systemPipeR - systemPipeR: A Multipurpose Workflow Management System for Reproducible Data Analysis
systemPipeR is a workflow management environment for reproducible data analysis that integrates R with command-line software. It enables researchers to design, execute, and report complex workflows on local machines and HPC systems. The framework combines R-based analysis with external tools through a Common Workflow Language (CWL) interface, manages workflow dependencies and restart capabilities, and automatically generates reproducible scientific analysis reports. The companion package systemPipeRdata provides ready-to-use workflow templates that simplify workflow setup and customization. Alternatively, workflow templates can be loaded from dedicated GitHub repositories.
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geneticsinfrastructuredataimportsequencingrnaseqriboseqchipseqmethylseqsnpgeneexpressioncoveragegenesetenrichmentalignmentqualitycontrolimmunooncologyreportwritingworkflowstepworkflowmanagement
11.75 score 52 stars 3 dependents 710 scripts 2.8k downloadsChemmineR - 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.
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cheminformaticsbiomedicalinformaticspharmacogeneticspharmacogenomicsmicrotitreplateassaycellbasedassaysvisualizationinfrastructuredataimportclusteringproteomicsmetabolomicscpp
9.21 score 17 stars 14 dependents 1.7k downloadssystemPipeRdata - systemPipeRdata: Workflow templates and sample data
systemPipeRdata complements the systemPipeR workflow management system (WMS) by offering a collection of pre-designed data analysis workflow templates. These templates are easily accessible and can be readily loaded onto a user's system with a single command. Once loaded, the WMS can immediately utilize these templates for efficient end-to-end analysis, serving a wide range of data analysis needs.
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geneticsinfrastructuredataimportsequencingrnaseqchipseqmethylseqsnpgeneexpressioncoveragegenesetenrichmentalignmentqualitycontrolimmunooncologyriboseqworkflowstepexperimenthubsoftwaredatapkg
8.63 score 9 stars 169 scriptsChemmineOB - 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.
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cheminformaticsbiomedicalinformaticspharmacogeneticspharmacogenomicsmicrotitreplateassaycellbasedassaysvisualizationinfrastructuredataimportclusteringproteomicsmetabolomicsopenbabelcpp
8.29 score 10 stars 1 dependents 102 scripts 992 downloadsbioassayR - Cross-target analysis of small molecule bioactivity
bioassayR is a computational tool that enables simultaneous analysis of thousands of bioassay experiments performed over a diverse set of compounds and biological targets. Unique features include support for large-scale cross-target analyses of both public and custom bioassays, generation of high throughput screening fingerprints (HTSFPs), and an optional preloaded database that provides access to a substantial portion of publicly available bioactivity data.
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immunooncologymicrotitreplateassaycellbasedassaysvisualizationinfrastructuredataimportbioinformaticsproteomicsmetabolomics
6.51 score 6 stars 49 scripts 519 downloadsfmcsR - 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.
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cheminformaticsbiomedicalinformaticspharmacogeneticspharmacogenomicsmicrotitreplateassaycellbasedassaysvisualizationinfrastructuredataimportclusteringproteomicsmetabolomicscpp
6.16 score 6 stars 1 dependents 768 downloadseiR - 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.
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cheminformaticsbiomedicalinformaticspharmacogeneticspharmacogenomicsmicrotitreplateassaycellbasedassaysvisualizationinfrastructuredataimportclusteringproteomicsmetabolomics
5.46 score 4 stars 12 scripts 529 downloadsdrugTargetInteractions - drugTargetInteractions: Mining the Druggable Genome
Utilities for identifying known drug-target interactions for a sets of query drug and/or target protein (gene) identifiers. The interaction information is obained from a series of drug/target databases.
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cheminformaticsbiomedicalinformaticspharmacogeneticspharmacogenomicsproteomicsmetabolomics
4.58 score 2 stars 16 scripts 437 downloads