{ "_id": "6a1d27901d7bb097a0a38260", "Package": "rifi", "Title": "'rifi' analyses data from rifampicin time series created by\nmicroarray or RNAseq", "Version": "1.17.1", "Authors@R": "c(person(\"Loubna\", \"Youssar\", email = \"lyoussar@gmail.com\", role = c(\"aut\", \"ctb\")), person(\"Walja\", \"Wanney\", email = \"jawalja@gmail.com\", role = c(\"aut\", \"ctb\")),person(\"Jens\", \"Georg\", email = \"jens.georg@biologie.uni-freiburg.de\", role = c(\"aut\", \"cre\")))", "Description": "'rifi' analyses data from rifampicin time series created\nby microarray or RNAseq. 'rifi' is a transcriptome data\nanalysis tool for the holistic identification of transcription\nand decay associated processes. The decay constants and the\ndelay of the onset of decay is fitted for each probe/bin.\nSubsequently, probes/bins of equal properties are combined into\nsegments by dynamic programming, independent of a existing\ngenome annotation. This allows to detect transcript segments of\ndifferent stability or transcriptional events within one\nannotated gene. In addition to the classic decay\nconstant/half-life analysis, 'rifi' detects processing sites,\ntranscription pausing sites, internal transcription start sites\nin operons, sites of partial transcription termination in\noperons, identifies areas of likely transcriptional\ninterference by the collision mechanism and gives an estimate\nof the transcription velocity. All data are integrated to give\nan estimate of continous transcriptional units, i.e. operons.\nComprehensive output tables and visualizations of the full\ngenome result and the individual fits for all probes/bins are\nproduced.", "VignetteBuilder": "knitr", "biocViews": "RNASeq, DifferentialExpression, GeneRegulation,\nTranscriptomics, Regression, Microarray, Software", "BugReports": "https://github.com/CyanolabFreiburg/rifi", "License": "GPL-3 + file LICENSE", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.1.12", "Language": "en-US", "Config/Bioconductor/UnsupportedPlatforms": "windows", "Config/pak/sysreqs": "cmake make libbz2-dev libicu-dev liblzma-dev\nlibxml2-dev libssl-dev xz-utils zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-05-29 18:37:31 UTC", "RemoteUrl": "https://github.com/bioc/rifi", "RemoteRef": "HEAD", "RemoteSha": "75de92622d1d34795969a366a250c13e8d98fa88", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 09:14:44 UTC", "User": "root" }, "Author": "Loubna Youssar [aut, ctb],\nWalja Wanney [aut, ctb],\nJens Georg [aut, cre]", "Maintainer": "Jens Georg ", "MD5sum": "2454c6f95f2efb015c6a6d1ca078c286", "_user": "bioc", "_type": "src", "_file": "rifi_1.17.1.tar.gz", "_fileid": "bb4ff337e7bef0a784ad6195d58c3658e5ff303941c18b55f7b2f7aedc36dcbb", "_filesize": 6920568, "_sha256": "bb4ff337e7bef0a784ad6195d58c3658e5ff303941c18b55f7b2f7aedc36dcbb", "_created": "2026-05-30T09:14:44.000Z", "_published": "2026-06-01T06:32:48.858Z", "_jobs": [ { "job": 78798335910, "time": 245, "config": "bioc-checks", "r": "4.6.0", "check": "WARNING", "artifact": "7307163438" }, { "job": 78798335749, "time": 622, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "7307201433" }, { "job": 78798335919, "time": 634, "config": "linux-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7307200685" }, { "job": 78798335715, "time": 395, "config": 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A SummarizedExperiment containing the output from rifi_penalties including the logbook and the four penalty objects as metadata.", "object": "penalties_e_coli", "file": "penalties_e_coli.RData", "class": [ "RangedSummarizedExperiment" ], "fields": [], "table": false, "tojson": false }, { "name": "penalties_minimal", "title": "The result of rifi_penalties for artificial example data A SummarizedExperiment containing the output from rifi_penalties including the logbook and the four penalty objects as metadata.", "object": "penalties_minimal", "file": "penalties_minimal.RData", "class": [ "RangedSummarizedExperiment" ], "fields": [], "table": false, "tojson": false }, { "name": "penalties_synechocystis_6803", "title": "The result of rifi_penalties for Synechocystis 6803 example data. A SummarizedExperiment containing the output from rifi_penalties including the logbook and the four penalty objects as metadata.", "object": "penalties_synechocystis_6803", "file": "penalties_synechocystis_6803.RData", "class": [ "RangedSummarizedExperiment" ], "fields": [], "table": false, "tojson": false }, { "name": "preprocess_e_coli", "title": "The result of rifi_preprocess for E.coli example data A SummarizedExperiment containing the output from rifi_penalties including the logbook and the four penalty objects as metadata. A list containing the output from rifi_preprocess, including the inp and the modified input_df.", "object": "preprocess_e_coli", "file": "preprocess_e_coli.RData", "class": [ "RangedSummarizedExperiment" ], "fields": [], "table": false, "tojson": false }, { "name": "preprocess_minimal", "title": "The result of rifi_preprocess for artificial example data A SummarizedExperiment containing the output from rifi_preprocess", "object": "preprocess_minimal", "file": "preprocess_minimal.RData", "class": [ "RangedSummarizedExperiment" ], "fields": [], "table": false, "tojson": false }, { "name": "preprocess_synechocystis_6803", "title": "The result of rifi_preprocess for Synechocystis 6803 example data is a A SummarizedExperiment containing the output of rifi_preprocess as an extention to rowRanges", "object": "preprocess_synechocystis_6803", "file": "preprocess_synechocystis_6803.RData", "class": [ "RangedSummarizedExperiment" ], "fields": [], "table": false, "tojson": false }, { "name": "res_minimal", "title": "The result of event_dataframe for E.coli artificial example. A data frame combining the processed genome annotation and a SummarizedExperiment data from rifi_stats. The dataframe is", "object": "res_minimal", "file": "res_minimal.RData", "class": [ "data.frame" ], "fields": [ "region", "gene", "locus_tag", "strand", "TU", "position", "FC_fragment_intensity", "FC_intensity", "p_value_intensity", "FC_fragment_HL", "FC_HL", "p_value_HL", "FC_HL_intensity_fragment", "FC_HL_intensity", "FC_HL_adapted", "p_value_Manova", "synthesis_ratio", "synthesis_ratio_event", "pausing_site", "iTSS_I", "event_ps_itss_p_value_Ttest", "ps_ts_fragment", "event_position", "event_duration", "delay_frg_slope", "p_value_slope", "delay", "half_life", "intensity" ], "rows": 24, "table": true, "tojson": true }, { "name": "stats_e_coli", "title": "The result of rifi_stats for E.coli example data A SummarizedExperiment containing the output from rifi_stats", "object": "stats_e_coli", "file": "stats_e_coli.RData", "class": [ "RangedSummarizedExperiment" ], "fields": [], "table": false, "tojson": false }, { "name": "stats_minimal", "title": "The result of rifi_stats for artificial example data A SummarizedExperiment containing the output of rifi_stats as an extention to rowRanges and metadata (gff file processed, see gff file documentation)", "object": "stats_minimal", "file": "stats_minimal.RData", "class": [ "RangedSummarizedExperiment" ], "fields": [], "table": false, "tojson": false }, { "name": "stats_synechocystis_6803", "title": "The result of rifi_stats for Synechocystis 6803 example data A SummarizedExperiment containing the output of rifi_stats as an extention to rowRanges", "object": "stats_synechocystis_6803", "file": "stats_synechocystis_6803.RData", "class": [ "RangedSummarizedExperiment" ], "fields": [], "table": false, "tojson": false }, { "name": "summary_e_coli", "title": "The result of rifi_summary for E.coli example data A SummarizedExperiment containing the output of rifi_stats as an extention to rowRanges", "object": "summary_e_coli", "file": "summary_e_coli.RData", "class": [ "RangedSummarizedExperiment" ], "fields": [], "table": false, "tojson": false }, { "name": "summary_minimal", "title": "The result of rifi_summary for artificial example data A SummarizedExperiment with the output from rifi_summary as metadata", "object": "summary_minimal", "file": "summary_minimal.RData", "class": [ "RangedSummarizedExperiment" ], "fields": [], "table": false, "tojson": false }, { "name": "summary_synechocystis_6803", "title": "The result of rifi_summary for Synechocystis 6803 example data A list containing the output from rifi_summary, including the fragment based data frame, bin based data frame, event data frame and the TI dataframe.", "object": "summary_synechocystis_6803", "file": "summary_synechocystis_6803.RData", "class": [ "RangedSummarizedExperiment" ], "fields": [], "table": false, "tojson": false }, { "name": "wrapper_e_coli", "title": "The result of rifi_wrapper for E.coli example data A list of SummarizedExperiment containing the output of rifi_wrapper. The list contains 6 elements of SummarizedExperiment output of rifi_preprocess, rifi_fit, rifi_penalties, rifi_fragmentation, rifi_stats and rifi_summary. The plot is generated from rifi_visualization. for more detail, please refer to each function separately.", "object": "wrapper_e_coli", "file": "wrapper_e_coli.RData", "class": [ "list" ], "fields": [], "table": false, "tojson": false }, { "name": "wrapper_minimal", "title": "The result of rifi_wrapper for E.coli artificial example. A list of SummarizedExperiment containing the output of rifi_wrapper. The list contains 6 elements of SummarizedExperiment output of rifi_preprocess, rifi_fit, rifi_penalties, rifi_fragmentation, rifi_stats and rifi_summary. The plot is generated from rifi_visualization. for more detail, please refer to each function separately.", "object": "wrapper_minimal", "file": "wrapper_minimal.RData", "class": [ "list" ], "fields": [], "table": false, "tojson": false }, { "name": "wrapper_summary_synechocystis_6803", "title": "The result of rifi_wrapper for summary_synechocystis_6803 example data A list of SummarizedExperiment containing the output of rifi_wrapper. The list contains 6 elements of SummarizedExperiment output of rifi_preprocess, rifi_fit, rifi_penalties, rifi_fragmentation, rifi_stats and rifi_summary. The plot is generated from rifi_visualization. for more detail, please refer to each function separately.", "object": "wrapper_summary_synechocystis_6803", "file": "wrapper_summary_synechocystis_6803.RData", "class": [ "list" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "apply_ancova", "title": "========================================================================= apply_ancova: apply_ancova checks the variances between 2 segments showing either pausing site (ps) or internal starting site (ITSS) independently.", "topics": [ "apply_ancova" ] }, { "page": "apply_event_position", "title": "========================================================================= apply_event_position: apply_event_position extracts event time duration for pausing site or iTSS", "topics": [ "apply_event_position" ] }, { "page": "apply_manova", "title": "========================================================================= apply_manova: apply_manova checks if the ratio of hl ratio and intensity ratio is statistically significant.", "topics": [ "apply_manova" ] }, { "page": "apply_t_test", "title": "========================================================================= apply_t_test: apply_t_test uses the statistical t_test to check if the fold-change of half -life (HL) fragments and the fold-change intensity fragments respectively are significant.", "topics": [ "apply_t_test" ] }, { "page": "apply_t_test_ti", "title": "========================================================================= apply_t_test_ti: apply_t_test_ti compares the mean of two neighboring TI fragments within the same TU.", "topics": [ "apply_t_test_ti" ] }, { "page": "apply_Ttest_delay", "title": "========================================================================= apply_Ttest_delay: apply_Ttest_delay checks the significance of the point between 2 segments showing pausing site (ps) and internal starting site (ITSS) independently", "topics": [ "apply_Ttest_delay" ] }, { "page": "check_input", "title": "========================================================================= Check_input: Check_input reviews the input given by the user", "topics": [ "check_input" ] }, { "page": "dataframe_summary", "title": "========================================================================= dataframe_summary: dataframe_summary creates two tables relating gene annotation to fragments", "topics": [ "dataframe_summary" ] }, { "page": "dataframe_summary_events", "title": "========================================================================= dataframe_summary_events: dataframe_summary_events creates one table with all events between the segments", "topics": [ "dataframe_summary_events" ] }, { "page": "dataframe_summary_events_HL_int", "title": "========================================================================= dataframe_summary_events_HL_int: dataframe_summary_events_HL_int creates one table with all events between the segments", "topics": [ "dataframe_summary_events_HL_int" ] }, { "page": "dataframe_summary_events_ps_itss", "title": "========================================================================= dataframe_summary_events_ps_itss: dataframe_summary_events_ps_itss creates one table with all events between the segments.", "topics": [ "dataframe_summary_events_ps_itss" ] }, { "page": "dataframe_summary_events_velocity", "title": "========================================================================= dataframe_summary_events_velocity: dataframe_summary_events_velocity creates one table with all events between the segments.", "topics": [ "dataframe_summary_events_velocity" ] }, { "page": "dataframe_summary_TI", "title": "========================================================================= dataframe_summary_TI: dataframe_summary_TI creates one table with all TI fragments,p_value and the coordinates", "topics": [ "dataframe_summary_TI" ] }, { "page": "event_dataframe", "title": "========================================================================= event_dataframe: event_dataframe creates a dataframe only with events", "topics": [ "event_dataframe" ] }, { "page": "example_input_e_coli", "title": "An example SummarizedExperiment from E. coli An example SummarizedExperiment from RNA-seq containing information about the intensities at all time points (assay). Seqnames, IRanges and strand columns (rowRanges)and colData with time point series and replicates.", "topics": [ "example_input_e_coli" ] }, { "page": "example_input_minimal", "title": "An artificial example SummarizedExperiment An example SummarizedExperiment containing information about the intensities at all time points (assay). Seqnames, IRanges and strand columns (rowRanges) and colData with time point series and replicates.", "topics": [ "example_input_minimal" ] }, { "page": "example_input_synechocystis_6803", "title": "An example input data frame from Synechocystis PCC 6803 A SummarizedExperiment from microarrays data containing information about the intensities at all time points (assay), Seqnames, IRanges and strand columns (rowRanges) and colData with time point series and averaged replicates.", "topics": [ "example_input_synechocystis_6803" ] }, { "page": "finding_PDD", "title": "========================================================================= finding_PDD: finding_PDD Flags potential candidates for post transcription decay", "topics": [ "finding_PDD" ] }, { "page": "finding_TI", "title": "========================================================================= finding_TI: finding_TI flags potential candidates for transcription interference", "topics": [ "finding_TI" ] }, { "page": "fit_e_coli", "title": "The result of rifi_fit for E.coli example data A SummarizedExperiment containing the output from rifi_fit as an extension of rowRanges and metadata.", "topics": [ "fit_e_coli" ] }, { "page": "fit_minimal", "title": "The artificial result of rifi_fit for artificial example data A SummarizedExperiment containing the output from rifi_fit.", "topics": [ "fit_minimal" ] }, { "page": "fit_synechocystis_6803", "title": "The result of rifi_fit for Synechocystis 6803 example data A SummarizedExperiment containing the output from rifi_fit as an extension of rowRanges and metadata.", "topics": [ "fit_synechocystis_6803" ] }, { "page": "fold_change", "title": "========================================================================= fold_change: fold_change sets a fold-change ratio between the neighboring fragments of Half-life (HL) and intensity", "topics": [ "fold_change" ] }, { "page": "fragment_delay", "title": "========================================================================= fragment_delay: fragment_delay performs the delay fragmentation", "topics": [ "fragment_delay" ] }, { "page": "fragment_HL", "title": "========================================================================= fragment_HL: fragment_HL performs the half_life fragmentation", "topics": [ "fragment_HL" ] }, { "page": "fragment_inty", "title": "========================================================================= fragment_inty: fragment_inty performs the intensity fragmentation", "topics": [ "fragment_inty" ] }, { "page": "fragment_TI", "title": "========================================================================= fragment_TI: fragment_TI performs the TI fragmentation", "topics": [ "fragment_TI" ] }, { "page": "fragmentation_e_coli", "title": "The result of rifi_fragmentation for E.coli example data A SummarizedExperiment containing the output from rifi_fragmentation as an extension of rowRanges", "topics": [ "fragmentation_e_coli" ] }, { "page": "fragmentation_minimal", "title": "The result of rifi_fragmentation for artificial example data A SummarizedExperiment containing the output from rifi_fragmentation as an extension of rowRanges and metadata.", "topics": [ "fragmentation_minimal" ] }, { "page": "fragmentation_synechocystis_6803", "title": "The result of rifi_fragmentation for Synechocystis 6803 example data A SummarizedExperiment containing the output from rifi_fragmentation as an extension fo rowRanges", "topics": [ "fragmentation_synechocystis_6803" ] }, { "page": "gff3_preprocess", "title": "========================================================================= gff3_preprocess: gff3_preprocess process gff3 file from database for multiple usage", "topics": [ "gff3_preprocess" ] }, { "page": "make_df", "title": "========================================================================= make_df: make_df adds important columns to the SummarizedExperiment object", "topics": [ "make_df" ] }, { "page": "make_pen", "title": "========================================================================= make_pen: make_pen assigns automatically a penalties", "topics": [ "make_pen" ] }, { "page": "nls2_fit", "title": "========================================================================= nls2_fit: nls2_fit estimates decay for each probe or bin", "topics": [ "nls2_fit" ] }, { "page": "penalties_e_coli", "title": "The result of rifi_penalties for E.coli example data. A SummarizedExperiment containing the output from rifi_penalties including the logbook and the four penalty objects as metadata.", "topics": [ "penalties_e_coli" ] }, { "page": "penalties_minimal", "title": "The result of rifi_penalties for artificial example data A SummarizedExperiment containing the output from rifi_penalties including the logbook and the four penalty objects as metadata.", "topics": [ "penalties_minimal" ] }, { "page": "penalties_synechocystis_6803", "title": "The result of rifi_penalties for Synechocystis 6803 example data. A SummarizedExperiment containing the output from rifi_penalties including the logbook and the four penalty objects as metadata.", "topics": [ "penalties_synechocystis_6803" ] }, { "page": "predict_ps_itss", "title": "========================================================================= predict_ps_itss: predict_ps_itss predicts pausing sites (ps) and internal starting sites (ITSS) between delay fragments.", "topics": [ "predict_ps_itss" ] }, { "page": "preprocess_e_coli", "title": "The result of rifi_preprocess for E.coli example data A SummarizedExperiment containing the output from rifi_penalties including the logbook and the four penalty objects as metadata. A list containing the output from rifi_preprocess, including the inp and the modified input_df.", "topics": [ "preprocess_e_coli" ] }, { "page": "preprocess_minimal", "title": "The result of rifi_preprocess for artificial example data A SummarizedExperiment containing the output from rifi_preprocess", "topics": [ "preprocess_minimal" ] }, { "page": "preprocess_synechocystis_6803", "title": "The result of rifi_preprocess for Synechocystis 6803 example data is a A SummarizedExperiment containing the output of rifi_preprocess as an extention to rowRanges", "topics": [ "preprocess_synechocystis_6803" ] }, { "page": "res_minimal", "title": "The result of event_dataframe for E.coli artificial example. A data frame combining the processed genome annotation and a SummarizedExperiment data from rifi_stats. The dataframe is", "topics": [ "res_minimal" ] }, { "page": "rifi_fit", "title": "========================================================================= rifi_fit: rifi_fit wraps conveniently all fitting steps", "topics": [ "rifi_fit" ] }, { "page": "rifi_fragmentation", "title": "========================================================================= rifi_fragmentation: rifi_fragmentation wraps conveniently all fragmentation steps", "topics": [ "rifi_fragmentation" ] }, { "page": "rifi_penalties", "title": "========================================================================= rifi_penalties: rifi_penalties wraps conveniently all penalty steps", "topics": [ "rifi_penalties" ] }, { "page": "rifi_preprocess", "title": "========================================================================= rifi_preprocess: rifi_preprocess wraps conveniently all pre-processing steps", "topics": [ "rifi_preprocess" ] }, { "page": "rifi_stats", "title": "rifi_stats wraps all statistical prediction steps conveniently", "topics": [ "rifi_stats" ] }, { "page": "rifi_summary", "title": "========================================================================= rifi_summary: rifi_summary wraps conveniently and summarize all rifi outputs", "topics": [ "rifi_summary" ] }, { "page": "rifi_visualization", "title": "========================================================================= rifi_visualization: rifi_visualization plots all the data with fragments and events from both strands", "topics": [ "rifi_visualization" ] }, { "page": "rifi_wrapper", "title": "========================================================================= rifi_wrapper: rifi_wrapper wraps conveniently all functions included on rifi workflow", "topics": [ "rifi_wrapper" ] }, { "page": "segment_pos", "title": "========================================================================= segment_pos: segment_pos divides all IDs by position into position_segments", "topics": [ "segment_pos" ] }, { "page": "stats_e_coli", "title": "The result of rifi_stats for E.coli example data A SummarizedExperiment containing the output from rifi_stats", "topics": [ "stats_e_coli" ] }, { "page": "stats_minimal", "title": "The result of rifi_stats for artificial example data A SummarizedExperiment containing the output of rifi_stats as an extention to rowRanges and metadata (gff file processed, see gff file documentation)", "topics": [ "stats_minimal" ] }, { "page": "stats_synechocystis_6803", "title": "The result of rifi_stats for Synechocystis 6803 example data A SummarizedExperiment containing the output of rifi_stats as an extention to rowRanges", "topics": [ "stats_synechocystis_6803" ] }, { "page": "summary_e_coli", "title": "The result of rifi_summary for E.coli example data A SummarizedExperiment containing the output of rifi_stats as an extention to rowRanges", "topics": [ "summary_e_coli" ] }, { "page": "summary_minimal", "title": "The result of rifi_summary for artificial example data A SummarizedExperiment with the output from rifi_summary as metadata", "topics": [ "summary_minimal" ] }, { "page": "summary_synechocystis_6803", "title": "The result of rifi_summary for Synechocystis 6803 example data A list containing the output from rifi_summary, including the fragment based data frame, bin based data frame, event data frame and the TI dataframe.", "topics": [ "summary_synechocystis_6803" ] }, { "page": "TI_fit", "title": "========================================================================= TI_fit: TI_fit estimates transcription interference and termination factor using nls function for probe or bin flagged as \"TI\".", "topics": [ "TI_fit" ] }, { "page": "TUgether", "title": "========================================================================= TUgether: TUgether combines delay fragments into TUs", "topics": [ "TUgether" ] }, { "page": "viz_pen_obj", "title": "========================================================================= viz_pen_obj: viz_pen_obj visualizes penalty objects", "topics": [ "viz_pen_obj" ] }, { "page": "wrapper_e_coli", "title": "The result of rifi_wrapper for E.coli example data A list of SummarizedExperiment containing the output of rifi_wrapper. The list contains 6 elements of SummarizedExperiment output of rifi_preprocess, rifi_fit, rifi_penalties, rifi_fragmentation, rifi_stats and rifi_summary. The plot is generated from rifi_visualization. for more detail, please refer to each function separately.", "topics": [ "wrapper_e_coli" ] }, { "page": "wrapper_minimal", "title": "The result of rifi_wrapper for E.coli artificial example. A list of SummarizedExperiment containing the output of rifi_wrapper. The list contains 6 elements of SummarizedExperiment output of rifi_preprocess, rifi_fit, rifi_penalties, rifi_fragmentation, rifi_stats and rifi_summary. The plot is generated from rifi_visualization. for more detail, please refer to each function separately.", "topics": [ "wrapper_minimal" ] }, { "page": "wrapper_summary_synechocystis_6803", "title": "The result of rifi_wrapper for summary_synechocystis_6803 example data A list of SummarizedExperiment containing the output of rifi_wrapper. The list contains 6 elements of SummarizedExperiment output of rifi_preprocess, rifi_fit, rifi_penalties, rifi_fragmentation, rifi_stats and rifi_summary. The plot is generated from rifi_visualization. for more detail, please refer to each function separately.", "topics": [ "wrapper_summary_synechocystis_6803" ] } ], "_readme": "https://github.com/bioc/rifi/raw/HEAD/README.md", "_rundeps": [ "abind", "askpass", "backports", "BH", "Biobase", "BiocBaseUtils", "BiocGenerics", "BiocIO", "BiocParallel", "Biostrings", "bitops", "boot", "broom", "car", "carData", "cigarillo", "cli", "codetools", "colorspace", "cowplot", "cpp11", "crayon", "curl", "DelayedArray", "Deriv", "doBy", "doMC", "dplyr", "egg", "farver", "foreach", "forecast", "formatR", "Formula", "fracdiff", "futile.logger", "futile.options", "generics", "GenomicAlignments", "GenomicRanges", "ggplot2", "glue", "gridExtra", "gtable", "httr", "IRanges", "isoband", "iterators", "jsonlite", "labeling", "lambda.r", "lattice", "lifecycle", "lme4", "lmtest", "magrittr", "MASS", "Matrix", "MatrixGenerics", "MatrixModels", "matrixStats", "mgcv", "microbenchmark", "mime", "minqa", "modelr", "nlme", "nloptr", "nls2", "nnet", "numDeriv", "openssl", "pbkrtest", "pillar", "pkgconfig", "plyr", "proto", "purrr", "quantreg", "R6", "rbibutils", "RColorBrewer", "Rcpp", "RcppArmadillo", "RcppEigen", "RCurl", "Rdpack", "reformulas", "reshape2", "restfulr", "Rhtslib", "rjson", "rlang", "Rsamtools", "rtracklayer", "S4Arrays", "S4Vectors", "S7", "scales", "Seqinfo", "snow", "SparseArray", "SparseM", "stringi", "stringr", "SummarizedExperiment", "survival", "sys", "tibble", "tidyr", "tidyselect", "timeDate", "urca", "utf8", "vctrs", "viridisLite", "withr", "XML", "XVector", "yaml", "zoo" ], "_vignettes": [ { "source": "vignette.Rmd", "filename": "vignette.html", "title": "rifi", "author": "Walja Wanney, Loubna Youssar and Jens Georg", "engine": "knitr::rmarkdown", "headings": [ "0. Installation", "I. Introduction", "1. Quickstart", "2. The output", "1. bin/probe based results", "2. fragment based results", "3. Transcription events", "4. Rifampicin relievable termination - TI instances", "5. rowRanges", "3. The whole genome visualization", "4. Troubleshooting", "1. Fit", "2. Penalties", "1. A high frequency of considerable long segments", "2. A high frequency of mini segments", "3. A high frequency of extreme high values", "5. Citing rifi", "II. rifi_preprocess", "1. The Input Data Frame", "2. check_input", "3. Filtration_Below_Background", "4. make_df", "5. segment_pos", "6. finding_PDD", "7. finding_TI", "8. rifi_preprocess", "III. rifi_fit", "1. nls2_fit", "2. TI_fit", "3. plot_nls2", "IV. rifi penalties", "1. make_pen", "1. fragment_delay_pen", "2. fragment_HL_pen", "3. fragment_inty_pen", "4. fragment_TI_pen", "2. viz_pen_obj", "V. rifi fragmentation", "1. fragment_delay", "2. fragment_HL", "3. fragment_inty", "4. TUgether", "5. fragment_TI", "VI. rifi_stats", "1. predict_ps_itss", "2. apply_Ttest_delay", "3. apply_ancova", "4. apply_event_position", "5. apply_t_test", "1. fragment_function", "2. t_test_function", "6. fold_change", "7. apply_manova", "8. apply_t_test_ti", "9. gff3_preprocess", "VII. rifi_summary", "1. event_dataframe", "1. position_function", "2. annotation_function_event", "3. strand_function", "2. dataframe_summary", "3. dataframe_summary_events", "4. dataframe_summary_events_HL_int", "5. dataframe_summary_events_ps_itss", "6. dataframe_summary_events_velocity", "7. dataframe_summary_TI", "VIII. rifi_visualization", "1. Annotation", "2. Delay", "3. Half-life", "4. Intensity/coverage", "5. Additional features", "IX. Additional functions", "1. score_fun_linear", "2. score_fun_ave", "3. score_fun_increasing", "X. References" ], "created": "2021-12-22 17:57:02", "modified": "2023-03-01 08:50:48", "commits": 42 } ], "_score": 4.903089986991944, "_indexed": true, "_nocasepkg": "rifi", "_universes": [ "bioc", "cyanolabfreiburg" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.17.1", "date": "2026-05-30T09:26:04.000Z", "distro": "noble", "commit": "75de92622d1d34795969a366a250c13e8d98fa88", "fileid": "0c38fe2eb4cb45e8612d1490e5c1e02c4bc6ffd03c5202dc163dc8db7d68a21b", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26664200594" }, { "r": "4.6.0", "os": "linux", "version": "1.17.1", "date": "2026-05-30T09:25:43.000Z", "distro": "noble", "commit": "75de92622d1d34795969a366a250c13e8d98fa88", "fileid": "94852d329987f3db8af65c7f62a10a264419b11567dfdc5f60f7949e5bb112a4", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26664200594" }, { "r": "4.5.3", "os": "mac", "version": "1.17.1", "date": "2026-05-30T12:52:14.000Z", "commit": "75de92622d1d34795969a366a250c13e8d98fa88", "fileid": "6276073c64c83092c980592b7df01c2e384a496901c6150c54759db99c6452a7", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26664200594" }, { "r": "4.6.0", "os": "mac", "version": "1.17.1", "date": "2026-05-30T12:51:44.000Z", "commit": "75de92622d1d34795969a366a250c13e8d98fa88", "fileid": "19097b027053efae64988cd6d44156bf38ad9a5c0c136516e1df605d5129dcea", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26664200594" }, { "r": "4.6.0", "os": "wasm", "version": "1.17.1", "date": "2026-05-30T09:24:56.000Z", "commit": "75de92622d1d34795969a366a250c13e8d98fa88", "fileid": "d6b674c7354a99f649668edff37570cba28197b505ae45587d1724cd930a4e2a", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26664200594" } ] }