Package: rifi 1.9.0

Jens Georg

rifi: 'rifi' analyses data from rifampicin time series created by microarray or RNAseq

'rifi' analyses data from rifampicin time series created by microarray or RNAseq. 'rifi' is a transcriptome data analysis tool for the holistic identification of transcription and decay associated processes. The decay constants and the delay of the onset of decay is fitted for each probe/bin. Subsequently, probes/bins of equal properties are combined into segments by dynamic programming, independent of a existing genome annotation. This allows to detect transcript segments of different stability or transcriptional events within one annotated gene. In addition to the classic decay constant/half-life analysis, 'rifi' detects processing sites, transcription pausing sites, internal transcription start sites in operons, sites of partial transcription termination in operons, identifies areas of likely transcriptional interference by the collision mechanism and gives an estimate of the transcription velocity. All data are integrated to give an estimate of continous transcriptional units, i.e. operons. Comprehensive output tables and visualizations of the full genome result and the individual fits for all probes/bins are produced.

Authors:Loubna Youssar [aut, ctb], Walja Wanney [aut, ctb], Jens Georg [aut, cre]

rifi_1.9.0.tar.gz

rifi_1.9.0.tgz(r-4.4-any)rifi_1.9.0.tgz(r-4.3-any)
rifi_1.9.0.tar.gz(r-4.5-noble)rifi_1.9.0.tar.gz(r-4.4-noble)
rifi_1.9.0.tgz(r-4.4-emscripten)rifi_1.9.0.tgz(r-4.3-emscripten)
rifi.pdf |rifi.html✨
rifi/json (API)

# Install 'rifi' in R:
install.packages('rifi', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/cyanolabfreiburg/rifi/issues

Datasets:
  • 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.
  • 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.
  • 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
  • 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.
  • 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
  • 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
  • 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.
  • 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.

On BioConductor:rifi-1.9.0(bioc 3.20)rifi-1.8.0(bioc 3.19)

bioconductor-package

38 exports 0.71 score 112 dependencies

Last updated 2 months agofrom:4a8fea2342

Exports:apply_ancovaapply_event_positionapply_manovaapply_t_testapply_t_test_tiapply_Ttest_delaycheck_inputdataframe_summarydataframe_summary_eventsdataframe_summary_events_HL_intdataframe_summary_events_ps_itssdataframe_summary_events_velocitydataframe_summary_TIevent_dataframefinding_PDDfinding_TIfold_changefragment_delayfragment_HLfragment_intyfragment_TIgff3_preprocessmake_dfmake_pennls2_fitpredict_ps_itssrifi_fitrifi_fragmentationrifi_penaltiesrifi_preprocessrifi_statsrifi_summaryrifi_visualizationrifi_wrappersegment_posTI_fitTUgetherviz_pen_obj

Dependencies:abindaskpassbackportsBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitopsbootbroomcarcarDataclicodetoolscolorspacecowplotcpp11crayoncurlDelayedArrayDerivdoBydoMCdplyreggfansifarverforeachformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesggplot2gluegridExtragtablehttrIRangesisobanditeratorsjsonlitelabelinglambda.rlatticelifecyclelme4magrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmgcvmicrobenchmarkmimeminqamodelrmunsellnlmenloptrnls2nnetnumDerivopensslpbkrtestpillarpkgconfigplyrprotopurrrquantregR6RColorBrewerRcppRcppEigenRCurlreshape2restfulrRhtslibrjsonrlangRsamtoolsrtracklayerS4ArraysS4VectorsscalessnowSparseArraySparseMstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselectUCSC.utilsutf8vctrsviridisLitewithrXMLXVectoryamlzlibbioc

rifi

Walja Wanney, Loubna Youssar and Jens Georg

Rendered fromvignette.Rmdusingknitr::rmarkdownon Jul 06 2024.

Last update: 2023-03-01
Started: 2021-12-22

Readme and manuals

Help Manual

Help pageTopics
========================================================================= apply_ancova: apply_ancova checks the variances between 2 segments showing either pausing site (ps) or internal starting site (ITSS) independently.apply_ancova
========================================================================= apply_event_position: apply_event_position extracts event time duration for pausing site or iTSSapply_event_position
========================================================================= apply_manova: apply_manova checks if the ratio of hl ratio and intensity ratio is statistically significant.apply_manova
========================================================================= 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
========================================================================= apply_t_test_ti: apply_t_test_ti compares the mean of two neighboring TI fragments within the same TU.apply_t_test_ti
========================================================================= apply_Ttest_delay: apply_Ttest_delay checks the significance of the point between 2 segments showing pausing site (ps) and internal starting site (ITSS) independentlyapply_Ttest_delay
========================================================================= Check_input: Check_input reviews the input given by the usercheck_input
========================================================================= dataframe_summary: dataframe_summary creates two tables relating gene annotation to fragmentsdataframe_summary
========================================================================= dataframe_summary_events: dataframe_summary_events creates one table with all events between the segmentsdataframe_summary_events
========================================================================= dataframe_summary_events_HL_int: dataframe_summary_events_HL_int creates one table with all events between the segmentsdataframe_summary_events_HL_int
========================================================================= dataframe_summary_events_ps_itss: dataframe_summary_events_ps_itss creates one table with all events between the segments.dataframe_summary_events_ps_itss
========================================================================= dataframe_summary_events_velocity: dataframe_summary_events_velocity creates one table with all events between the segments.dataframe_summary_events_velocity
========================================================================= dataframe_summary_TI: dataframe_summary_TI creates one table with all TI fragments,p_value and the coordinatesdataframe_summary_TI
========================================================================= event_dataframe: event_dataframe creates a dataframe only with eventsevent_dataframe
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_e_coli
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_minimal
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.example_input_synechocystis_6803
========================================================================= finding_PDD: finding_PDD Flags potential candidates for post transcription decayfinding_PDD
========================================================================= finding_TI: finding_TI flags potential candidates for transcription interferencefinding_TI
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_e_coli
The artificial result of rifi_fit for artificial example data A SummarizedExperiment containing the output from rifi_fit.fit_minimal
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.fit_synechocystis_6803
========================================================================= fold_change: fold_change sets a fold-change ratio between the neighboring fragments of Half-life (HL) and intensityfold_change
========================================================================= fragment_delay: fragment_delay performs the delay fragmentationfragment_delay
========================================================================= fragment_HL: fragment_HL performs the half_life fragmentationfragment_HL
========================================================================= fragment_inty: fragment_inty performs the intensity fragmentationfragment_inty
========================================================================= fragment_TI: fragment_TI performs the TI fragmentationfragment_TI
The result of rifi_fragmentation for E.coli example data A SummarizedExperiment containing the output from rifi_fragmentation as an extension of rowRangesfragmentation_e_coli
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_minimal
The result of rifi_fragmentation for Synechocystis 6803 example data A SummarizedExperiment containing the output from rifi_fragmentation as an extension fo rowRangesfragmentation_synechocystis_6803
========================================================================= gff3_preprocess: gff3_preprocess process gff3 file from database for multiple usagegff3_preprocess
========================================================================= make_df: make_df adds important columns to the SummarizedExperiment objectmake_df
========================================================================= make_pen: make_pen assigns automatically a penaltiesmake_pen
========================================================================= nls2_fit: nls2_fit estimates decay for each probe or binnls2_fit
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_e_coli
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_minimal
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.penalties_synechocystis_6803
========================================================================= predict_ps_itss: predict_ps_itss predicts pausing sites (ps) and internal starting sites (ITSS) between delay fragments.predict_ps_itss
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_e_coli
The result of rifi_preprocess for artificial example data A SummarizedExperiment containing the output from rifi_preprocesspreprocess_minimal
The result of rifi_preprocess for Synechocystis 6803 example data is a A SummarizedExperiment containing the output of rifi_preprocess as an extention to rowRangespreprocess_synechocystis_6803
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 isres_minimal
========================================================================= rifi_fit: rifi_fit wraps conveniently all fitting stepsrifi_fit
========================================================================= rifi_fragmentation: rifi_fragmentation wraps conveniently all fragmentation stepsrifi_fragmentation
========================================================================= rifi_penalties: rifi_penalties wraps conveniently all penalty stepsrifi_penalties
========================================================================= rifi_preprocess: rifi_preprocess wraps conveniently all pre-processing stepsrifi_preprocess
rifi_stats wraps all statistical prediction steps convenientlyrifi_stats
========================================================================= rifi_summary: rifi_summary wraps conveniently and summarize all rifi outputsrifi_summary
========================================================================= rifi_visualization: rifi_visualization plots all the data with fragments and events from both strandsrifi_visualization
========================================================================= rifi_wrapper: rifi_wrapper wraps conveniently all functions included on rifi workflowrifi_wrapper
========================================================================= segment_pos: segment_pos divides all IDs by position into position_segmentssegment_pos
The result of rifi_stats for E.coli example data A SummarizedExperiment containing the output from rifi_statsstats_e_coli
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_minimal
The result of rifi_stats for Synechocystis 6803 example data A SummarizedExperiment containing the output of rifi_stats as an extention to rowRangesstats_synechocystis_6803
The result of rifi_summary for E.coli example data A SummarizedExperiment containing the output of rifi_stats as an extention to rowRangessummary_e_coli
The result of rifi_summary for artificial example data A SummarizedExperiment with the output from rifi_summary as metadatasummary_minimal
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.summary_synechocystis_6803
========================================================================= TI_fit: TI_fit estimates transcription interference and termination factor using nls function for probe or bin flagged as "TI".TI_fit
========================================================================= TUgether: TUgether combines delay fragments into TUsTUgether
========================================================================= viz_pen_obj: viz_pen_obj visualizes penalty objectsviz_pen_obj
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_e_coli
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_minimal
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.wrapper_summary_synechocystis_6803