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ribiosUtils: Swiss-army knife for computational biology tasks in drug discovery

Introduction

ribiosUtils is a R package that performs various routine tasks for bioinformatics and computational biology research in drug discovery. It is distributed under the GPL-3 license.

Installation

Install the devel version from GitHub

Run following commands in the R console.

library(devtools)
devtools::install_github("bedapub/ribiosUtils")

Install the stable version on CRAN

The CRAN version is temporarily not available due to pending changes.

install.packages("ribiosUtils")

History

ribiosUtils is part of the ribios software suite (ribios stands for R interface to BIOS). It started as a R implementation of the BIOS library, publicly known as Bioinfo-C library, developed by Clemens Broger et al. at F. Hoffmann-La Roche for many years. Since its inception in 2012, many functionalities have been added, which are implemented in either C (or C++) or R.

Jitao David Zhang maintains and develops ribiosUtils and other ribios packages. The work is dedicated to the memory of Clemens Broger, a pioneer of bioinformatics and cheminformatics in drug discovery, a man true to himself.

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Version

Install

install.packages('ribiosUtils')

Monthly Downloads

2

Version

1.7.7

License

GPL-3

Issues

Pull Requests

Stars

Forks

Repository

https://github.com/bedapub/ribiosUtils

Homepage

https://bedapub.github.io/ribiosUtils/

Maintainer

Jitao David Zhang

Last Published

February 3rd, 2026

Functions in ribiosUtils (1.7.7)

Get the base and extension(s) of file name(s)

Make the first alphabet of strings uppercase

Proportion of cumulative sum over sum

Shorten strings to strings with a fix width of characters

Get a factor vector for a data.frame

Cut a vector of numbers into interval factors.

equateWellLabelWidth

Format labels for wells in microwell plates to equal widths

Convert factor columns in a data.frame into character strings

cumOverlapCoefficient

Cumulative overlap coefficient

cutreeIntoOrderedGroups

Cut a tree into groups of ordered sizes

Invert the names and elements of a list

Checks existing directory

identicalMatrix

Test whether two matrices are identical by values and by dim names

identicalMatrixValue

Test whether two matrices have the same numerica values given certain accuracy

Case-insensitive match and pmatch

Print head and tail elements of a vector

head/tail function for matrix or data.frame

Ensure the Truth of R Expressions and Print Defined Error Message if NOT

Whether an integer is odd (or even)

Tell whether an object is an error

isRocheCompoundID

Tell whether a character string is a Roche compound ID

Return last characters from strings

Calculate the Jaccard Index between two vectors

Convert a long-format data frame into matrix

Match a column in data.frame to a master vector

Load a library mutedly and quit (die) in case of failing

isTopOrIncAndNotExcl

Logical vector of being top or included and not excluded

Transform a list of character strings into a data.frame

listOverlapCoefficient

Pairwise overlap coefficient of lists

KEEP ROWS WITH THE MAXIMUM STATISTIC

Multiple matching

Reorder the groups by their group size

Multiple identical

Replace NA with FALSE

matchColumnName

Match a given vector to column names of a data.frame or matrix

Operations for multiple sets

mergeInfreqLevelsByCumsumprop

Merge infrequent levels by setting the threshold of the proportion of cumulative sum over sum a.k.a. cumsumprop

Transform a matrix into a long-format data.frame

naivePairwiseDist

Calculate pairwise distances between each pair of items in a list

Print BEDAinfo object

Print a decimal number in procent format

Transform p-values to continuous scores

Transform p-values to continuous scores with the quantile function of the normal distribution

overlapCoefficient

Overlap coefficient, also known as Szymkiewicz-Simpson coefficient

pairwiseOverlapDistance

Calculate pairwise overlap coefficients between each pair of items in a list

Overwrite a directory

Transform p-values to continuous scores with the absolute-log10 transformation

pairwiseJaccardIndex

Calculate pairwise Jaccard Indices between each pair of items in a list

Rearrange columns to put some columns to far left

Encode a password

relevelsByNotNamedVec

Relevel a factor by a unnamed vector.

Reload a package

Decode password with function implemented with pwencode

relevelsByNamedVec

Relevel a factor by a named vector.

Relevel a factor by a named or unnamed vector.

Quitely Quit with Messages

Quietly runs a system command

The functions registerLog and doLog provide a simple mechanism to handle loggings (printing text messages to files or other types of connections) in R.

Sort numeric factor levels by values

A temporary file which (1) every machine in the cluster has access to and (2) there is sufficient space

removeColumnsByFunc

Remove rows or column by function

removeRowsWithNA

Remove rows in a matrix that contains one or more NAs

replaceColumnName

Replace column names in data.frame

removeColumnsWithNA

Remove columns in a matrix that contains one or more NAs

Remove invariable columns from a data frame or matrix

A temporary directory which (1) every machine in the cluster has access to and (2) has sufficient space

ribiosUtils-package

ribiosUtils: Utilities from and Interface to the 'Bioinfo-C' ('BIOS') Library

replaceZeroPvalue

Replace p-values of zero

rowscale.matrix

Scale a matrix by row

Reverse rank order

Extract core identifiers from Roche compound IDs

Return a matrix that highlights reverse rank orders of features of interest by column

Reverse setdiff

Scale a table by row

S3 method for row-scaling

Remove temporary files at a specified time interval from now

Get reverse rank orders in each column

Repeat garbage-collecting until all resource is freed

sortAndFilterByCumsumprop

Sort a numeric vector and filter by a threshold of cumsumprop

Shorten strings to a given number of characters

Tokenize strings by character

Sort data.frame rows by values in specified columns

Keep silent by suppressing warnings and messages

Functions for command-line Rscript debugging

shortenRocheCompoundID

Shorten Roche compounds identifiers

Sort matrix by dim names

Prepare R for an interactive script

subsetByColumnName

Subset a data.frame by column name, allowing differences in cases

wellIndex2position

Translate well index numbers to well positions

Make a vector free of NA and unique

Write text as log to a connection

Trim leading and tailing spaces from string

Summarizing rows/columns by a factor

Length of unique elements in a vector

Print messages conditional on the verbose level

System user name

Print BEDA project information

applyTopOrIncAndNotExclFilter

Apply isTopOrIncAndNotExcl filter to a matrix

biomicsPstorePath2URL

Translate BiOmics-Pathology pstore path to URL

assertColumnName

Assert whether the required column names exist

assertDesignContrast

Check dimensionality of both design and contrast matrix

Set boundaries for numeric values, or perform a 0-1 normalization.

Convert string-valued data frame or matrix into a numeric matrix

Check dimensionality of contrast matrix

Testing whether several objects are all identical with each other

Check dimensionality of design matrix

cbindByRownames

Column bind by rownames

Check whether file(s) exist

Print the chosen few items of a long vector

Count tokens by splitting strings

Compare two vectors by set operations

Calculate correlation coefficients using common rows of the two matrices

cumJaccardIndex

Cumulative Jaccard Index

closeLoggerConnections

Close connections to all loggers This function closes all open connections set up by loggers It is automatically run at the end of the R session (setup by registerLog)

Create a directory if it does not exist, and then make sure the creation was successful.

columnOverlapCoefficient

Pairwise jaccard/overlap coefficient can be calculated efficiently using matrix Pairwise overlap coefficient of binary matrix by column