{ "_id": "6a1bcf971d7bb097a0a1405e", "Package": "scHiCcompare", "Title": "Differential Analysis of Single-cell Hi-C Data", "Version": "1.4.0", "Authors@R": "c(\nperson(given = \"My\", family = \"Nguyen\",\nemail = \"hamy.12398@gmail.com\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0009-0003-1118-7085\")),\nperson(given = \"Mikhail\",\nfamily = \"Dozmorov\",\nrole = c(\"aut\"),\nemail = \"mikhail.dozmorov@gmail.com\",\ncomment = c(ORCID = \"0000-0002-0086-8358\")))", "Description": "This package provides functions for differential chromatin\ninteraction analysis between two single-cell Hi-C data groups.\nIt includes tools for imputation, normalization, and\ndifferential analysis of chromatin interactions. The package\nimplements pooling techniques for imputation and offers methods\nto normalize and test for differential interactions across\nsingle-cell Hi-C datasets.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "LazyData": "false", "RoxygenNote": "7.3.2", "VignetteBuilder": "knitr", "biocViews": "Software, SingleCell, HiC, Sequencing, Normalization", "BugReports": "https://github.com/dozmorovlab/ScHiCcompare/issues", "URL": "https://github.com/dozmorovlab/ScHiCcompare", "Config/pak/sysreqs": "cmake make libicu-dev libssl-dev libx11-dev\nzlib1g-dev", "Repository": "https://bioc-release.r-universe.dev", "Date/Publication": "2026-04-28 13:04:58 UTC", "RemoteUrl": "https://github.com/bioc/scHiCcompare", "RemoteRef": "RELEASE_3_23", "RemoteSha": "e578bc9cae9d8c4d6b4321176b9a3b7027019aa8", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 11:01:05 UTC", "User": "root" }, "Author": "My Nguyen [aut, cre] (ORCID: ),\nMikhail Dozmorov [aut] (ORCID: )", "Maintainer": "My Nguyen ", "MD5sum": "e83b5a22ef41310e56344945cdadf268", "_user": "bioc-release", "_type": "src", "_file": "scHiCcompare_1.4.0.tar.gz", "_fileid": "38a8b4bc0c9cdef71fb2fec56ee2b9b33600450d58b2b1bb6413c9c86e53bc76", "_filesize": 1218251, "_sha256": "38a8b4bc0c9cdef71fb2fec56ee2b9b33600450d58b2b1bb6413c9c86e53bc76", "_created": "2026-05-30T11:01:05.000Z", "_published": "2026-05-31T06:05:11.150Z", "_jobs": [ { "job": 78703938002, "time": 210, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "7307767694" }, { "job": 78703937972, "time": 397, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "7307785201" }, { "job": 78703937893, "time": 367, "config": "linux-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7307782087" }, { "job": 78703937888, "time": 176, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "7309471046" }, { "job": 78703937909, "time": 171, "config": "macos-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "7309470163" }, { "job": 78703937918, "time": 290, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7307705100" }, { "job": 78703937991, "time": 164, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7307763790" }, { "job": 78703937797, "time": 285, "config": "windows-devel", "r": "4.7.0", "check": "WARNING", "artifact": "7314275129" }, { "job": 78703937899, "time": 281, "config": "windows-oldrel", "r": "4.5.3", "check": "WARNING", "artifact": "7307774625" }, { "job": 78703937858, "time": 326, "config": "windows-release", "r": "4.6.0", "check": "WARNING", "artifact": "7307778884" } ], "_bioccheck": { "error": 0, "warning": 0, "note": 7 }, "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26681019696", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/scHiCcompare", "_commit": { "id": "e578bc9cae9d8c4d6b4321176b9a3b7027019aa8", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n", "time": 1777381498 }, "_maintainer": { "name": "My Nguyen", "email": "hamy.12398@gmail.com", "login": "hamy12398", "description": "", "uuid": 93464589 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.5.0", "role": "Depends" }, { "package": "grDevices", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "gtools", "role": "Imports" }, { "package": "HiCcompare", "role": "Imports" }, { "package": "lattice", "role": "Imports" }, { "package": "mclust", "role": "Imports" }, { "package": "mice", "role": "Imports" }, { "package": "miceadds", "role": "Imports" }, { "package": "ranger", "role": "Imports" }, { "package": "rstatix", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "data.table", "role": "Imports" }, { "package": "BiocParallel", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "DT", "role": "Suggests" }, { "package": "gridExtra", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.5.0", "bioc": "3.24" }, { "branch": "release", "version": "1.4.0", "bioc": "3.23" } ], "_topics": [ "software", "singlecell", "hic", "sequencing", "normalization", "chromatin", "schi-c", "single-cell" ], "_stars": 0, "_contributors": [ { "user": "hamy12398", "count": 211, "uuid": 93464589 }, { "user": "mdozmorov", "count": 12, "uuid": 864945 }, { "user": "wallbpg", "count": 6, "uuid": 122574468 }, { "user": "petehaitch", "count": 2, "uuid": 1049741 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 243, "source": "https://www.bioconductor.org/packages/stats/bioc/scHiCcompare" }, "_devurl": "https://github.com/dozmorovlab/schiccompare", "_searchresults": 6, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "extra/scHiCcompare.html", "manual.pdf" ], "_homeurl": "https://github.com/dozmorovlab/schiccompare", "_realowner": "bioc", "_cranurl": false, "_exports": [ "plot_HiCmatrix_heatmap", "plot_imputed_distance_diagnostic", "print.scHiCcompare", "pseudo_bulkHic", "read_files", "scHiC_bulk_compare", "scHiC_table", "scHiCcompare", "scHiCcompare_impute" ], "_datasets": [ { "name": "ODC.bandnorm_chr20_1", "title": "scHi-C data from oligodendrocyte (ODC) cell type - chromosome 20 at 1 MB resolution", "object": "ODC.bandnorm_chr20_1", "file": "ODC.bandnorm_chr20_1.rda", "class": [ "data.frame" ], "fields": [ "chr1", "start1", "chr2", "start2", "IF" ], "rows": 335, "table": true, "tojson": true }, { "name": "scHiC.table_MG_chr22", "title": "scHi-C table from microglia (MG) cell type - chromosome 22 at 1 MB resolution", "object": "scHiC.table_MG_chr22", "file": "scHiC.table_MG_chr22.rda", "class": [ "data.frame" ], "fields": [ "cell", "chr", "region1", "region2", "IF_1", "IF_2", "IF_3", "IF_4", "IF_5", "IF_6", "IF_7", "IF_8", "IF_9", "IF_10" ], "rows": 666, "table": true, "tojson": true }, { "name": "scHiC.table_ODC_chr22", "title": "scHi-C table from oligodendrocyte (ODC) cell type - chromosome 22 at 1 MB resolution", "object": "scHiC.table_ODC_chr22", "file": "scHiC.table_ODC_chr22.rda", "class": [ "data.frame" ], "fields": [ "cell", "chr", "region1", "region2", "IF_1", "IF_2", "IF_3", "IF_4", "IF_5", "IF_6", "IF_7", "IF_8", "IF_9", "IF_10" ], "rows": 666, "table": true, "tojson": true } ], "_help": [ { "page": "ODC.bandnorm_chr20_1", "title": "scHi-C data from oligodendrocyte (ODC) cell type - chromosome 20 at 1 MB resolution", "topics": [ "ODC.bandnorm_chr20_1" ] }, { "page": "plot_HiCmatrix_heatmap", "title": "Plot Hi-C Interaction Matrix Heatmap", "topics": [ "plot_HiCmatrix_heatmap" ] }, { "page": "plot_imputed_distance_diagnostic", "title": "Plot Imputed Distance Diagnostic", "topics": [ "plot_imputed_distance_diagnostic" ] }, { "page": "print.scHiCcompare", "title": "Print method for `scHiCcompare` objects", "topics": [ "print.scHiCcompare" ] }, { "page": "pseudo_bulkHic", "title": "Generate Pseudo-bulk Hi-C Data", "topics": [ "pseudo_bulkHic" ] }, { "page": "read_files", "title": "Read Files for scHi-C Dataset", "topics": [ "read_files" ] }, { "page": "scHiC_bulk_compare", "title": "Compare Bulk Hi-C Data", "topics": [ "scHiC_bulk_compare" ] }, { "page": "scHiC_table", "title": "Create scHiC Interaction Frequency Table", "topics": [ "scHiC_table" ] }, { "page": "scHiC.table_MG_chr22", "title": "scHi-C table from microglia (MG) cell type - chromosome 22 at 1 MB resolution", "topics": [ "scHiC.table_MG_chr22" ] }, { "page": "scHiC.table_ODC_chr22", "title": "scHi-C table from oligodendrocyte (ODC) cell type - chromosome 22 at 1 MB resolution", "topics": [ "scHiC.table_ODC_chr22" ] }, { "page": "scHiCcompare", "title": "ScHiCcompare: Differential Analysis of Single-Cell Hi-C Data", "topics": [ "scHiCcompare" ] }, { "page": "scHiCcompare_impute", "title": "Random Forest Imputation with Pooling options for scHi-C Data", "topics": [ "scHiCcompare_impute" ] } ], "_readme": "https://github.com/bioc/scHiCcompare/raw/RELEASE_3_23/README.md", "_rundeps": [ "abind", "backports", "BH", "Biobase", "BiocGenerics", "biocmake", "BiocParallel", "bit", "bit64", "boot", "broom", "car", "carData", "cli", "clipr", "codetools", "colorspace", "corrplot", "cowplot", "cpp11", "crayon", "data.table", "DBI", "DelayedArray", "Deriv", "dir.expiry", "doBy", "dplyr", "farver", "filelock", "forcats", "foreach", "forecast", "formatR", "Formula", "fracdiff", "futile.logger", "futile.options", "generics", "GenomicRanges", "ggplot2", "glmnet", "glue", "gridExtra", "gtable", "gtools", "haven", "HiCcompare", "hms", "InteractionSet", "IRanges", "isoband", "iterators", "jomo", "KernSmooth", "labeling", "lambda.r", "lattice", "lifecycle", "lme4", "lmtest", "magrittr", "MASS", "Matrix", "MatrixGenerics", "MatrixModels", "matrixStats", "mclust", "mgcv", "mice", "miceadds", "microbenchmark", "minqa", "mitml", "mitools", "modelr", "nlme", "nloptr", "nnet", "numDeriv", "ordinal", "pan", "pbkrtest", "pheatmap", "pillar", "pkgconfig", "prettyunits", "progress", "purrr", "quantreg", "R6", "ranger", "rbibutils", "RColorBrewer", "Rcpp", "RcppArmadillo", "RcppEigen", "Rdpack", "readr", "reformulas", "rhdf5", "rhdf5filters", "Rhdf5lib", "rlang", "rpart", "rstatix", "S4Arrays", "S4Vectors", "S7", "scales", "Seqinfo", "shape", "snow", "SparseArray", "SparseM", "stringi", "stringr", "SummarizedExperiment", "survival", "tibble", "tidyr", "tidyselect", "timeDate", "tzdb", "ucminf", "urca", "utf8", "vctrs", "viridisLite", "vroom", "withr", "XVector", "zoo" ], "_vignettes": [ { "source": "ScHiCcompare.Rmd", "filename": "ScHiCcompare.html", "title": "scHiCcompare Vignette", "author": "My Nguyen, Mikhail Dozmorov", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Installation", "scHiCcompare function", "Overview", "Input", "Prepare input folders", "Example of real analysis", "Output", "Output objects from the R function", "Externally saved output files", "Example of output", "Helper functions", "Heatmap HiC matrix plot", "Imputation Diagnostic plot", "Others", "Download scHiC data", "Import scHiC data in R", "Session Info" ], "created": "2024-10-07 16:38:25", "modified": "2025-04-01 07:03:01", "commits": 47 } ], "_score": 4.477121254719663, "_indexed": false, "_nocasepkg": "schiccompare", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/scHiCcompare", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.4.0", "date": "2026-05-30T11:13:33.000Z", "distro": "noble", "commit": "e578bc9cae9d8c4d6b4321176b9a3b7027019aa8", "fileid": "87d97635d2b654276c8f319c68ea89be7c2190c28309536e6ef55002cd537f7a", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26681019696" }, { "r": "4.6.0", "os": "linux", "version": "1.4.0", "date": "2026-05-30T11:13:02.000Z", "distro": "noble", "commit": "e578bc9cae9d8c4d6b4321176b9a3b7027019aa8", "fileid": "69ad99aca25d512f0b5812e9fe3122f7a0b0a3e6331315c9602456ad6bec5bbb", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26681019696" }, { "r": "4.5.3", "os": "mac", "version": "1.4.0", "date": "2026-05-30T16:01:33.000Z", "commit": "e578bc9cae9d8c4d6b4321176b9a3b7027019aa8", "fileid": "230bdd95a25edb487dbd3d03238f88221c788b3e4e136d50c7640878dacf81e9", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26681019696" }, { "r": "4.6.0", "os": "mac", "version": "1.4.0", "date": "2026-05-30T16:01:24.000Z", "commit": "e578bc9cae9d8c4d6b4321176b9a3b7027019aa8", "fileid": "3b2c8a50f31dd01591c30d7e31b224ec1a90a1c41709ba1b902843c84e7c3505", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26681019696" }, { "r": "4.6.0", "os": "wasm", "version": "1.4.0", "date": "2026-05-30T11:12:29.000Z", "commit": "e578bc9cae9d8c4d6b4321176b9a3b7027019aa8", "fileid": "1acf92e200df133ed3b3330f0b4f3b97413f57419bb44e6e3ea8d9979c398ebc", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26681019696" }, { "r": "4.7.0", "os": "win", "version": "1.4.0", "date": "2026-05-31T06:01:42.000Z", "commit": "e578bc9cae9d8c4d6b4321176b9a3b7027019aa8", "fileid": "d5f74f7419bb1cd47eba768de14270531d53e750b65564d49ede6a743a4975e9", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26681019696" }, { "r": "4.5.3", "os": "win", "version": "1.4.0", "date": "2026-05-30T11:11:30.000Z", "commit": "e578bc9cae9d8c4d6b4321176b9a3b7027019aa8", "fileid": "01d8a28b27706cbf7f77226e3fb08833a5c4e5df56451a174b4d22272ac57ffc", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26681019696" }, { "r": "4.6.0", "os": "win", "version": "1.4.0", "date": "2026-05-30T11:11:13.000Z", "commit": "e578bc9cae9d8c4d6b4321176b9a3b7027019aa8", "fileid": "6aaa1a51d0a382ce85c51952685c93bbc7121f5a83e84808b3fe10991d0f0550", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26681019696" } ] }