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12 of 5,674 resources
This package provides an interface to the 'samtools', 'bcftools', and 'tabix' utilities for manipulating SAM (Sequence Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed tab-delimited (tabix) files.
A molecular informatics toolkit with an integration of bioinformatics and chemoinformatics tools for drug discovery.
This package provides an R wrapper around the popular bowtie short read aligner and around SpliceMap, a de novo splice junction discovery and alignment tool. The package is used by the QuasR bioconductor package. We recommend to use the QuasR package instead of using Rbowtie directly.
More than 9900 annotated position frequency matrices from 14 public sources, for multiple organisms.
The miaViz package implements functions to visualize TreeSummarizedExperiment objects especially in the context of microbiome analysis. Part of the mia family of R/Bioconductor packages.
The `miaTime` package provides tools for microbiome time series analysis based on (Tree)SummarizedExperiment infrastructure.
Microbiome time series simulation with generalized Lotka-Volterra model, Self-Organized Instability (SOI), and other models. Hubbell's Neutral model is used to determine the abundance matrix. The resulting abundance matrix is applied to (Tree)SummarizedExperiment objects.
mia implements tools for microbiome analysis based on the SummarizedExperiment, SingleCellExperiment and TreeSummarizedExperiment infrastructure. Data wrangling and analysis in the context of taxonomic data is the main scope. Additional functions for common task are implemented such as community indices calculation and summarization.
Utility package to facilitate integration and analysis of EBI MGnify data in R. The package can be used to import microbial data for instance into TreeSummarizedExperiment (TreeSE). In TreeSE format, the data is directly compatible with miaverse framework.
Utility package to facilitate integration and analysis of EBI HoloFood data in R. This package streamlines access to the resource, allowing for direct loading of data into formats optimized for downstream analytics.
Fast and efficient reading and writing of mass spectrometry imaging data files. Supports imzML and Analyze 7.5 formats. Provides ontologies for mass spectrometry imaging.
Implements statistical & computational tools for analyzing mass spectrometry imaging datasets, including methods for efficient pre-processing, spatial segmentation, and classification.