{ "_id": "6af03a3cf4a180a2e271cb32", "Package": "FindIT2", "Title": "find influential TF and Target based on multi-omics data", "Version": "1.18.0", "Authors@R": "c(\nperson(\"Guandong\", \"Shang\", role = c(\"aut\", \"cre\"),\nemail = \"shangguandong1996@163.com\",\ncomment = c(ORCID = \"0000-0002-9509-0314\"))\n)", "Description": "This package implements functions to find influential TF\nand target based on different input type. It have five module:\nMulti-peak multi-gene annotaion(mmPeakAnno module), Calculate\nregulation potential(calcRP module), Find influential Target\nbased on ChIP-Seq and RNA-Seq data(Find influential Target\nmodule), Find influential TF based on different input(Find\ninfluential TF module), Calculate peak-gene or peak-peak\ncorrelation(peakGeneCor module). And there are also some other\nuseful function like integrate different source information,\ncalculate jaccard similarity for your TF.", "License": "Artistic-2.0", "URL": "https://github.com/shangguandong1996/FindIT2", "BugReports": "https://support.bioconductor.org/t/FindIT2", "biocViews": "Software, Annotation, ChIPSeq, ATACSeq, GeneRegulation,\nMultipleComparison, GeneTarget", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.1.2", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "Config/pak/sysreqs": "make libbz2-dev libicu-dev liblzma-dev libpng-dev\nlibxml2-dev libssl-dev xz-utils zlib1g-dev", "Repository": "Bioconductor 3.23", "Date/Publication": "2026-04-28 12:56:26 UTC", "RemoteUrl": "https://github.com/bioc/FindIT2", "RemoteRef": "RELEASE_3_23", "RemoteSha": "e7a0d39113ce7a959d424ce2c354c3d3f56de51a", "NeedsCompilation": "no", "Packaged": { "Date": "2026-11-08 08:30:33 UTC", "User": "root" }, "Author": "Guandong Shang [aut, cre] (ORCID:\n)", "Maintainer": "Guandong Shang ", "_user": "bioc-release", "_type": "src", "_file": "FindIT2_1.18.0.tar.gz", "_fileid": "https://r2.ropensci.org/e55797a1d54c42ca379d0b9dc43be9db1b2a9e5dfd9eddd17bff8743ebeeb1bb", "_filesize": 2173295, "_sha256": "e55797a1d54c42ca379d0b9dc43be9db1b2a9e5dfd9eddd17bff8743ebeeb1bb", "_expires": "2027-02-16T09:00:42.000Z", "_created": "2026-11-08T08:30:33.000Z", "_published": "2026-11-08T09:00:44.764Z", "_upstream": "https://github.com/bioc/FindIT2", "_status": "success", "_maintainer": { "name": "Guandong Shang", "email": "shangguandong1996@163.com", "login": "shangguandong1996", "description": "Postgraduate, interested in Epigenomics and Bioinformatics", "uuid": 22555126, "orcid": "0000-0002-9509-0314" }, "_jobs": [ { "job": 128677017152, "time": 224, "config": "bioc-checks", "r": "4.6.2", "check": "NOTE", "artifact": "13610737174" }, { "job": 128677017195, "time": 474, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "13610991076" }, { "job": 128677017157, "time": 455, "config": "linux-release-x86_64", "r": "4.6.2", "check": "OK", "artifact": "13610319971" }, { "job": 128677017166, "time": 351, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "13611521966" }, { "job": 128677017189, "time": 461, "config": "macos-release-arm64", "r": "4.6.2", "check": "OK", "artifact": "13611047291" }, { "job": 128675752600, "time": 354, "config": "source", "r": "4.6.2", "check": "OK", "artifact": "13610766252" }, { "job": 128677017214, "time": 155, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "13609649562" }, { "job": 128677017160, "time": 366, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "13609929005" }, { "job": 128677017207, "time": 370, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "13611210394" }, { "job": 128677017218, "time": 342, "config": "windows-release-x86_64", "r": "4.6.2", "check": "OK", "artifact": "13611090599" } ], "_bioccheck": { "error": 0, "warning": 0, "note": 13 }, "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/42462853596", "_commit": { "id": "e7a0d39113ce7a959d424ce2c354c3d3f56de51a", "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": 1777380986 }, "_distro": "resolute", "_host": "GitHub-Actions", "_registered": true, "_dependencies": [ { "package": "GenomicRanges", "role": "Depends" }, { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "withr", "role": "Imports" }, { "package": "BiocGenerics", "role": "Imports" }, { "package": "Seqinfo", "role": "Imports" }, { "package": "rtracklayer", "role": "Imports" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "GenomicFeatures", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "patchwork", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "BiocParallel", "role": "Imports" }, { "package": "qvalue", "role": "Imports" }, { "package": "stringr", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "ggrepel", "role": "Imports" }, { "package": "tibble", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "SummarizedExperiment", "role": "Imports" }, { "package": "MultiAssayExperiment", "role": "Imports" }, { "package": "IRanges", "role": "Imports" }, { "package": "progress", "role": "Imports" }, { "package": "purrr", "role": "Imports" }, { "package": "glmnet", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "sessioninfo", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "TxDb.Athaliana.BioMart.plantsmart28", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2026-18", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.19.0", "bioc": "3.24", "repository": "bioc", "r": "4.6.0" }, { "branch": "release", "version": "1.18.0", "bioc": "3.23", "repository": "bioc", "r": "4.6.0" } ], "_topics": [ "software", "annotation", "chipseq", "atacseq", "generegulation", "multiplecomparison", "genetarget" ], "_stars": 6, "_contributors": [ { "user": "shangguandong1996", "count": 72, "uuid": 22555126 }, { "user": "jwokaty", "count": 6, "uuid": 1744257 }, { "user": "nturaga", "count": 4, "uuid": 2746443 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 485, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 488, "source": "https://www.bioconductor.org/packages/stats/bioc/FindIT2" }, "_devurl": "https://github.com/shangguandong1996/findit2", "_searchresults": 11, "_rbuild": "4.6.2", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/FindIT2.html", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md" ], "_homeurl": "https://github.com/shangguandong1996/findit2", "_realowner": "bioc", "_cranurl": false, "_exports": [ "calcRP_coverage", "calcRP_region", "calcRP_TFHit", "enhancerPromoterCor", "findIT_enrichFisher", "findIT_enrichWilcox", "findIT_MARA", "findIT_regionRP", "findIT_TFHit", "findIT_TTPair", "getAssocPairNumber", "integrate_ChIP_RNA", "integrate_replicates", "jaccard_findIT_enrichFisher", "jaccard_findIT_TTpair", "loadPeakFile", "mm_geneBound", "mm_geneScan", "mm_nearestGene", "peakGeneCor", "plot_annoDistance", "plot_peakGeneAlias_summary", "plot_peakGeneCor" ], "_datasets": [ { "name": "ATAC_normCount", "title": "ATAC normCount of E50h-72h in Chr5", "object": "ATAC_normCount", "file": "ATAC_normCount.rda", "class": [ "matrix", "array" ], "fields": [ "E5_0h_R1", "E5_0h_R2", "E5_4h_R1", "E5_4h_R2", "E5_8h_R1", "E5_8h_R2", "E5_16h_R1", "E5_16h_R2", "E5_24h_R1", "E5_24h_R2", "E5_48h_R1", "E5_48h_R2", "E5_48h_R3", "E5_72h_R1", "E5_72h_R2", "E5_72h_R3" ], "rows": 5902, "table": true, "tojson": true }, { "name": "RNA_normCount", "title": "RNA normCount of E50h-72h in Chr5", "object": "RNA_normCount", "file": "RNA_normCount.rda", "class": [ "data.frame" ], "fields": [ "E5_0h_R1", "E5_0h_R2", "E5_4h_R1", "E5_4h_R2", "E5_4h_R3", "E5_8h_R1", "E5_8h_R2", "E5_16h_R1", "E5_16h_R2", "E5_24h_R1", "E5_24h_R2", "E5_48h_R1", "E5_48h_R2", "E5_72h_R1", "E5_72h_R2", "E5_72h_R3" ], "rows": 8236, "table": true, "tojson": true }, { "name": "RNADiff_LEC2_GR", "title": "RNA diff result from LEC2_GR VS LEC2_DMSO", "object": "RNADiff_LEC2_GR", "file": "RNADiff_LEC2_GR.rda", "class": [ "data.frame" ], "fields": [ "gene_id", "log2FoldChange", "padj" ], "rows": 8236, "table": true, "tojson": true }, { "name": "test_featureSet", "title": "test_featureSet", "object": "test_featureSet", "file": "test_featureSet.rda", "class": [ "character" ], "fields": [], "table": false, "tojson": true }, { "name": "test_geneSet", "title": "test_geneSet", "object": "test_geneSet", "file": "test_geneSet.rda", "class": [ "character" ], "fields": [], "table": false, "tojson": true }, { "name": "TF_target_database", "title": "TF-target database", "object": "TF_target_database", "file": "TF_target_database.rda", "class": [ "data.frame" ], "fields": [ "TF_id", "target_gene" ], "rows": 7549, "table": true, "tojson": true } ], "_help": [ { "page": "ATAC_normCount", "title": "ATAC normCount of E50h-72h in Chr5", "topics": [ "ATAC_normCount" ] }, { "page": "calcRP_coverage", "title": "calcRP_coverage", "topics": [ "calcRP_coverage" ] }, { "page": "calcRP_region", "title": "calcRP_region", "topics": [ "calcRP_region" ] }, { "page": "calcRP_TFHit", "title": "calcRP_TFHit", "topics": [ "calcRP_TFHit" ] }, { "page": "enhancerPromoterCor", "title": "enhancerPromoterCor", "topics": [ "enhancerPromoterCor" ] }, { "page": "findIT_enrichFisher", "title": "findI(nfluential)T(F)_enrichFisher", "topics": [ "findIT_enrichFisher" ] }, { "page": "findIT_enrichWilcox", "title": "findIT_enrichWilcox", "topics": [ "findIT_enrichWilcox" ] }, { "page": "findIT_MARA", "title": "findIT_MARA", "topics": [ "findIT_MARA" ] }, { "page": "findIT_regionRP", "title": "findI(nfluential)T(F)_regionRP", "topics": [ "findIT_regionRP" ] }, { "page": "findIT_TFHit", "title": "findI(nfluential)T(F)_TFHit", "topics": [ "findIT_TFHit" ] }, { "page": "findIT_TTPair", "title": "findI(nfluential)T(F)_T(F)T(arget)Pair", "topics": [ "findIT_TTPair" ] }, { "page": "getAssocPairNumber", "title": "getAssocPairNumber", "topics": [ "getAssocPairNumber" ] }, { "page": "integrate_ChIP_RNA", "title": "integrate_ChIP_RNA", "topics": [ "integrate_ChIP_RNA" ] }, { "page": "integrate_replicates", "title": "integrate_replicates", "topics": [ "integrate_replicates" ] }, { "page": "jaccard_findIT_enrichFisher", "title": "jaccard_findIT_enrichFisher", "topics": [ "jaccard_findIT_enrichFisher" ] }, { "page": "jaccard_findIT_TTpair", "title": "jaccard_findIT_TTpair", "topics": [ "jaccard_findIT_TTpair" ] }, { "page": "loadPeakFile", "title": "loadPeakFile", "topics": [ "loadPeakFile" ] }, { "page": "mm_geneBound", "title": "mm_geneBound", "topics": [ "mm_geneBound" ] }, { "page": "mm_geneScan", "title": "mm_geneScan", "topics": [ "mm_geneScan" ] }, { "page": "mm_nearestGene", "title": "mm_nearestGene", "topics": [ "mm_nearestGene" ] }, { "page": "peakGeneCor", "title": "peakGeneCor", "topics": [ "peakGeneCor" ] }, { "page": "plot_annoDistance", "title": "plot_annoDistance", "topics": [ "plot_annoDistance" ] }, { "page": "plot_peakGeneAlias_summary", "title": "plot_peakGeneAlias_summary", "topics": [ "plot_peakGeneAlias_summary" ] }, { "page": "plot_peakGeneCor", "title": "plot_peakGeneCor", "topics": [ "plot_peakGeneCor" ] }, { "page": "RNA_normCount", "title": "RNA normCount of E50h-72h in Chr5", "topics": [ "RNA_normCount" ] }, { "page": "RNADiff_LEC2_GR", "title": "RNA diff result from LEC2_GR VS LEC2_DMSO", "topics": [ "RNADiff_LEC2_GR" ] }, { "page": "test_featureSet", "title": "test_featureSet", "topics": [ "test_featureSet" ] }, { "page": "test_geneSet", "title": "test_geneSet", "topics": [ "test_geneSet" ] }, { "page": "TF_target_database", "title": "TF-target database", "topics": [ "TF_target_database" ] } ], "_readme": "https://github.com/bioc/FindIT2/raw/RELEASE_3_23/README.md", "_rundeps": [ "abind", "AnnotationDbi", "askpass", "BH", "Biobase", "BiocBaseUtils", "BiocGenerics", "BiocIO", "BiocParallel", "Biostrings", "bit", "bit64", "bitops", "blob", "cachem", "cigarillo", "cli", "codetools", "cpp11", "crayon", "curl", "DBI", "DelayedArray", "dplyr", "farver", "fastmap", "foreach", "formatR", "futile.logger", "futile.options", "generics", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "ggplot2", "ggrepel", "glmnet", "glue", "gtable", "hms", "httr", "IRanges", "isoband", "iterators", "jsonlite", "KEGGREST", "labeling", "lambda.r", "lattice", "lifecycle", "magrittr", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "mime", "MultiAssayExperiment", "openssl", "patchwork", "pillar", "pkgconfig", "plyr", "png", "prettyunits", "progress", "purrr", "qvalue", "R6", "RColorBrewer", "Rcpp", "RcppEigen", "RCurl", "reshape2", "restfulr", "Rhtslib", "rjson", "rlang", "Rsamtools", "RSQLite", "rtracklayer", "S4Arrays", "S4Vectors", "S7", "scales", "Seqinfo", "shape", "snow", "SparseArray", "stringi", "stringr", "SummarizedExperiment", "survival", "sys", "tibble", "tidyr", "tidyselect", "utf8", "vctrs", "viridisLite", "withr", "XML", "XVector", "yaml" ], "_vignettes": [ { "source": "FindIT2.Rmd", "filename": "FindIT2.html", "title": "FindIT2:Find influential TF and influential Target", "author": "Guandong Shang", "engine": "knitr::rmarkdown", "headings": [ "Basics", "Install FindIT2", "Citation", "Acknowledgments", "Introduction", "Multi-peak multi-gene annotation", "annotate peak using nearest mode", "find realted peak using gene Bound mode", "find related peak using gene scan mode", "Calculate regulation potential(RP)", "calculate RP using mmAnno", "Calculate RP using bw file", "Calculate RP using mmAnno result and peakScore matrix", "Find influential target", "Find influential TF", "Find IT of input peak based on wilcox test", "Find IT of input peak based on fisher test", "Find IT of input genes based on fisher test", "Find IT of input genes based on TF hit", "Find IT of input genes based on region RP", "Find IT of input genes based on motif activity response", "integrate result", "Calculate feature correlation", "Calculate peak gene correlation", "Calculate enhancer promoter correlation", "Integrate result", "Session info", "References" ], "created": "2021-06-08 08:49:05", "modified": "2022-05-10 08:24:03", "commits": 11 } ], "_score": 4.819543935541869, "_indexed": false, "_nocasepkg": "findit2", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/FindIT2", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.18.0", "date": "2026-11-08T08:34:54.000Z", "distro": "resolute", "commit": "e7a0d39113ce7a959d424ce2c354c3d3f56de51a", "fileid": "https://r2.ropensci.org/d7d005de342c6ba2c82e0f8c138eb6357fead3e890355d40e0a75fad5e850c3a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/42462853596" }, { "r": "4.6.2", "os": "linux", "version": "1.18.0", "date": "2026-11-08T08:35:32.000Z", "distro": "resolute", "commit": "e7a0d39113ce7a959d424ce2c354c3d3f56de51a", "fileid": "https://r2.ropensci.org/44d05f576476ef4ddbdb2e0cdd87cc783df984863372cf68f05988acf74f6d56", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/42462853596" }, { "r": "4.5.3", "os": "mac", "version": "1.18.0", "date": "2026-11-08T08:53:48.000Z", "commit": "e7a0d39113ce7a959d424ce2c354c3d3f56de51a", "fileid": "https://r2.ropensci.org/a5fd117d98f926424f49653ca0f84e4b3b88f64b3c59211a742adc13de866e02", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/42462853596" }, { "r": "4.6.2", "os": "mac", "version": "1.18.0", "date": "2026-11-08T08:55:12.000Z", "commit": "e7a0d39113ce7a959d424ce2c354c3d3f56de51a", "fileid": "https://r2.ropensci.org/d9bbe6296c742ad3fd1e1fe18fd3c7b0d3af6641653a39ad608e5d98b7cf72ba", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/42462853596" }, { "r": "4.6.0", "os": "wasm", "version": "1.18.0", "date": "2026-11-08T08:33:48.000Z", "commit": "e7a0d39113ce7a959d424ce2c354c3d3f56de51a", "fileid": "https://r2.ropensci.org/9ebe012b8342e53970024e19ee2798c4fbf1c42bf2a45994b0ebb112085ddcf2", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/42462853596" }, { "r": "4.7.0", "os": "win", "version": "1.18.0", "date": "2026-11-08T08:33:15.000Z", "commit": "e7a0d39113ce7a959d424ce2c354c3d3f56de51a", "fileid": "https://r2.ropensci.org/80da291a87f5962be49fd0d23e177b11b218080ce92792e0433f5973eaf6f58a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/42462853596" }, { "r": "4.5.3", "os": "win", "version": "1.18.0", "date": "2026-11-08T08:33:03.000Z", "commit": "e7a0d39113ce7a959d424ce2c354c3d3f56de51a", "fileid": "https://r2.ropensci.org/95f4b2970f5aeaa87582807094aa1e51fd515c179430a3e6cc5c6628dbd15326", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/42462853596" }, { "r": "4.6.2", "os": "win", "version": "1.18.0", "date": "2026-11-08T08:33:03.000Z", "commit": "e7a0d39113ce7a959d424ce2c354c3d3f56de51a", "fileid": "https://r2.ropensci.org/dd16bf009e463dd5d18298ede16cbb1c4359843ca8dee580fc42b591f87423f3", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/42462853596" } ] }