Package: rifiComparative 1.7.0

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_1.7.0.tar.gz

rifiComparative_1.7.0.tgz(r-4.4-any)rifiComparative_1.7.0.tgz(r-4.3-any)
rifiComparative_1.7.0.tar.gz(r-4.5-noble)rifiComparative_1.7.0.tar.gz(r-4.4-noble)
rifiComparative_1.7.0.tgz(r-4.4-emscripten)rifiComparative_1.7.0.tgz(r-4.3-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-1.7.0(bioc 3.21)rifiComparative-1.6.0(bioc 3.20)

rnaseq differentialexpression generegulation transcriptomics microarray software

4.00 score 135 downloads 11 exports 163 dependencies

Last updated 2 months agofrom:0e250a5c2e. Checks:OK: 1 NOTE: 3. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Dec 14 2024
R-4.5-linux	NOTE	Dec 14 2024
R-4.4-mac	NOTE	Dec 14 2024
R-4.3-mac	NOTE	Dec 14 2024

Exports:adjusting_HLToInt figures_fun fragmentation gff3_preprocess joining_data_column joining_data_row loading_fun make_pen penalties rifi_visualization_comparison statistics

Dependencies:abind askpass base64enc BH Biobase BiocGenerics BiocIO BiocParallel Biostrings bitops brew brio bslib cachem callr cli clipr codetools colorspace commonmark cowplot cpp11 crayon credentials curl DelayedArray desc devtools diffobj digest doMC downlit dplyr DTA egg ellipsis evaluate fansi farver fastmap fontawesome foreach formatR fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicRanges gert ggplot2 ggrepel gh gitcreds glue gridExtra gtable highr htmltools htmlwidgets httpuv httr httr2 ini IRanges isoband iterators jquerylib jsonlite knitr labeling lambda.r later lattice lifecycle LSD magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime miniUI munsell nlme nnet openssl pillar pkgbuild pkgconfig pkgdown pkgload plyr praise prettyunits processx profvis promises ps purrr R6 ragg rappdirs rcmdcheck RColorBrewer Rcpp RCurl remotes reshape2 restfulr Rhtslib rjson rlang rmarkdown roxygen2 rprojroot Rsamtools rstudioapi rtracklayer rversions S4Arrays S4Vectors sass scales scatterplot3d sessioninfo shiny snow sourcetools SparseArray stringi stringr SummarizedExperiment sys systemfonts testthat textshaping tibble tidyselect tinytex UCSC.utils urlchecker usethis utf8 vctrs viridisLite waldo whisker withr writexl xfun XML xml2 xopen xtable XVector yaml zip zlibbioc

rifiComparative

Loubna Youssar

Rendered fromrifiComparative.Rmdusingknitr::rmarkdownon Dec 14 2024.

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
adjusting_HLToInt Creates one table merging HL and intensity fragments with genome annotation	adjusting_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 frame	data_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 frame	df_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 frame	df_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 plots	figures_fun
The result of fragmentation for df_comb_minimal example data A data frame containing the output of fragmentation as a data frame	fragment_int
fragmentation: Conveniently wraps all fragmentation steps	fragmentation
gff3_preprocess processes gff3 file from database	gff3_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 column	joining_data_column
joining_data_row joins two data frames by row	joining_data_row
loading_fun loads the data of all conditions	loading_fun
make_pen assigns automatically penalties	make_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 steps	penalties
The result of penalties for df_comb_minimal example data A data frame containing the output of penalties as a data frame	penalties_df
rifi_visualization_comparison plots the segments and genome annotation	rifi_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 test	statistics
The result of statistics for fragment_int example data A data frame containing the output of statistics as a data frame	stats_df_comb_minimal
An example SummarizedExperiment from Synechosystis PCC 6803 first condition obtained from rifi_statistics and used as input for rifiComparative	stats_se_cdt1
An example SummarizedExperiment from Synechosystis PCC 6803 second condition obtained from rifi_statistics and used as input for rifiComparative	stats_se_cdt2