Package: rifi 1.17.1

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_1.17.1.tar.gz

rifi_1.17.1.tgz(r-4.6-any)rifi_1.17.1.tgz(r-4.5-any)
rifi_1.17.1.tar.gz(r-4.7-any)rifi_1.17.1.tar.gz(r-4.6-any)
rifi_1.17.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
rifi/json (API)

# Install 'rifi' in R:

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

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-1.17.1(bioc 3.24)rifi-1.16.0(bioc 3.23)

rnaseq differentialexpression generegulation transcriptomics regression microarray software

4.78 score 1 scripts 38 exports 120 dependencies

Last updated from:75de92622d. Checks:5 WARNING, 2 OK, 3 FAIL. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	242
linux-devel-x86_64	WARNING	622
source / vignettes	OK	342
linux-release-x86_64	WARNING	594
macos-release-arm64	WARNING	293
macos-oldrel-arm64	WARNING	320
windows-devel	FAIL	117
windows-release	FAIL	118
windows-oldrel	FAIL	100
wasm-release	OK	217

Exports:apply_ancova apply_event_position apply_manova apply_t_test apply_t_test_ti apply_Ttest_delay check_input dataframe_summary dataframe_summary_events dataframe_summary_events_HL_int dataframe_summary_events_ps_itss dataframe_summary_events_velocity dataframe_summary_TI event_dataframe finding_PDD finding_TI fold_change fragment_delay fragment_HL fragment_inty fragment_TI gff3_preprocess make_df make_pen nls2_fit predict_ps_itss rifi_fit rifi_fragmentation rifi_penalties rifi_preprocess rifi_stats rifi_summary rifi_visualization rifi_wrapper segment_pos TI_fit TUgether viz_pen_obj

Dependencies: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 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

rifi

Rendered fromvignette.Rmdusingknitr::rmarkdown

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

Help page	Topics
========================================================================= 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 iTSS	apply_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) independently	apply_Ttest_delay
========================================================================= Check_input: Check_input reviews the input given by the user	check_input
========================================================================= dataframe_summary: dataframe_summary creates two tables relating gene annotation to fragments	dataframe_summary
========================================================================= dataframe_summary_events: dataframe_summary_events creates one table with all events between the segments	dataframe_summary_events
========================================================================= dataframe_summary_events_HL_int: dataframe_summary_events_HL_int creates one table with all events between the segments	dataframe_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 coordinates	dataframe_summary_TI
========================================================================= event_dataframe: event_dataframe creates a dataframe only with events	event_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 decay	finding_PDD
========================================================================= finding_TI: finding_TI flags potential candidates for transcription interference	finding_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 intensity	fold_change
========================================================================= fragment_delay: fragment_delay performs the delay fragmentation	fragment_delay
========================================================================= fragment_HL: fragment_HL performs the half_life fragmentation	fragment_HL
========================================================================= fragment_inty: fragment_inty performs the intensity fragmentation	fragment_inty
========================================================================= fragment_TI: fragment_TI performs the TI fragmentation	fragment_TI
The result of rifi_fragmentation for E.coli example data A SummarizedExperiment containing the output from rifi_fragmentation as an extension of rowRanges	fragmentation_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 rowRanges	fragmentation_synechocystis_6803
========================================================================= gff3_preprocess: gff3_preprocess process gff3 file from database for multiple usage	gff3_preprocess
========================================================================= make_df: make_df adds important columns to the SummarizedExperiment object	make_df
========================================================================= make_pen: make_pen assigns automatically a penalties	make_pen
========================================================================= nls2_fit: nls2_fit estimates decay for each probe or bin	nls2_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_preprocess	preprocess_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 rowRanges	preprocess_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 is	res_minimal
========================================================================= rifi_fit: rifi_fit wraps conveniently all fitting steps	rifi_fit
========================================================================= rifi_fragmentation: rifi_fragmentation wraps conveniently all fragmentation steps	rifi_fragmentation
========================================================================= rifi_penalties: rifi_penalties wraps conveniently all penalty steps	rifi_penalties
========================================================================= rifi_preprocess: rifi_preprocess wraps conveniently all pre-processing steps	rifi_preprocess
rifi_stats wraps all statistical prediction steps conveniently	rifi_stats
========================================================================= rifi_summary: rifi_summary wraps conveniently and summarize all rifi outputs	rifi_summary
========================================================================= rifi_visualization: rifi_visualization plots all the data with fragments and events from both strands	rifi_visualization
========================================================================= rifi_wrapper: rifi_wrapper wraps conveniently all functions included on rifi workflow	rifi_wrapper
========================================================================= segment_pos: segment_pos divides all IDs by position into position_segments	segment_pos
The result of rifi_stats for E.coli example data A SummarizedExperiment containing the output from rifi_stats	stats_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 rowRanges	stats_synechocystis_6803
The result of rifi_summary for E.coli example data A SummarizedExperiment containing the output of rifi_stats as an extention to rowRanges	summary_e_coli
The result of rifi_summary for artificial example data A SummarizedExperiment with the output from rifi_summary as metadata	summary_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 TUs	TUgether
========================================================================= viz_pen_obj: viz_pen_obj visualizes penalty objects	viz_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

Package: rifi 1.17.1

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

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