{ "_id": "6ae1a414327abcdf86863e4d", "Package": "scMaSigPro", "Type": "Package", "Title": "Differential Expression Analysis Along Single-Cell Trajectories", "Version": "0.6.0", "Authors@R": "c(\nperson(\"Ana\", \"Conesa\", role = \"aut\", email = \"ana.conesa@csic.es\",\ncomment = c(ORCID = \"0000-0001-9597-311X\")),\nperson(\"María José\", \"Nueda\", role = \"aut\", email = \"mj.nueda@ua.es\",\ncomment = c(ORCID = \"0000-0002-1666-4771\")),\nperson(\"Priyansh\", \"Srivastava\", role = c(\"aut\", \"cre\"),\nemail = \"spriyansh29@gmail.com\",\ncomment = c(ORCID = \"0000-0003-2618-5296\")),\nperson(\"Marta\", \"Benegas Coll\", role = \"aut\", email = \"martabc22@gmail.com\",\ncomment = c(ORCID = \"0009-0004-9886-2828\")),\nperson(\"European Union\", role = \"fnd\",\ncomment = \"Horizon 2020 Marie Skłodowska-Curie Grant Agreement No 953407\"))", "Description": "Identifies genes whose expression changes along\nsingle-cell pseudotime and differs between the branching paths\nof a trajectory. Cells are pseudo-bulked into pseudotime bins\nthat preserve their ordering, and the polynomial generalised\nlinear model of the 'maSigPro' package is fitted to the binned\ncounts with a negative binomial family and size-factor offsets.\nMethods are described in Srivastava et al. (2024)\n.", "License": "GPL (>= 2)", "Encoding": "UTF-8", "Language": "en-GB", "Roxygen": "list(markdown = TRUE)", "Config/testthat/edition": "3", "URL": "https://github.com/BioBam/scMaSigPro/,\nhttps://spriyansh.github.io/scMaSigPro/", "biocViews": "Clustering, Regression, TimeCourse, DifferentialExpression,\nGeneExpression, RNASeq, Sequencing, Software, SingleCell,\nTranscriptomics, MultipleComparison, Visualization", "BugReports": "https://github.com/BioBam/scMaSigPro/issues", "VignetteBuilder": "knitr", "Config/roxygen2/version": "8.1.0", "Config/pak/sysreqs": "zlib1g-dev", "Repository": "https://spriyansh.r-universe.dev", "Date/Publication": "2026-10-28 06:55:07 UTC", "RemoteUrl": "https://github.com/spriyansh/scMaSigPro", "RemoteRef": "HEAD", "RemoteSha": "f7b543ea6091ac73db96185a10dc625866b1c08d", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-28 07:18:26 UTC", "User": "root" }, "Author": "Ana Conesa [aut] (ORCID: ),\nMaría José Nueda [aut] (ORCID: ),\nPriyansh Srivastava [aut, cre] (ORCID:\n),\nMarta Benegas Coll [aut] (ORCID:\n),\nEuropean Union [fnd] (Horizon 2020 Marie Skłodowska-Curie Grant\nAgreement No 953407)", "Maintainer": "Priyansh Srivastava ", "_user": "spriyansh", "_type": "src", "_file": "scMaSigPro_0.6.0.tar.gz", "_fileid": "https://r2.ropensci.org/9bc99ce394300f60e96571ec50cc608a8d9745a93b03dec5563d0b2126b30f7a", "_filesize": 3096913, "_sha256": "9bc99ce394300f60e96571ec50cc608a8d9745a93b03dec5563d0b2126b30f7a", "_expires": "2027-02-05T07:28:18.000Z", "_created": "2026-10-28T07:18:26.000Z", "_published": "2026-10-28T07:28:20.320Z", "_upstream": "https://github.com/spriyansh/scMaSigPro", "_status": "success", "_maintainer": { "name": "Priyansh Srivastava", "email": "spriyansh29@gmail.com", "login": "spriyansh", "orcid": "0000-0003-2618-5296", "twitter": "@spriyansh29", "description": "Computational Biologist", "uuid": 34842808 }, "_jobs": [ { "job": 122685380530, "time": 410, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "12799471964" }, { "job": 122685380553, "time": 487, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "12799566124" }, { "job": 122685380465, "time": 168, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "FAIL", "artifact": "" }, { "job": 122685380463, "time": 510, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "12798687922" }, { "job": 122682340391, "time": 538, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "12797779963" }, { "job": 122685380407, "time": 251, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "12798418903" }, { "job": 122685380418, "time": 340, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "12799177339" }, { "job": 122685380535, "time": 68, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "FAIL", "artifact": "" }, { "job": 122685380435, "time": 486, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "12799527011" } ], "_buildurl": "https://github.com/r-universe/spriyansh/actions/runs/40648190362", "_commit": { "id": "f7b543ea6091ac73db96185a10dc625866b1c08d", "author": "Priyansh Srivastava <34842808+spriyansh@users.noreply.github.com>", "committer": "GitHub ", "message": "P6/process (#47)\n\n* ci: run the checks on pull requests, only in spriyansh/scMaSigPro\n\nR-CMD-check, lint, test-coverage, r-universe and pr-commands move back\ninto .github/workflows. Every job runs only when the repository is\nspriyansh/scMaSigPro, so the same files run no job in any other copy,\nsuch as BioBam/scMaSigPro after a sync; pkgdown.yaml gets the same\ncondition. The checks also run on pull requests to main, a new push to a\npull request cancels the run of its previous commit, and each workflow\nasks for read access to the contents only (pr-commands: write access to\nthe contents and pull requests).\n\ntest-coverage prints the total coverage and uploads the report to\nCodecov only when the CODECOV_TOKEN secret exists, so it passes without\nit. The R-universe build skips macOS and Windows, which R-CMD-check\ncovers and where R-universe would also check the previous R release,\nwhich the package does not support. In codecov.yml the project status\nis no longer informational: it fails when the coverage falls below its\ntarget of 80 %, like the patch status below 85 %.\n\n* ci: move the Dependabot configuration to .github and group its updates\n\ndependabot.yml moves to .github/, where Dependabot reads it, and its\nweekly updates of the GitHub Actions come in one pull request. The\nfolder of parked workflows and its README go.\n\n* build: give the authors' names as the article does and add the funder\n\nAuthors@R spells \"María José Nueda\" and \"Marta Benegas Coll\" as the\narticle does and lists the European Union as funder (role \"fnd\"), with\nthe Horizon 2020 Marie Skłodowska-Curie grant agreement No 953407. The\npackage help page lists them the same way. The spell check reads the\nnames of Authors@R as whole strings, so inst/WORDLIST lists \"Benegas\"\nand \"María\".\n\n* docs: add a contributing guide and a code of conduct\n\nCONTRIBUTING.md explains where to report a problem, how to propose a\nchange, the checks that a pull request runs, the code style, the tests\nand the comparison with maSigPro", "time": 1793170507 }, "_distro": "resolute", "_host": "GitHub-Actions", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.6.0", "role": "Depends" }, { "package": "methods", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "Matrix", "role": "Imports" }, { "package": "S4Vectors", "version": ">= 0.40.2", "role": "Imports" }, { "package": "SummarizedExperiment", "role": "Imports" }, { "package": "SingleCellExperiment", "version": ">= 1.24.0", "role": "Imports" }, { "package": "MASS", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "BiocParallel", "role": 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"topics": [ "plotIntersect" ] }, { "page": "plotTrend", "title": "Plot the trend of a gene", "concept": [ "plots" ], "topics": [ "plotTrend" ] }, { "page": "plotTrendCluster", "title": "Plot the trends of the clusters", "concept": [ "plots" ], "topics": [ "plotTrendCluster" ] }, { "page": "predictors", "title": "Design matrix of the polynomial model", "concept": [ "accessors" ], "topics": [ "predictors", "predictors,ScMaSigPro-method", "predictors<-", "predictors<-,ScMaSigPro-method" ] }, { "page": "queryCoeff", "title": "Query the coefficients of the selected models", "concept": [ "results" ], "topics": [ "queryCoeff" ] }, { "page": "sc.cluster.trend", "title": "Cluster the significant genes", "concept": [ "workflow steps" ], "topics": [ "sc.cluster.trend" ] }, { "page": "sc.filter", "title": "List the significant genes", "concept": [ "workflow steps" ], "topics": [ "sc.filter" ] }, { "page": "sc.p.vector", "title": "Test the full model of each gene", "concept": [ "workflow steps" ], 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belong to several paths?", "Raw or normalised counts?", "How many cells and bins are enough?", "The paths have different lengths. 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Can I still use it?", "How do I get the results into my SingleCellExperiment?", "How long does an analysis take?", "Citing scMaSigPro", "Session information" ], "created": "2026-10-27 22:38:44", "modified": "2026-10-27 22:38:44", "commits": 1 }, { "source": "masigpro-and-class.Rmd", "filename": "masigpro-and-class.html", "title": "maSigPro and the ScMaSigPro class", "author": "Priyansh Srivastava", "engine": "knitr::rmarkdown", "headings": [ "The ScMaSigPro object", "Two resolutions and the results", "Cells and bins", "The design", "The results", "The settings", "Objects from earlier versions", "Equivalence with maSigPro", "A Gaussian model on microarray data", "A negative binomial model on counts", "What scMaSigPro adds", "Session information", "References" ], "created": "2026-10-27 22:38:44", "modified": "2026-10-27 22:38:44", "commits": 1 }, { "source": "model-and-tuning.Rmd", "filename": "model-and-tuning.html", "title": "Model and tuning", "author": "Priyansh Srivastava", 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