R-universe search: cheminformatics

bioc

limma:Linear Models for Microarray and Omics Data

Data analysis, linear models and differential expression for omics data.

Maintained by Gordon Smyth. Last updated 5 days ago.

exonarray geneexpression transcription alternativesplicing differentialexpression differentialsplicing genesetenrichment dataimport bayesian clustering regression timecourse microarray micrornaarray mrnamicroarray onechannel proprietaryplatforms twochannel sequencing rnaseq batcheffect multiplecomparison normalization preprocessing qualitycontrol biomedicalinformatics cellbiology cheminformatics epigenetics functionalgenomics genetics immunooncology metabolomics proteomics systemsbiology transcriptomics

10.0 match 13.81 score 16k scripts 585 dependents

bioc

ChemmineR:Cheminformatics Toolkit for R

ChemmineR is a cheminformatics package for analyzing drug-like small molecule data in R. Its latest version contains functions for efficient processing of large numbers of molecules, physicochemical/structural property predictions, structural similarity searching, classification and clustering of compound libraries with a wide spectrum of algorithms. In addition, it offers visualization functions for compound clustering results and chemical structures.

Maintained by Thomas Girke. Last updated 5 months ago.

cheminformatics biomedicalinformatics pharmacogenetics pharmacogenomics microtitreplateassay cellbasedassays visualization infrastructure dataimport clustering proteomics metabolomics cpp

13.8 match 14 stars 9.42 score 253 scripts 12 dependents

bioc

ChemmineOB:R interface to a subset of OpenBabel functionalities

ChemmineOB provides an R interface to a subset of cheminformatics functionalities implemented by the OpelBabel C++ project. OpenBabel is an open source cheminformatics toolbox that includes utilities for structure format interconversions, descriptor calculations, compound similarity searching and more. ChemineOB aims to make a subset of these utilities available from within R. For non-developers, ChemineOB is primarily intended to be used from ChemmineR as an add-on package rather than used directly.

Maintained by Thomas Girke. Last updated 5 months ago.

cheminformatics biomedicalinformatics pharmacogenetics pharmacogenomics microtitreplateassay cellbasedassays visualization infrastructure dataimport clustering proteomics metabolomics openbabel cpp

10.8 match 10 stars 7.87 score 77 scripts 1 dependents

bioc

biodb:biodb, a library and a development framework for connecting to chemical and biological databases

The biodb package provides access to standard remote chemical and biological databases (ChEBI, KEGG, HMDB, ...), as well as to in-house local database files (CSV, SQLite), with easy retrieval of entries, access to web services, search of compounds by mass and/or name, and mass spectra matching for LCMS and MSMS. Its architecture as a development framework facilitates the development of new database connectors for local projects or inside separate published packages.

Maintained by Pierrick Roger. Last updated 5 months ago.

software infrastructure dataimport kegg biology cheminformatics chemistry databases cpp

10.0 match 11 stars 7.85 score 24 scripts 6 dependents

bioc

Rcpi:Molecular Informatics Toolkit for Compound-Protein Interaction in Drug Discovery

A molecular informatics toolkit with an integration of bioinformatics and chemoinformatics tools for drug discovery.

Maintained by Nan Xiao. Last updated 5 months ago.

software dataimport datarepresentation featureextraction cheminformatics biomedicalinformatics proteomics go systemsbiology bioconductor bioinformatics drug-discovery feature-extraction fingerprint molecular-descriptors protein-sequences

10.0 match 37 stars 7.81 score 29 scripts

bioc

AlpsNMR:Automated spectraL Processing System for NMR

Reads Bruker NMR data directories both zipped and unzipped. It provides automated and efficient signal processing for untargeted NMR metabolomics. It is able to interpolate the samples, detect outliers, exclude regions, normalize, detect peaks, align the spectra, integrate peaks, manage metadata and visualize the spectra. After spectra proccessing, it can apply multivariate analysis on extracted data. Efficient plotting with 1-D data is also available. Basic reading of 1D ACD/Labs exported JDX samples is also available.

Maintained by Sergio Oller Moreno. Last updated 5 months ago.

software preprocessing visualization classification cheminformatics metabolomics dataimport

10.0 match 15 stars 7.59 score 12 scripts 1 dependents

bioc

fmcsR:Mismatch Tolerant Maximum Common Substructure Searching

The fmcsR package introduces an efficient maximum common substructure (MCS) algorithms combined with a novel matching strategy that allows for atom and/or bond mismatches in the substructures shared among two small molecules. The resulting flexible MCSs (FMCSs) are often larger than strict MCSs, resulting in the identification of more common features in their source structures, as well as a higher sensitivity in finding compounds with weak structural similarities. The fmcsR package provides several utilities to use the FMCS algorithm for pairwise compound comparisons, structure similarity searching and clustering.

Maintained by Thomas Girke. Last updated 5 months ago.

cheminformatics biomedicalinformatics pharmacogenetics pharmacogenomics microtitreplateassay cellbasedassays visualization infrastructure dataimport clustering proteomics metabolomics cpp

10.0 match 5 stars 7.03 score 60 scripts 1 dependents

bioc

BridgeDbR:Code for using BridgeDb identifier mapping framework from within R

Use BridgeDb functions and load identifier mapping databases in R. It uses GitHub, Zenodo, and Figshare if you use this package to download identifier mappings files.

Maintained by Egon Willighagen. Last updated 4 months ago.

software annotation metabolomics cheminformatics bioconductor-package bridgedb genes identifiers life-sciences metabolites proteins openjdk

10.0 match 4 stars 6.97 score 43 scripts

ethanbass

chromConverter:Chromatographic File Converter

Reads chromatograms from binary formats into R objects. Currently supports conversion of 'Agilent ChemStation', 'Agilent MassHunter', 'Shimadzu LabSolutions', 'ThermoRaw', and 'Varian Workstation' files as well as various text-based formats. In addition to its internal parsers, chromConverter contains bindings to parsers in external libraries, such as 'Aston' <https://github.com/bovee/aston>, 'Entab' <https://github.com/bovee/entab>, 'rainbow' <https://rainbow-api.readthedocs.io/>, and 'ThermoRawFileParser' <https://github.com/compomics/ThermoRawFileParser>.

Maintained by Ethan Bass. Last updated 9 days ago.

cheminformatics chromatography fair-data gc-fid hplc hplc-dad hplc-uv metabolomics metabolomics-data open-data open-science

10.0 match 33 stars 6.35 score 16 scripts 2 dependents

ethanbass

chromatographR:Chromatographic Data Analysis Toolset

Tools for high-throughput analysis of HPLC-DAD/UV chromatograms (or similar data). Includes functions for preprocessing, alignment, peak-finding and fitting, peak-table construction, data-visualization, etc. Preprocessing and peak-table construction follow the rough formula laid out in 'alsace' (Wehrens, R., Bloemberg, T.G., and Eilers P.H.C., 2015. <doi:10.1093/bioinformatics/btv299>. Alignment of chromatograms is available using parametric time warping (as implemented in the 'ptw' package) (Wehrens, R., Bloemberg, T.G., and Eilers P.H.C. 2015. <doi:10.1093/bioinformatics/btv299>) or variable penalty dynamic time warping (as implemented in 'VPdtw') (Clifford, D., & Stone, G. 2012. <doi:10.18637/jss.v047.i08>). Peak-finding uses the algorithm by Tom O'Haver <https://terpconnect.umd.edu/~toh/spectrum/PeakFindingandMeasurement.htm>. Peaks are then fitted to a gaussian or exponential-gaussian hybrid peak shape using non-linear least squares (Lan, K. & Jorgenson, J. W. 2001. <doi:10.1016/S0021-9673(01)00594-5>). See the vignette for more details and suggested workflow.

Maintained by Ethan Bass. Last updated 8 days ago.

bioinformatics cheminformatics chromatography gc-fid hplc hplc-dad hplc-pda hplv-uv metabolomics open-data open-science reproducibility reproducible-research

10.0 match 18 stars 6.33 score 8 scripts 1 dependents

bioc

rcellminer:rcellminer: Molecular Profiles, Drug Response, and Chemical Structures for the NCI-60 Cell Lines

The NCI-60 cancer cell line panel has been used over the course of several decades as an anti-cancer drug screen. This panel was developed as part of the Developmental Therapeutics Program (DTP, http://dtp.nci.nih.gov/) of the U.S. National Cancer Institute (NCI). Thousands of compounds have been tested on the NCI-60, which have been extensively characterized by many platforms for gene and protein expression, copy number, mutation, and others (Reinhold, et al., 2012). The purpose of the CellMiner project (http://discover.nci.nih.gov/ cellminer) has been to integrate data from multiple platforms used to analyze the NCI-60 and to provide a powerful suite of tools for exploration of NCI-60 data.

Maintained by Augustin Luna. Last updated 5 months ago.

acgh cellbasedassays copynumbervariation geneexpression pharmacogenomics pharmacogenetics mirna cheminformatics visualization software systemsbiology

10.0 match 5.71 score 113 scripts

bioc

eiR:Accelerated similarity searching of small molecules

The eiR package provides utilities for accelerated structure similarity searching of very large small molecule data sets using an embedding and indexing approach.

Maintained by Thomas Girke. Last updated 1 months ago.

cheminformatics biomedicalinformatics pharmacogenetics pharmacogenomics microtitreplateassay cellbasedassays visualization infrastructure dataimport clustering proteomics metabolomics

10.0 match 3 stars 5.51 score 12 scripts

bioc

ASICS:Automatic Statistical Identification in Complex Spectra

With a set of pure metabolite reference spectra, ASICS quantifies concentration of metabolites in a complex spectrum. The identification of metabolites is performed by fitting a mixture model to the spectra of the library with a sparse penalty. The method and its statistical properties are described in Tardivel et al. (2017) <doi:10.1007/s11306-017-1244-5>.

Maintained by Gaëlle Lefort. Last updated 5 months ago.

software dataimport cheminformatics metabolomics

10.0 match 5.18 score 30 scripts

bioc

fobitools:Tools for Manipulating the FOBI Ontology

A set of tools for interacting with the Food-Biomarker Ontology (FOBI). A collection of basic manipulation tools for biological significance analysis, graphs, and text mining strategies for annotating nutritional data.

Maintained by Pol Castellano-Escuder. Last updated 4 months ago.

massspectrometry metabolomics software visualization biomedicalinformatics graphandnetwork annotation cheminformatics pathways genesetenrichment biological-intrerpretation biological-knowledge biological-significance-analysis enrichment-analysis food-biomarker-ontology knowledge-graph nutrition obofoundry ontology text-mining

10.0 match 1 stars 5.08 score 5 scripts

bioc

seahtrue:Seahtrue revives XF data for structured data analysis

Seahtrue organizes oxygen consumption and extracellular acidification analysis data from experiments performed on an XF analyzer into structured nested tibbles.This allows for detailed processing of raw data and advanced data visualization and statistics. Seahtrue introduces an open and reproducible way to analyze these XF experiments. It uses file paths to .xlsx files. These .xlsx files are supplied by the userand are generated by the user in the Wave software from Agilent from the assay result files (.asyr). The .xlsx file contains different sheets of important data for the experiment; 1. Assay Information - Details about how the experiment was set up. 2. Rate Data - Information about the OCR and ECAR rates. 3. Raw Data - The original raw data collected during the experiment. 4. Calibration Data - Data related to calibrating the instrument. Seahtrue focuses on getting the specific data needed for analysis. Once this data is extracted, it is prepared for calculations through preprocessing. To make sure everything is accurate, both the initial data and the preprocessed data go through thorough checks.

Maintained by Vincent de Boer. Last updated 5 months ago.

cellbasedassays functionalprediction datarepresentation dataimport cellbiology cheminformatics metabolomics microtitreplateassay visualization qualitycontrol batcheffect experimentaldesign preprocessing go

10.0 match 5.04 score 2 scripts

bioc

rmelting:R Interface to MELTING 5

R interface to the MELTING 5 program (https://www.ebi.ac.uk/biomodels/tools/melting/) to compute melting temperatures of nucleic acid duplexes along with other thermodynamic parameters.

Maintained by J. Aravind. Last updated 5 months ago.

biomedicalinformatics cheminformatics bioconductor bioinformatics melting-temperature openjdk

10.0 match 2 stars 4.78 score 10 scripts

bioc

customCMPdb:Customize and Query Compound Annotation Database

This package serves as a query interface for important community collections of small molecules, while also allowing users to include custom compound collections.

Maintained by Yuzhu Duan. Last updated 5 months ago.

software cheminformatics annotationhubsoftware

10.0 match 2 stars 4.78 score 4 scripts

cct-datascience

volcalc:Calculate Volatility of Chemical Compounds

Calculate estimated relative volatility index values for organic compounds based on functional group contributions. Calculation uses the SIMPOL.1 method in Prankow and Asher (2008) <doi:10.5194/acp-8-2773-2008> or modified SIMPOL.1 method as in Meredith et al. (2023) <doi:10.5194/acp-8-2773-2008>.

Maintained by Kristina Riemer. Last updated 6 months ago.

cheminformatics chemometrics metabolomics

10.0 match 5 stars 4.48 score 7 scripts

bioc

drugTargetInteractions:Drug-Target Interactions

Provides utilities for identifying drug-target interactions for sets of small molecule or gene/protein identifiers. The required drug-target interaction information is obained from a local SQLite instance of the ChEMBL database. ChEMBL has been chosen for this purpose, because it provides one of the most comprehensive and best annotatated knowledge resources for drug-target information available in the public domain.

Maintained by Thomas Girke. Last updated 5 months ago.

cheminformatics biomedicalinformatics pharmacogenetics pharmacogenomics proteomics metabolomics

10.0 match 1 stars 4.34 score 11 scripts

bioc

MWASTools:MWASTools: an integrated pipeline to perform metabolome-wide association studies

MWASTools provides a complete pipeline to perform metabolome-wide association studies. Key functionalities of the package include: quality control analysis of metabonomic data; MWAS using different association models (partial correlations; generalized linear models); model validation using non-parametric bootstrapping; visualization of MWAS results; NMR metabolite identification using STOCSY; and biological interpretation of MWAS results.

Maintained by Andrea Rodriguez-Martinez. Last updated 5 months ago.

metabolomics lipidomics cheminformatics systemsbiology qualitycontrol

10.0 match 3.78 score 5 scripts 1 dependents

bioc

CONSTANd:Data normalization by matrix raking

Normalizes a data matrix `data` by raking (using the RAS method by Bacharach, see references) the Nrows by Ncols matrix such that the row means and column means equal 1. The result is a normalized data matrix `K=RAS`, a product of row mulipliers `R` and column multipliers `S` with the original matrix `A`. Missing information needs to be presented as `NA` values and not as zero values, because CONSTANd is able to ignore missing values when calculating the mean. Using CONSTANd normalization allows for the direct comparison of values between samples within the same and even across different CONSTANd-normalized data matrices.

Maintained by Dirk Valkenborg. Last updated 5 months ago.

massspectrometry cheminformatics normalization preprocessing differentialexpression genetics transcriptomics proteomics

10.0 match 3.78 score 5 scripts

ethanbass

mzinspectr:Read and Analyze Mass Spectrometry Alignment Files

A few functions for analyzing MS-DIAL alignments in R. Includes functions for feature normalization, subtraction of blanks, and mass library (msp) search.

Maintained by Ethan Bass. Last updated 5 months ago.

cheminformatics gc-ms lc-ms metabolomics

10.0 match 3 stars 2.78 score

bioc

roastgsa:Rotation based gene set analysis

This package implements a variety of functions useful for gene set analysis using rotations to approximate the null distribution. It contributes with the implementation of seven test statistic scores that can be used with different goals and interpretations. Several functions are available to complement the statistical results with graphical representations.

Maintained by Adria Caballe. Last updated 5 months ago.

microarray preprocessing normalization geneexpression survival transcription sequencing transcriptomics bayesian clustering regression rnaseq micrornaarray mrnamicroarray functionalgenomics systemsbiology immunooncology differentialexpression genesetenrichment batcheffect multiplecomparison qualitycontrol timecourse metabolomics proteomics epigenetics cheminformatics exonarray onechannel twochannel proprietaryplatforms cellbiology biomedicalinformatics alternativesplicing differentialsplicing dataimport pathways

10.0 match 2.30 score

varungiri

RxnSim:Functions to Compute Chemical and Chemical Reaction Similarity

Methods to compute chemical similarity between two or more reactions and molecules. Allows masking of chemical substructures for weighted similarity computations. Uses packages 'rCDK' and 'fingerprint' for cheminformatics functionality. Methods for reaction similarity and sub-structure masking are as described in: Giri et al. (2015) <doi:10.1093/bioinformatics/btv416>.

Maintained by Varun Giri. Last updated 2 years ago.

openjdk

0.5 match 2 stars 3.18 score 15 scripts