Package: rifiComparative 1.11.0

Loubna Youssar

rifiComparative: 'rifiComparative' compares the output of rifi from two different conditions.

'rifiComparative' is a continuation of rifi package. It compares two conditions output of rifi using half-life and mRNA at time 0 segments. As an input for the segmentation, the difference between half-life of both condtions and log2FC of the mRNA at time 0 are used. The package provides segmentation, statistics, summary table, fragments visualization and some additional useful plots for further anaylsis.

Authors:Loubna Youssar [aut, cre], Jens cre Georg [aut]

rifiComparative_1.11.0.tar.gz

rifiComparative_1.11.0.tgz(r-4.6-any)rifiComparative_1.11.0.tgz(r-4.5-any)
rifiComparative_1.11.0.tar.gz(r-4.6-any)rifiComparative_1.11.0.tar.gz(r-4.5-any)
rifiComparative_1.11.0.tgz(r-4.5-emscripten)
rifiComparative.pdf |rifiComparative.html✨
rifiComparative/json (API)
NEWS

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

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

Datasets:
  • annot_g - The result of gff3_preprocessing of gff3 file A list containing all necessary information from a gff file for adjusting_HLToInt and visualization.
  • data_combined_minimal - The result of joining_by_row for inp_s and inp_f example data A data frame containing the output of joining_by_row as a data frame
  • df_comb_minimal - The result of joining_by_column for data_combined_minimal example data A data frame containing the output of joining_by_row as a data frame
  • df_mean_minimal - The result of adjusting_HLToInt for stats_df_comb_minimal and annotation example data A data frame containing the output of adjusting_HLToInt as a data frame
  • differential_expression - An example data frame from Synechosystis PCC 6803 differential probes expression obtained from limma package and only interesting variables were selected. The data frame was used entirely.
  • fragment_int - The result of fragmentation for df_comb_minimal example data A data frame containing the output of fragmentation as a data frame
  • inp_f - The result of loading_fun for stats_se_cdt2 example data Two data frame containing the output of loading_fun as second element of a list.
  • inp_s - The result of loading_fun for stats_se_cdt1 example data Two data frame containing the output of loading_fun as first element of a list.
  • pen_HL - The result of penalties for df_comb_minimal example data. A list containing the output from penalties including the logbook and two penalty objects.
  • pen_int - The result of penalties for df_comb_minimal example data. A list containing the output from penalties including the logbook and two penalty objects.
  • penalties_df - The result of penalties for df_comb_minimal example data A data frame containing the output of penalties as a data frame
  • stats_df_comb_minimal - The result of statistics for fragment_int example data A data frame containing the output of statistics as a data frame
  • stats_se_cdt1 - An example SummarizedExperiment from Synechosystis PCC 6803 first condition obtained from rifi_statistics and used as input for rifiComparative
  • stats_se_cdt2 - An example SummarizedExperiment from Synechosystis PCC 6803 second condition obtained from rifi_statistics and used as input for rifiComparative

On BioConductor:rifiComparative-1.11.0(bioc 3.23)rifiComparative-1.10.0(bioc 3.22)

rnaseqdifferentialexpressiongeneregulationtranscriptomicsmicroarraysoftware

4.00 score 248 downloads 11 exports 158 dependencies

Last updated from:fbe68f4789. Checks:5 NOTE, 2 OK, 3 FAIL. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE230
linux-devel-x86_64NOTE685
source / vignettesOK530
linux-release-x86_64NOTE625
macos-release-arm64NOTE380
macos-oldrel-arm64NOTE489
windows-develFAIL136
windows-releaseFAIL114
windows-oldrelFAIL107
wasm-releaseOK209

Exports:adjusting_HLToIntfigures_funfragmentationgff3_preprocessjoining_data_columnjoining_data_rowloading_funmake_penpenaltiesrifi_visualization_comparisonstatistics

Dependencies:abindaskpassbase64encBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitopsbrewbriobslibcachemcallrcigarilloclicliprcodetoolscommonmarkcowplotcpp11crayoncredentialscurlDelayedArraydescdevtoolsdiffobjdigestdoMCdownlitdplyrDTAeggellipsisevaluatefansifarverfastmapfontawesomeforeachformatRfsfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicRangesgertggplot2ggrepelghgitcredsgluegridExtragtablehighrhtmltoolshtmlwidgetshttpuvhttrhttr2iniIRangesisobanditeratorsjquerylibjsonliteknitrlabelinglambda.rlaterlatticelifecycleLSDmagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeminiUInnetopensslotelpakpillarpkgbuildpkgconfigpkgdownpkgloadplyrpraiseprettyunitsprocessxprofvispromisespspurrrR6raggrappdirsrcmdcheckRColorBrewerRcppRCurlreshape2restfulrRhtslibrjsonrlangrmarkdownroxygen2rprojrootRsamtoolsrstudioapirtracklayerrversionsS4ArraysS4VectorsS7sassscalesscatterplot3dSeqinfosessioninfoshinysnowsourcetoolsSparseArraystringistringrSummarizedExperimentsyssystemfontstestthattextshapingtibbletidyselecttinytexurlcheckerusethisutf8vctrsviridisLitewaldowhiskerwithrwritexlxfunXMLxml2xopenxtableXVectoryamlzip

rifiComparative

Loubna Youssar

Rendered fromrifiComparative.Rmdusingknitr::rmarkdownon Apr 03 2026.

Last update: 2023-04-30
Started: 2022-09-06

Readme and manuals

Help Manual

Help pageTopics
adjusting_HLToInt Creates one table merging HL and intensity fragments with genome annotationadjusting_HLToInt
The result of gff3_preprocessing of gff3 file A list containing all necessary information from a gff file for adjusting_HLToInt and visualization.annot_g
The result of joining_by_row for inp_s and inp_f example data A data frame containing the output of joining_by_row as a data framedata_combined_minimal
The result of joining_by_column for data_combined_minimal example data A data frame containing the output of joining_by_row as a data framedf_comb_minimal
The result of adjusting_HLToInt for stats_df_comb_minimal and annotation example data A data frame containing the output of adjusting_HLToInt as a data framedf_mean_minimal
An example data frame from Synechosystis PCC 6803 differential probes expression obtained from limma package and only interesting variables were selected. The data frame was used entirely.differential_expression
'figures_fun': generates several plotsfigures_fun
The result of fragmentation for df_comb_minimal example data A data frame containing the output of fragmentation as a data framefragment_int
fragmentation: Conveniently wraps all fragmentation stepsfragmentation
gff3_preprocess processes gff3 file from databasegff3_preprocess
The result of loading_fun for stats_se_cdt2 example data Two data frame containing the output of loading_fun as second element of a list.inp_f
The result of loading_fun for stats_se_cdt1 example data Two data frame containing the output of loading_fun as first element of a list.inp_s
joining_data_column joins two data frames by columnjoining_data_column
joining_data_row joins two data frames by rowjoining_data_row
loading_fun loads the data of all conditionsloading_fun
make_pen assigns automatically penaltiesmake_pen
The result of penalties for df_comb_minimal example data. A list containing the output from penalties including the logbook and two penalty objects.pen_HL
The result of penalties for df_comb_minimal example data. A list containing the output from penalties including the logbook and two penalty objects.pen_int
penalties wraps conveniently all penalty stepspenalties
The result of penalties for df_comb_minimal example data A data frame containing the output of penalties as a data framepenalties_df
rifi_visualization_comparison plots the segments and genome annotationrifi_visualization_comparison
============================================================================= rifiComparative: rifiComparative a successor package of rifi. It compares 2 rifi outputs from 2 different conditions of the same organism.rifiComparative
statistics check segments significance using statistical teststatistics
The result of statistics for fragment_int example data A data frame containing the output of statistics as a data framestats_df_comb_minimal
An example SummarizedExperiment from Synechosystis PCC 6803 first condition obtained from rifi_statistics and used as input for rifiComparativestats_se_cdt1
An example SummarizedExperiment from Synechosystis PCC 6803 second condition obtained from rifi_statistics and used as input for rifiComparativestats_se_cdt2