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

What is ribiosUtils?

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

Run following commands in the R console.

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

History

ribiosUtils is part of the ribios software suite (ribios stands for R interface to BIOS). The package was previously a sub-directory of the ribios project. 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 in 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

11

Version

1.5-6

License

GPL-3

Issues

Pull Requests

Stars

Forks

Repository

https://github.com/bedapub/ribiosUtils

Maintainer

Jitao David Zhang

Last Published

March 6th, 2020

Functions in ribiosUtils (1.5-6)

Print the chosen few items of a long vector

columnOverlapCoefficient

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

getDefaultFontFamily

Get default font family

Shorten strings to strings with a fix width of characters

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)

cumOverlapCoefficient

Cumulative overlap coefficient

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

Proportion of cumulative sum over sum

Get a factor vector for a data.frame

head/tail function for matrix or data.frame

Cut a vector of numbers into interval factors.

Convert a long-format data frame into matrix

Convert factor columns in a data.frame into character strings

cumJaccardIndex

Cumulative Jaccard Index

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

identicalMatrixValue

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

Transform a list of character strings into a data.frame

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

listOverlapCoefficient

Pairwise overlap coefficient of lists

Calculate the Jaccard Index between two vectors

isRocheCompoundID

Tell whether a character string is a Roche compound ID

Replace NA with FALSE

Sort numeric factor levels by values

pairwiseOverlapDistance

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

Open a device as a file preparing for plotting in the file

Quietly runs a system command

rowscale.matrix

Scale a matrix by row

KEEP ROWS WITH THE MAXIMUM STATISTIC

pairwiseJaccardIndex

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

Case-insensitive match and pmatch

Reverse setdiff

Keep silent by suppressing warnings and messages

Shorten strings to a given number of characters

matchColumnName

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

Match a column in data.frame to a master vector

Transform a matrix into a long-format data.frame

System user name

Print messages conditional on the verbose level

Print head and tail elements of a vector

Count tokens by splitting strings

Compare two vectors by set operations

identicalMatrix

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

Checks existing directory

Tell whether an object is an error

Multiple matching

Operations for multiple sets

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

Print a decimal number in procent format

naivePairwiseDist

Calculate pairwise distances between each pair of items in a list

overlapCoefficient

Overlap coefficient, also known as Szymkiewicz-Simpson coefficient

Relevel a factor by a named or unnamed vector.

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

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

Print BEDAinfo object

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

Transform p-values to continuous scores

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

Sort matrix by dim names

Reload a package

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

Tokenize strings by character

Remove temporary files at a specified time interval from now

Repeat garbage-collecting until all resource is freed

relevelsByNotNamedVec

Relevel a factor by a unnamed vector.

Remove invariable columns from a data frame or matrix

relevelsByNamedVec

Relevel a factor by a named vector.

replaceColumnName

Replace column names in data.frame

mergeInfreqLevelsByCumsumprop

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

subsetByColumnName

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

Write text as log to a connection

sortAndFilterByCumsumprop

Sort a numeric vector and filter by a threshold of cumsumprop

Sort data.frame rows by values in specified columns

Extract core identifiers from Roche compound IDs

Prepare R for an interactive script

Rearrange columns to put some columns to far left

Encode a password

Decode password with function implemented with pwencode

S3 method for row-scaling

Multiple identical

Quitely Quit with Messages

Functions for command-line Rscript debugging

Trim leading and tailing spaces from string

Summarizing rows/columns by a factor

Length of unique elements in a vector

Make a vector free of NA and unique

Check dimensionality of design matrix

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

Check dimensionality of contrast matrix

Print BEDA project information

Testing whether several objects are all identical with each other

Check whether file(s) exist

assertColumnName

Assert whether the required column names exist

assertDesignContrast

Check dimensionality of both design and contrast matrix

biomicsPstorePath2URL

Translate BiOmics-Pathology pstore path to URL