{ "_id": "6a5cf3a49baadeef8ab52911", "Package": "lemur", "Type": "Package", "Title": "Latent Embedding Multivariate Regression", "Version": "1.11.2", "Authors@R": "person(\"Constantin\", \"Ahlmann-Eltze\", email = \"artjom31415@googlemail.com\", \nrole = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-3762-068X\"))", "Description": "Fit a latent embedding multivariate regression (LEMUR)\nmodel to multi-condition single-cell data. The model provides a\nparametric description of single-cell data measured with\ntreatment vs. control or more complex experimental designs. The\nparametric model is used to (1) align conditions, (2) predict\nlog fold changes between conditions for all cells, and (3)\nidentify cell neighborhoods with consistent log fold changes.\nFor those neighborhoods, a pseudobulked differential expression\ntest is conducted to assess which genes are significantly\nchanged.", "URL": "https://github.com/const-ae/lemur", "BugReports": "https://github.com/const-ae/lemur/issues", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "LazyData": "false", "Config/testthat/edition": "3", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.3", "biocViews": "Transcriptomics, DifferentialExpression, SingleCell,\nDimensionReduction, Regression", "VignetteBuilder": "quarto", "Config/pak/sysreqs": "libssl-dev zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-07-19 12:27:06 UTC", "RemoteUrl": "https://github.com/bioc/lemur", "RemoteRef": "HEAD", "RemoteSha": "086bf8b84284127db477e5456ca469621dc290ba", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-07-19 15:43:39 UTC", "User": "root" }, "Author": "Constantin Ahlmann-Eltze [aut, cre] (ORCID:\n)", "Maintainer": "Constantin Ahlmann-Eltze ", "_user": "bioc", "_type": "src", "_file": "lemur_1.11.2.tar.gz", "_fileid": "https://r2.ropensci.org/06f99e44b872d731657e5a883f0eef743615c7997349d7119386f54ee326a4cf", "_filesize": 3440699, "_sha256": "06f99e44b872d731657e5a883f0eef743615c7997349d7119386f54ee326a4cf", "_expires": "2026-10-27T15:56:18.000Z", "_created": "2026-07-19T15:43:39.000Z", "_published": "2026-07-19T15:56:20.571Z", "_bioccheck": { "error": 0, "warning": 2, "note": 7 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/29693238181", "_status": "success", "_upstream": "https://github.com/bioc/lemur", "_commit": { "id": "086bf8b84284127db477e5456ca469621dc290ba", "author": "const-ae ", "committer": "const-ae ", "message": "Merge remote-tracking branch 'bioc/devel' into devel\n", "time": 1784464026 }, "_maintainer": { "name": "Constantin Ahlmann-Eltze", "email": "artjom31415@googlemail.com", "login": "const-ae", "bluesky": "@const-ae.bsky.social", "orcid": "0000-0002-3762-068X", "description": "Postdoc, Biostats, R", "uuid": 5359014 }, "_distro": "resolute", "_jobs": [ { "job": 88210091171, "time": 222, "config": "bioc-checks", "r": "4.6.1", "check": "WARNING", "artifact": "8444304981" }, { "job": 88210091202, "time": 333, "config": "linux-devel-arm64", "r": "4.7.0", "check": "ERROR", "artifact": "8444324195" }, { "job": 88210091211, "time": 430, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "ERROR", "artifact": "8444339230" }, { "job": 88210091203, "time": 337, "config": "linux-release-arm64", "r": "4.6.1", "check": "WARNING", "artifact": "8444324659" }, { "job": 88210091200, "time": 460, "config": "linux-release-x86_64", "r": "4.6.1", "check": "WARNING", "artifact": "8444344395" }, { "job": 88210091222, "time": 228, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "8444305765" }, { "job": 88210091249, "time": 369, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "WARNING", "artifact": "8444329351" }, { "job": 88210091213, "time": 236, "config": "macos-release-arm64", "r": "4.6.1", "check": "WARNING", "artifact": "8444307296" }, { "job": 88210091217, "time": 682, "config": "macos-release-x86_64", "r": "4.6.1", "check": "WARNING", "artifact": "8444379340" }, { "job": 88209557997, "time": 371, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8444268209" }, { "job": 88210091173, "time": 182, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8444298349" }, { "job": 88210091199, "time": 364, "config": "windows-devel", "r": "4.7.0", "check": "ERROR", "artifact": "8444328790" }, { "job": 88210091210, "time": 340, "config": "windows-oldrel", "r": "4.5.3", "check": "WARNING", "artifact": "8444324919" }, { "job": 88210091206, "time": 389, "config": "windows-release", "r": "4.6.1", "check": "WARNING", "artifact": "8444332766" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "RcppArmadillo", "role": "LinkingTo" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "irlba", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "SingleCellExperiment", "role": "Imports" }, { "package": "SummarizedExperiment", "role": "Imports" }, { "package": "rlang", "version": ">= 1.1.0", "role": "Imports" }, { "package": "vctrs", "version": ">= 0.6.0", "role": "Imports" }, { "package": "glmGamPoi", "version": ">= 1.12.0", "role": "Imports" }, { "package": "BiocGenerics", "role": "Imports" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "Matrix", "role": "Imports" }, { "package": "DelayedMatrixStats", "role": "Imports" }, { "package": "HDF5Array", "role": "Imports" }, { "package": "MatrixGenerics", "role": "Imports" }, { "package": "matrixStats", "role": "Imports" }, { "package": "Rcpp", "role": "Imports" }, { "package": "limma", "role": "Imports" }, { "package": "BiocNeighbors", "role": "Imports" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "tidyverse", "role": "Suggests" }, { "package": "uwot", "role": "Suggests" }, { "package": "dplyr", "role": "Suggests" }, { "package": "edgeR", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "quarto", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-08", "n": 4 }, { "week": "2026-12", "n": 6 }, { "week": "2026-20", "n": 1 }, { "week": "2026-21", "n": 3 }, { "week": "2026-29", "n": 3 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.11.1", "bioc": "3.24" }, { "branch": "release", "version": "1.9.0", "bioc": "3.23" } ], "_topics": [ "transcriptomics", "differentialexpression", "singlecell", "dimensionreduction", "regression", "quarto", "openblas", "cpp" ], "_stars": 102, "_contributors": [ { "user": "const-ae", "count": 456, "uuid": 5359014 }, { "user": "wolfganghuber", "count": 31, "uuid": 5198414 }, { "user": "jwokaty", "count": 12, "uuid": 1744257 }, { "user": "hpages", "count": 1, "uuid": 8810451 }, { "user": "bisaloo", "count": 1, "uuid": 10783929 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 449, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 328, "source": "https://www.bioconductor.org/packages/stats/bioc/lemur" }, "_devurl": "https://github.com/const-ae/lemur", "_searchresults": 121, "_quarto": true, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/lemur.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "LICENSE", "manual.pdf" ], "_homeurl": "https://github.com/const-ae/lemur", "_realowner": "bioc", "_cranurl": false, "_exports": [ ".lemur_fit", "align_by_grouping", "align_harmony", "compute_contrasts", "design", "find_de_neighborhoods", "lemur", "project_on_lemur_fit", "residuals", "test_de", "vars" ], "_datasets": [ { "name": "glioblastoma_example_data", "title": "The 'glioblastoma_example_data' dataset", "object": "glioblastoma_example_data", "file": "glioblastoma_example_data.rda", "class": [ "SingleCellExperiment" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "cash-lemur_fit-method", "title": "Access values from a 'lemur_fit'", "topics": [ "$,lemur_fit-method", "$<-,lemur_fit-method", ".DollarNames.lemur_fit", "dollar_methods" ] }, { "page": "align_harmony", "title": "Enforce additional alignment of cell clusters beyond the direct differential embedding", "topics": [ "align_by_grouping", "align_harmony" ] }, { "page": "compute_contrasts", "title": "Predict log fold changes between conditions for each cell. Both names 'compute_contrasts' and 'test_de' bind to the same function, but the former is more evocative.", "topics": [ "compute_contrasts", "test_de" ] }, { "page": "find_de_neighborhoods", "title": "Find differential expression neighborhoods", "topics": [ "find_de_neighborhoods" ] }, { "page": "glioblastoma_example_data", "title": "The 'glioblastoma_example_data' dataset", "topics": [ "glioblastoma_example_data" ] }, { "page": "lemur", "title": "Main function to fit the latent embedding multivariate regression (LEMUR) model", "topics": [ "lemur" ] }, { "page": "lemur_fit", "title": "The 'lemur_fit' class", "topics": [ ".lemur_fit", "design,lemur_fit-method", "lemur_fit", "lemur_fit-class", "[,lemur_fit,ANY,ANY,ANY-method" ] }, { "page": "predict.lemur_fit", "title": "Predict values from 'lemur_fit' object", "topics": [ "predict.lemur_fit" ] }, { "page": "project_on_lemur_fit", "title": "Project new data onto the latent spaces of an existing lemur fit", "topics": [ "project_on_lemur_fit" ] }, { "page": "residuals-lemur_fit-method", "title": "Predict values from 'lemur_fit' object", "topics": [ "residuals,lemur_fit-method" ] }, { "page": "test_global", "title": "Differential embedding for each condition", "topics": [ "test_global" ] } ], "_readme": "https://github.com/bioc/lemur/raw/HEAD/README.md", "_rundeps": [ "abind", "assorthead", "beachmat", "Biobase", "BiocGenerics", "biocmake", "BiocNeighbors", "cli", "DelayedArray", "DelayedMatrixStats", "dir.expiry", "filelock", "generics", "GenomicRanges", "glmGamPoi", "glue", "h5mread", "HDF5Array", "IRanges", "irlba", "lattice", "lifecycle", "limma", "Matrix", "MatrixGenerics", "matrixStats", "Rcpp", "RcppArmadillo", "rhdf5", "rhdf5filters", "Rhdf5lib", "rlang", "S4Arrays", "S4Vectors", "Seqinfo", "SingleCellExperiment", "SparseArray", "sparseMatrixStats", "statmod", "SummarizedExperiment", "vctrs", "XVector" ], "_sysdeps": [ { "shlib": "libblas", "package": "libopenblas0-pthread", "source": "openblas", "version": "0.3.32+ds-5", "name": "openblas", "homepage": "https://www.openblas.net/", "description": "Optimized BLAS (linear algebra) library (shared lib, pthread)" }, { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "16-20260322-1ubuntu1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" } ], "_vignettes": [ { "source": "Introduction.qmd", "filename": "Introduction.html", "title": "Introduction", "engine": "quarto::html", "headings": [ "Latent Embedding Multivariate Regression (LEMUR)", "Installation", "A note to users", "Overview", "A worked through example", "Using cell type annotation", "FAQ", "I have already integrated my data using Harmony / MNN / Seurat. Can I call lemur directly with the aligned data?", "Can I call lemur with sctransformed instead of log-transformed data?", "My data appears less integrated after calling lemur than before. What is happening?!", "The conditions still separate if I plot the data using UMAP / t-SNE, even after calling align_harmony / align_neighbors. What should I do?", "How do I make lemur faster?", "Session Info" ], "created": "2026-02-18 16:34:22", "modified": "2026-03-20 14:59:53", "commits": 6 } ], "_score": 8.091385542078369, "_indexed": true, "_nocasepkg": "lemur", "_universes": [ "bioc", "const-ae" ], "_previous": "1.11.1", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.11.2", "date": "2026-07-19T15:47:28.000Z", "distro": "resolute", "arch": "aarch64", "commit": "086bf8b84284127db477e5456ca469621dc290ba", "fileid": "https://r2.ropensci.org/dd713d134424f0943f74f19f1490810a465c9ede88e32f10d4b749e75617bf9a", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29693238181" }, { "r": "4.7.0", "os": "linux", "version": "1.11.2", "date": "2026-07-19T15:48:28.000Z", "distro": "resolute", "arch": "x86_64", "commit": "086bf8b84284127db477e5456ca469621dc290ba", "fileid": "https://r2.ropensci.org/372cf10ed2bf75e529eb3e69132067e30a16049b2635d79eefe12f60685919e6", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29693238181" }, { "r": "4.6.1", "os": "linux", "version": "1.11.2", "date": "2026-07-19T15:47:33.000Z", "distro": "resolute", "arch": "aarch64", "commit": "086bf8b84284127db477e5456ca469621dc290ba", "fileid": "https://r2.ropensci.org/998aadf7ac1f4aa1fd8327faf1628b27c6d8f55b2845173ffe6bc989a1584d1b", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29693238181" }, { "r": "4.6.1", "os": "linux", "version": "1.11.2", "date": "2026-07-19T15:48:45.000Z", "distro": "resolute", "arch": "x86_64", "commit": "086bf8b84284127db477e5456ca469621dc290ba", "fileid": "https://r2.ropensci.org/16a504fa2e8b72f63bf135480e20d77c7830713f7e8431bf7b6e2d1245916c3a", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29693238181" }, { "r": "4.5.3", "os": "mac", "version": "1.11.2", "date": "2026-07-19T15:46:25.000Z", "arch": "aarch64", "commit": "086bf8b84284127db477e5456ca469621dc290ba", "fileid": "https://r2.ropensci.org/bc94fdc8b39c7aa94946d610fa1b4f1dca89288c307378f1735d3387c6bf370c", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29693238181" }, { "r": "4.5.3", "os": "mac", "version": "1.11.2", "date": "2026-07-19T15:46:56.000Z", "arch": "x86_64", "commit": "086bf8b84284127db477e5456ca469621dc290ba", "fileid": "https://r2.ropensci.org/0e6fbaba79fc9af9bef3f13c5c41e17893c2e0eb93f72d52c363e6233cd01236", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29693238181" }, { "r": "4.6.1", "os": "mac", "version": "1.11.2", "date": "2026-07-19T15:46:34.000Z", "arch": "aarch64", "commit": "086bf8b84284127db477e5456ca469621dc290ba", "fileid": "https://r2.ropensci.org/58be256fda2ffdae6f35cbd23a4308e7f618dc8e281f82650bf743d76dabf600", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29693238181" }, { "r": "4.6.1", "os": "mac", "version": "1.11.2", "date": "2026-07-19T15:49:08.000Z", "arch": "x86_64", "commit": "086bf8b84284127db477e5456ca469621dc290ba", "fileid": "https://r2.ropensci.org/7893b5d3bd6292237c3e41b331548d4b115f549ed012d2a938ed753475f81c14", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29693238181" }, { "r": "4.6.0", "os": "wasm", "version": "1.11.2", "date": "2026-07-19T15:47:24.000Z", "arch": "emscripten", "commit": "086bf8b84284127db477e5456ca469621dc290ba", "fileid": "https://r2.ropensci.org/0c35b08d0f8f44521d4317882ee5e5561390dab935c2ec3ed7639940c7d0edd1", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29693238181" }, { "r": "4.7.0", "os": "win", "version": "1.11.2", "date": "2026-07-19T15:46:18.000Z", "arch": "x86_64", "commit": "086bf8b84284127db477e5456ca469621dc290ba", "fileid": "https://r2.ropensci.org/c474cb14028dc288750e2689c278855b749c0e42077229dac7e1400869bad26e", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29693238181" }, { "r": "4.5.3", "os": "win", "version": "1.11.2", "date": "2026-07-19T15:46:18.000Z", "arch": "x86_64", "commit": "086bf8b84284127db477e5456ca469621dc290ba", "fileid": "https://r2.ropensci.org/6bcc773874f54bc85dc32634753db72ea5d2c673fc2e4b847af05bdcec1952af", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29693238181" }, { "r": "4.6.1", "os": "win", "version": "1.11.2", "date": "2026-07-19T15:46:45.000Z", "arch": "x86_64", "commit": "086bf8b84284127db477e5456ca469621dc290ba", "fileid": "https://r2.ropensci.org/f28ce7465c54bea477a9c73cc6f313df09b8c4899c56ee24c2515da29c274bd8", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29693238181" } ] }