TI_fit                  =========================================================================
                        TI_fit: TI_fit estimates transcription
                        interference and termination factor using nls
                        function for probe or bin flagged as "TI".
TUgether                =========================================================================
                        TUgether: TUgether combines delay fragments
                        into TUs
apply_Ttest_delay       =========================================================================
                        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
apply_ancova            =========================================================================
                        apply_ancova: apply_ancova checks the variances
                        between 2 segments showing either pausing site
                        (ps) or internal starting site (ITSS)
                        independently.
apply_event_position    =========================================================================
                        apply_event_position: apply_event_position
                        extracts event time duration for pausing site
                        or iTSS
apply_manova            =========================================================================
                        apply_manova: apply_manova checks if the ratio
                        of hl ratio and intensity ratio is
                        statistically significant.
apply_t_test            =========================================================================
                        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.
apply_t_test_ti         =========================================================================
                        apply_t_test_ti: apply_t_test_ti compares the
                        mean of two neighboring TI fragments within the
                        same TU.
check_input             =========================================================================
                        Check_input: Check_input reviews the input
                        given by the user
dataframe_summary       =========================================================================
                        dataframe_summary: dataframe_summary creates
                        two tables relating gene annotation to
                        fragments
dataframe_summary_TI    =========================================================================
                        dataframe_summary_TI: dataframe_summary_TI
                        creates one table with all TI fragments,p_value
                        and the coordinates
dataframe_summary_events
                        =========================================================================
                        dataframe_summary_events:
                        dataframe_summary_events creates one table with
                        all events between the segments
dataframe_summary_events_HL_int
                        =========================================================================
                        dataframe_summary_events_HL_int:
                        dataframe_summary_events_HL_int creates one
                        table with all events between the segments
dataframe_summary_events_ps_itss
                        =========================================================================
                        dataframe_summary_events_ps_itss:
                        dataframe_summary_events_ps_itss creates one
                        table with all events between the segments.
dataframe_summary_events_velocity
                        =========================================================================
                        dataframe_summary_events_velocity:
                        dataframe_summary_events_velocity creates one
                        table with all events between the segments.
event_dataframe         =========================================================================
                        event_dataframe: event_dataframe creates a
                        dataframe only with events
example_input_e_coli    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.
example_input_minimal   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.
example_input_synechocystis_6803
                        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.
finding_PDD             =========================================================================
                        finding_PDD: finding_PDD Flags potential
                        candidates for post transcription decay
finding_TI              =========================================================================
                        finding_TI: finding_TI flags potential
                        candidates for transcription interference
fit_e_coli              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.
fit_minimal             The artificial result of rifi_fit for
                        artificial example data A SummarizedExperiment
                        containing the output from rifi_fit.
fit_synechocystis_6803
                        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.
fold_change             =========================================================================
                        fold_change: fold_change sets a fold-change
                        ratio between the neighboring fragments of
                        Half-life (HL) and intensity
fragment_HL             =========================================================================
                        fragment_HL: fragment_HL performs the half_life
                        fragmentation
fragment_TI             =========================================================================
                        fragment_TI: fragment_TI performs the TI
                        fragmentation
fragment_delay          =========================================================================
                        fragment_delay: fragment_delay performs the
                        delay fragmentation
fragment_inty           =========================================================================
                        fragment_inty: fragment_inty performs the
                        intensity fragmentation
fragmentation_e_coli    The result of rifi_fragmentation for E.coli
                        example data A SummarizedExperiment containing
                        the output from rifi_fragmentation as an
                        extension of rowRanges
fragmentation_minimal   The result of rifi_fragmentation for artificial
                        example data A SummarizedExperiment containing
                        the output from rifi_fragmentation as an
                        extension of rowRanges and metadata.
fragmentation_synechocystis_6803
                        The result of rifi_fragmentation for
                        Synechocystis 6803 example data A
                        SummarizedExperiment containing the output from
                        rifi_fragmentation as an extension fo rowRanges
gff3_preprocess         =========================================================================
                        gff3_preprocess: gff3_preprocess process gff3
                        file from database for multiple usage
make_df                 =========================================================================
                        make_df: make_df adds important columns to the
                        SummarizedExperiment object
make_pen                =========================================================================
                        make_pen: make_pen assigns automatically a
                        penalties
nls2_fit                =========================================================================
                        nls2_fit: nls2_fit estimates decay for each
                        probe or bin
penalties_e_coli        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.
penalties_minimal       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.
penalties_synechocystis_6803
                        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.
predict_ps_itss         =========================================================================
                        predict_ps_itss: predict_ps_itss predicts
                        pausing sites (ps) and internal starting sites
                        (ITSS) between delay fragments.
preprocess_e_coli       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.
preprocess_minimal      The result of rifi_preprocess for artificial
                        example data A SummarizedExperiment containing
                        the output from rifi_preprocess
preprocess_synechocystis_6803
                        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
res_minimal             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
rifi_fit                =========================================================================
                        rifi_fit: rifi_fit wraps conveniently all
                        fitting steps
rifi_fragmentation      =========================================================================
                        rifi_fragmentation: rifi_fragmentation wraps
                        conveniently all fragmentation steps
rifi_penalties          =========================================================================
                        rifi_penalties: rifi_penalties wraps
                        conveniently all penalty steps
rifi_preprocess         =========================================================================
                        rifi_preprocess: rifi_preprocess wraps
                        conveniently all pre-processing steps
rifi_stats              rifi_stats wraps all statistical prediction
                        steps conveniently
rifi_summary            =========================================================================
                        rifi_summary: rifi_summary wraps conveniently
                        and summarize all rifi outputs
rifi_visualization      =========================================================================
                        rifi_visualization: rifi_visualization plots
                        all the data with fragments and events from
                        both strands
rifi_wrapper            =========================================================================
                        rifi_wrapper: rifi_wrapper wraps conveniently
                        all functions included on rifi workflow
segment_pos             =========================================================================
                        segment_pos: segment_pos divides all IDs by
                        position into position_segments
stats_e_coli            The result of rifi_stats for E.coli example
                        data A SummarizedExperiment containing the
                        output from rifi_stats
stats_minimal           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)
stats_synechocystis_6803
                        The result of rifi_stats for Synechocystis 6803
                        example data A SummarizedExperiment containing
                        the output of rifi_stats as an extention to
                        rowRanges
summary_e_coli          The result of rifi_summary for E.coli example
                        data A SummarizedExperiment containing the
                        output of rifi_stats as an extention to
                        rowRanges
summary_minimal         The result of rifi_summary for artificial
                        example data A SummarizedExperiment with the
                        output from rifi_summary as metadata
summary_synechocystis_6803
                        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.
viz_pen_obj             =========================================================================
                        viz_pen_obj: viz_pen_obj visualizes penalty
                        objects
wrapper_e_coli          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.
wrapper_minimal         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.
wrapper_summary_synechocystis_6803
                        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.
