.4.1         \n\n    loaded via a namespace (and not attached):\n     [1] bitops_1.0-6       colorspace_1.2-2   dichromat_2.0-0    digest_0.6.3      \n     [5] evaluate_0.4.7     formatR_0.9        genefilter_1.42.0  geneplotter_1.38.0\n     [9] gtable_0.1.2       IRanges_1.18.3     labeling_0.2       munsell_0.4.2     \n    [13] proto_0.3-10       RColorBrewer_1.0-5 reshape2_1.2.2     splines_3.0.1     \n    [17] stats4_3.0.1       stringr_0.6.2      survival_2.37-4    tcltk_3.0.1       \n    [21] tools_3.0.1        XML_3.95-0.2      \n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdgrtwo%2Fbarseqg3","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fdgrtwo%2Fbarseqg3","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdgrtwo%2Fbarseqg3/lists"}