{ "_id": "6a1000a8acfb0bcc41c7b432", "Package": "oCELLoc", "Title": "Predicts Suitable Cell Types in Spatial Transcriptomics and\nscRNA-seq Data", "Version": "1.0.0", "Authors@R": "c(\nperson(given = \"Afeefa\",\nfamily = \"Zainab\",\nemail = \"afeeffazainab@gmail.com\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0003-3357-8661\")),\nperson(\"Vladyslav\", \"Honcharuk\",\nemail = \"vladyslav.s.honcharuk@gmail.com\",\nrole = \"aut\",\ncomment = c(ORCID = \"0000-0002-7464-500X\")),\nperson(\"Alexis\", \"Vandenbon\",\nemail = \"alexisvdb@infront.kyoto-u.ac.jp\",\nrole = \"aut\",\ncomment = c(ORCID = \"0000-0003-2180-5732\")))", "Description": "Picks the suitable cell types in spatial and scRNA-seq\ndata using shrinkage methods. The package includes curated\nreference gene expression profiles for human and mouse cell\ntypes, facilitating immediate application to common spatial\ntranscriptomics or scRNA datasets. Additionally, users can\ninput custom reference data to support tissue- or\nexperiment-specific analyses.", "License": "MIT + file LICENSE", "URL": "https://doi.org/10.64898/2025.12.11.693812", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.3", "LazyData": "true", "Config/pak/sysreqs": "libicu-dev", "Repository": "https://afeefa-zainab.r-universe.dev", "Date/Publication": "2025-12-17 06:21:45 UTC", "RemoteUrl": "https://github.com/afeefa-zainab/ocelloc", "RemoteRef": "HEAD", "RemoteSha": "f4b22bb7e46a22377a636e8158733339f6a8df92", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-22 07:03:38 UTC", "User": "root" }, "Author": "Afeefa Zainab [aut, cre] (ORCID:\n),\nVladyslav Honcharuk [aut] (ORCID:\n),\nAlexis Vandenbon [aut] (ORCID: )", "Maintainer": "Afeefa Zainab ", "MD5sum": "db7c5cc588e958b95212b3108039c620", "_user": "afeefa-zainab", "_type": "src", "_file": "oCELLoc_1.0.0.tar.gz", "_fileid": "eb9a75fb71948c6d8813fc1ca36011541b4ba9536d914bc937b8d55b1f8cb531", "_filesize": 3378990, "_sha256": "eb9a75fb71948c6d8813fc1ca36011541b4ba9536d914bc937b8d55b1f8cb531", "_created": "2026-05-22T07:03:38.000Z", "_published": "2026-05-22T07:07:20.737Z", "_distro": "noble", "_jobs": [ { "job": 77332322047, "time": 127, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7154709051" }, { "job": 77332322002, "time": 137, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7154711987" }, { "job": 77332322038, "time": 166, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7154716921" }, { "job": 77332322029, "time": 125, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7154702874" }, { "job": 77331857852, "time": 214, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7154673641" }, { "job": 77332322014, "time": 114, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7154705471" }, { "job": 77332322108, "time": 79, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7154695877" }, { "job": 77332322026, "time": 84, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7154697995" }, { "job": 77332322015, "time": 73, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7154694520" } ], "_buildurl": "https://github.com/r-universe/afeefa-zainab/actions/runs/26273377353", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/afeefa-zainab/ocelloc", "_commit": { "id": "f4b22bb7e46a22377a636e8158733339f6a8df92", "author": "Vladyslav Honcharuk <77810055+vladyslav-honcharuk@users.noreply.github.com>", "committer": "GitHub ", "message": "Revise README for scRNA-seq support and citation\n\nUpdated package description and title to include scRNA-seq data. Added citation information for publications.", "time": 1765952505 }, "_maintainer": { "name": "Afeefa Zainab", "email": "afeeffazainab@gmail.com", "login": "afeefa-zainab", "description": "", "uuid": 202893633, "orcid": "0000-0003-3357-8661" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "glmnet", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "reshape2", "role": "Imports" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "afeefa-zainab", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-48", "n": 1 }, { "week": "2025-51", "n": 2 } ], "_tags": [], "_stars": 1, "_contributors": [ { "user": "vladyslav-honcharuk", "count": 3, "uuid": 77810055 } ], "_userbio": { "uuid": 202893633, "type": "user", "name": "Afeefa ZAINAB" }, "_downloads": { "count": 462, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/oCELLoc" }, "_devurl": "https://github.com/afeefa-zainab/ocelloc", "_searchresults": 0, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/oCELLoc.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/afeefa-zainab/ocelloc", "_realowner": "afeefa-zainab", "_cranurl": true, "_releases": [ { "version": "1.0.0", "date": "2025-12-22" } ], "_exports": [ "predict_cell_types" ], "_datasets": [ { "name": "human_ref", "title": "Human Cell Type Reference Data", "object": "human_ref", "class": [ "matrix", "array" ], "fields": [ "lamp5 GABAergic cortical interneuron_CL:4023011", "sncg GABAergic cortical interneuron_CL:4023015", "caudal ganglionic eminence derived GABAergic cortical interneuron_CL:4023070", "vip GABAergic cortical interneuron_CL:4023016", "L5 extratelencephalic projecting glutamatergic cortical neuron_CL:4023041", "near-projecting glutamatergic cortical neuron_CL:4023012", "corticothalamic-projecting glutamatergic cortical neuron_CL:4023013", "L6b glutamatergic cortical neuron_CL:4023038", "astrocyte of the cerebral cortex_CL:0002605", "microglial cell_CL:0000129", "oligodendrocyte_CL:0000128", "oligodendrocyte precursor cell_CL:0002453", "L2/3-6 intratelencephalic projecting glutamatergic cortical neuron_CL:4023040", "chandelier pvalb GABAergic cortical interneuron_CL:4023036", "pvalb GABAergic cortical interneuron_CL:4023018", "sst GABAergic cortical interneuron_CL:4023017", "macrophage_CL:0000235", "monocyte_CL:0000576", "liver dendritic cell_CL:2000055", "mature NK T cell_CL:0000814", "endothelial cell of hepatic sinusoid_CL:1000398", "fibroblast_CL:0000057", "hepatocyte_CL:0000182", "intrahepatic cholangiocyte_CL:0002538", "neutrophil_CL:0000775", "plasma cell_CL:0000786", "T cell_CL:0000084", "endothelial cell_CL:0000115", "smooth muscle cell_CL:0000192", "ciliated cell_CL:0000064", "secretory cell_CL:0000151", "basal cell_CL:0000646", "mast cell_CL:0000097", "mucus secreting cell_CL:0000319", "CD8-positive, alpha-beta T cell_CL:0000625", "serous cell of epithelium of trachea_CL:1000330", "ionocyte_CL:0005006", "tracheal goblet cell_CL:1000329", "B cell_CL:0000236", "CD4-positive, alpha-beta T cell_CL:0000624", "erythrocyte_CL:0000232", "CD4-positive, alpha-beta memory T cell_CL:0000897", "CD8-positive, alpha-beta cytokine secreting effector T cell_CL:0000908", "naive B cell_CL:0000788", "memory B cell_CL:0000787", "classical monocyte_CL:0000860", "type I NK T cell_CL:0000921", "CD141-positive myeloid dendritic cell_CL:0002394", "platelet_CL:0000233", "naive thymus-derived CD4-positive, alpha-beta T cell_CL:0000895", "non-classical monocyte_CL:0000875", "plasmacytoid dendritic cell_CL:0000784", "hematopoietic stem cell_CL:0000037", "basophil_CL:0000767", "effector CD8-positive, alpha-beta T cell_CL:0001050", "effector CD4-positive, alpha-beta T cell_CL:0001044", "innate lymphoid cell_CL:0001065", "regulatory T cell_CL:0000815", "CD1c-positive myeloid dendritic cell_CL:0002399", "intermediate monocyte_CL:0002393", "stromal cell_CL:0000499", "acinar cell of salivary gland_CL:0002623", "CD4-positive helper T cell_CL:0000492", "pericyte_CL:0000669", "adventitial cell_CL:0002503", "endothelial cell of lymphatic vessel_CL:0002138", "duct epithelial cell_CL:0000068", "myoepithelial cell_CL:0000185", "CD8-positive, alpha-beta memory T cell_CL:0000909", "naive thymus-derived CD8-positive, alpha-beta T cell_CL:0000900", "epithelial cell_CL:0000066", "leukocyte_CL:0000738", "vein endothelial cell_CL:0002543", "endothelial cell of artery_CL:1000413", "capillary endothelial cell_CL:0002144", "tongue muscle cell_CL:0002673", "luminal epithelial cell of mammary gland_CL:0002326", "fibroblast of breast_CL:4006000", "vascular associated smooth muscle cell_CL:0000359", "epithelial cell of uterus_CL:0002149", "myometrial cell_CL:0002366", "ciliated epithelial cell_CL:0000067", "conjunctival epithelial cell_CL:1000432", "eye photoreceptor cell_CL:0000287", "Mueller cell_CL:0000636", "stem cell_CL:0000034", "epithelial cell of lacrimal sac_CL:1000436", "corneal epithelial cell_CL:0000575", "melanocyte_CL:0000148", "dendritic cell_CL:0000451", "retinal bipolar neuron_CL:0000748", "retinal blood vessel endothelial cell_CL:0002585", "keratocyte_CL:0002363", "retinal pigment epithelial cell_CL:0002586", "erythroid lineage cell_CL:0000764", "surface ectodermal cell_CL:0000114", "radial glial cell_CL:0000681", "myofibroblast cell_CL:0000186", "mesenchymal stem cell_CL:0000134", "muscle cell_CL:0000187", "CD8-positive, alpha-beta cytotoxic T cell_CL:0000794", "Langerhans cell_CL:0000453", "erythroid progenitor cell_CL:0000038", "granulocyte_CL:0000094", "common myeloid progenitor_CL:0000049", "cardiac endothelial cell_CL:0010008", "cardiac muscle cell_CL:0000746", "native cell_CL:0000003", "fibroblast of cardiac tissue_CL:0002548", "pancreatic acinar cell_CL:0002064", "myeloid cell_CL:0000763", "pancreatic stellate cell_CL:0002410", "pancreatic ductal cell_CL:0002079", "type B pancreatic cell_CL:0000169", "basal cell of prostate epithelium_CL:0002341", "club cell_CL:0000158", "luminal cell of prostate epithelium_CL:0002340", "keratinocyte_CL:0000312", "endothelial cell of vascular tree_CL:0002139", "skeletal muscle satellite stem cell_CL:0008011", "tendon cell_CL:0000388", "fast muscle cell_CL:0000190", "slow muscle cell_CL:0000189", "mesothelial cell_CL:0000077", "salivary gland cell_CL:0009005", "naive regulatory T cell_CL:0002677", "T follicular helper cell_CL:0002038", "DN4 thymocyte_CL:0000808", "medullary thymic epithelial cell_CL:0002365", "fat cell_CL:0000136", "bladder urothelial cell_CL:1001428", "enterocyte of epithelium of large 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"erythrocyte_CL:0000232", "cardiac neuron_CL:0010022", "naive T cell_CL:0000898", "hematopoietic precursor cell_CL:0008001", "monocyte_CL:0000576", "megakaryocyte-erythroid progenitor cell_CL:0000050", "granulocytopoietic cell_CL:0002191", "promonocyte_CL:0000559", "granulocyte_CL:0000094", "proerythroblast_CL:0000547", "natural killer cell_CL:0000623", "erythroblast_CL:0000765", "macrophage_CL:0000235", "precursor B cell_CL:0000817", "late pro-B cell_CL:0002048", "immature B cell_CL:0000816", "naive B cell_CL:0000788", "plasma cell_CL:0000786", "basophil_CL:0000767", "erythroid progenitor cell, mammalian_CL:0001066", "T cell_CL:0000084", "luminal epithelial cell of mammary gland_CL:0002326", "B cell_CL:0000236", "stromal cell_CL:0000499", "basal cell_CL:0000646", "endothelial cell_CL:0000115", "mesenchymal stem cell of adipose tissue_CL:0002570", "myeloid cell_CL:0000763", "epithelial cell_CL:0000066", "kidney proximal convoluted tubule epithelial cell_CL:1000838", "mesangial cell_CL:0000650", "kidney loop of Henle thick ascending limb epithelial cell_CL:1001106", "kidney distal convoluted tubule epithelial cell_CL:1000849", "kidney loop of Henle ascending limb epithelial cell_CL:1001016", "kidney collecting duct principal cell_CL:1001431", "lymphocyte_CL:0000542", "fenestrated cell_CL:0000666", "epithelial cell of proximal tubule_CL:0002306", "brush cell_CL:0002204", "plasmatocyte_CL:0000394", "kidney cortex artery cell_CL:1001045", "kidney capillary endothelial cell_CL:1000892", "fibroblast_CL:0000057", "hepatocyte_CL:0000182", "endothelial cell of hepatic sinusoid_CL:1000398", "Kupffer cell_CL:0000091", "hepatic stellate cell_CL:0000632", "plasmacytoid dendritic cell_CL:0000784", "myeloid leukocyte_CL:0000766", "non-classical monocyte_CL:0000875", "alveolar macrophage_CL:0000583", "myeloid dendritic cell_CL:0000782", "CD8-positive, alpha-beta T cell_CL:0000625", "classical monocyte_CL:0000860", "bronchial smooth muscle cell_CL:0002598", "mature NK T cell_CL:0000814", "pulmonary interstitial fibroblast_CL:0002241", "intermediate monocyte_CL:0002393", "neutrophil_CL:0000775", "adventitial cell_CL:0002503", "CD4-positive, alpha-beta T cell_CL:0000624", "vein endothelial cell_CL:0002543", "fibroblast of lung_CL:0002553", "regulatory T cell_CL:0000815", "dendritic cell_CL:0000451", "smooth muscle cell of the pulmonary artery_CL:0002591", "pericyte_CL:0000669", "type II pneumocyte_CL:0002063", "ciliated columnar cell of tracheobronchial tree_CL:0002145", "endothelial cell of lymphatic vessel_CL:0002138", "mesenchymal stem cell_CL:0000134", "Schwann cell_CL:0002573", "skeletal muscle satellite cell_CL:0000594", "cell of skeletal muscle_CL:0000188", "type B pancreatic cell_CL:0000169", "pancreatic D cell_CL:0000173", "pancreatic A cell_CL:0000171", "pancreatic acinar cell_CL:0002064", "pancreatic PP cell_CL:0002275", "pancreatic ductal cell_CL:0002079", "immature NK T cell_CL:0000914", "macrophage dendritic cell progenitor_CL:0002009", 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