GenomicRanges - Representation and manipulation of genomic intervals

The ability to efficiently represent and manipulate genomic annotations and alignments is playing a central role when it comes to analyzing high-throughput sequencing data (a.k.a. NGS data). The GenomicRanges package defines general purpose containers for storing and manipulating genomic intervals and variables defined along a genome. More specialized containers for representing and manipulating short alignments against a reference genome, or a matrix-like summarization of an experiment, are defined in the GenomicAlignments and SummarizedExperiment packages, respectively. Both packages build on top of the GenomicRanges infrastructure.

Last updated 7 days ago

geneticsinfrastructuredatarepresentationsequencingannotationgenomeannotationcoveragebioconductor-packagecore-package

17.85 score 45 stars 1.3k packages 14k scripts 87k downloads

BiocParallel - Bioconductor facilities for parallel evaluation

This package provides modified versions and novel implementation of functions for parallel evaluation, tailored to use with Bioconductor objects.

Last updated 24 days ago

infrastructurebioconductor-packagecore-package

17.11 score 67 stars 1.1k packages 6.3k scripts 82k downloads

Biobase - Biobase: Base functions for Bioconductor

Functions that are needed by many other packages or which replace R functions.

Last updated 24 days ago

infrastructurebioconductor-packagecore-package

16.48 score 9 stars 1.8k packages 7.0k scripts 93k downloads

S4Vectors - Foundation of vector-like and list-like containers in Bioconductor

The S4Vectors package defines the Vector and List virtual classes and a set of generic functions that extend the semantic of ordinary vectors and lists in R. Package developers can easily implement vector-like or list-like objects as concrete subclasses of Vector or List. In addition, a few low-level concrete subclasses of general interest (e.g. DataFrame, Rle, Factor, and Hits) are implemented in the S4Vectors package itself (many more are implemented in the IRanges package and in other Bioconductor infrastructure packages).

Last updated 7 days ago

infrastructuredatarepresentationbioconductor-packagecore-package

16.10 score 18 stars 1.8k packages 1.0k scripts 110k downloads

IRanges - Foundation of integer range manipulation in Bioconductor

Provides efficient low-level and highly reusable S4 classes for storing, manipulating and aggregating over annotated ranges of integers. Implements an algebra of range operations, including efficient algorithms for finding overlaps and nearest neighbors. Defines efficient list-like classes for storing, transforming and aggregating large grouped data, i.e., collections of atomic vectors and DataFrames.

Last updated 7 days ago

infrastructuredatarepresentationbioconductor-packagecore-package

16.09 score 22 stars 1.8k packages 2.1k scripts 105k downloads

BiocGenerics - S4 generic functions used in Bioconductor

The package defines many S4 generic functions used in Bioconductor.

Last updated 8 days ago

infrastructurebioconductor-packagecore-package

14.04 score 12 stars 2.2k packages 606 scripts 108k downloads

Spectra - Spectra Infrastructure for Mass Spectrometry Data

The Spectra package defines an efficient infrastructure for storing and handling mass spectrometry spectra and functionality to subset, process, visualize and compare spectra data. It provides different implementations (backends) to store mass spectrometry data. These comprise backends tuned for fast data access and processing and backends for very large data sets ensuring a small memory footprint.

Last updated 1 days ago

infrastructureproteomicsmassspectrometrymetabolomicsbioconductorhacktoberfestmass-spectrometry

12.85 score 38 stars 33 packages 215 scripts 3.3k downloads

MsCoreUtils - Core Utils for Mass Spectrometry Data

MsCoreUtils defines low-level functions for mass spectrometry data and is independent of any high-level data structures. These functions include mass spectra processing functions (noise estimation, smoothing, binning, baseline estimation), quantitative aggregation functions (median polish, robust summarisation, ...), missing data imputation, data normalisation (quantiles, vsn, ...), misc helper functions, that are used across high-level data structure within the R for Mass Spectrometry packages.

Last updated 24 days ago

infrastructureproteomicsmassspectrometrymetabolomicsbioconductormass-spectrometryutils

10.66 score 16 stars 67 packages 40 scripts 5.9k downloads

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.

Last updated 24 days ago

cheminformaticsbiomedicalinformaticspharmacogeneticspharmacogenomicsmicrotitreplateassaycellbasedassaysvisualizationinfrastructuredataimportclusteringproteomicsmetabolomics

10.34 score 13 stars 13 packages 228 scripts 1.4k downloads

AnnotationFilter - Facilities for Filtering Bioconductor Annotation Resources

This package provides class and other infrastructure to implement filters for manipulating Bioconductor annotation resources. The filters will be used by ensembldb, Organism.dplyr, and other packages.

Last updated 24 days ago

annotationinfrastructuresoftwarebioconductor-packagecore-package

10.19 score 5 stars 161 packages 44 scripts 18k downloads

MetaboCoreUtils - Core Utils for Metabolomics Data

MetaboCoreUtils defines metabolomics-related core functionality provided as low-level functions to allow a data structure-independent usage across various R packages. This includes functions to calculate between ion (adduct) and compound mass-to-charge ratios and masses or functions to work with chemical formulas. The package provides also a set of adduct definitions and information on some commercially available internal standard mixes commonly used in MS experiments.

Last updated 24 days ago

infrastructuremetabolomicsmassspectrometrymass-spectrometry

9.54 score 9 stars 34 packages 50 scripts 3.0k downloads

ProtGenerics - Generic infrastructure for Bioconductor mass spectrometry packages

S4 generic functions and classes needed by Bioconductor proteomics packages.

Last updated 24 days ago

infrastructureproteomicsmassspectrometrybioconductormass-spectrometrymetabolomics

9.38 score 8 stars 187 packages 4 scripts 19k downloads

MsBackendMgf - Mass Spectrometry Data Backend for Mascot Generic Format (mgf) Files

Mass spectrometry (MS) data backend supporting import and export of MS/MS spectra data from Mascot Generic Format (mgf) files. Objects defined in this package are supposed to be used with the Spectra Bioconductor package. This package thus adds mgf file support to the Spectra package.

Last updated 2 days ago

infrastructureproteomicsmassspectrometrymetabolomicsdataimport

7.16 score 5 stars 3 packages 32 scripts 701 downloads

MsBackendMsp - Mass Spectrometry Data Backend for NIST msp Files

Mass spectrometry (MS) data backend supporting import and handling of MS/MS spectra from NIST MSP Format (msp) files. Import of data from files with different MSP *flavours* is supported. Objects from this package add support for MSP files to Bioconductor's Spectra package. This package is thus not supposed to be used without the Spectra package that provides a complete infrastructure for MS data handling.

Last updated 24 days ago

infrastructureproteomicsmassspectrometrymetabolomicsdataimportmass-spectrometry

6.68 score 5 stars 1 packages 32 scripts 395 downloads

tima - Taxonomically Informed Metabolite Annotation

This package provides the infrastructure to perform Taxonomically Informed Metabolite Annotation.

Last updated 6 hours ago

metabolite annotationchemotaxonomyscoring systemnatural productscomputational metabolomicstaxonomic distancespecialized metabolome

6.26 score 9 stars 1 packages 32 scripts