This package allows building the hierarchy of domains starting from Hi-C data. Each hierarchical level is identified by a minimum value of physical insulation between neighboring domains.

Infernal ("INFERence of RNA ALignment") is a tool for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation of a special case of profile stochastic context-free grammars called covariance models (CMs). A CM is like a sequence profile, but it scores a combination of sequence consensus and RNA secondary structure consensus, so in many cases, it is more capable of identifying RNA homologs that conserve their secondary structure more than their primary sequence.

This package provides the kentUtils, a selection of bioinformatics utilities used in combination with the UCSC genome browser.

This package lets you read and write files in Generic Feature Format (GFF) with Biopython integration.

MultiQC is a tool to aggregate bioinformatics results across many samples into a single report. It contains modules for a large number of common bioinformatics tools.

This package provides an implementation of chunked, compressed, N-dimensional arrays for R, Zarr specification version 2 (2024) <doi:10.5281/zenodo.11320255>.

This library contains the genomics components of the Bio++ phylogenetics library. It is part of the Bio++ project.

This package provides a client for the OmniPath web service and many other resources. It also includes functions to transform and pretty print some of the downloaded data, functions to access a number of other resources such as BioPlex, ConsensusPathDB, EVEX, Gene Ontology, Guide to Pharmacology (IUPHAR/BPS), Harmonizome, HTRIdb, Human Phenotype Ontology, InWeb InBioMap, KEGG Pathway, Pathway Commons, Ramilowski et al. 2015, RegNetwork, ReMap, TF census, TRRUST and Vinayagam et al. 2011. Furthermore, OmnipathR features a close integration with the NicheNet method for ligand activity prediction from transcriptomics data, and its R implementation nichenetr.

PiGx is a collection of genomics pipelines. It includes the following pipelines:

• PiGx BSseq for raw fastq read data of bisulfite experiments

• PiGx RNAseq for RNAseq samples

• PiGx scRNAseq for single cell dropseq analysis

• PiGx ChIPseq for reads from ChIPseq experiments

All pipelines are easily configured with a simple sample sheet and a descriptive settings file. The result is a set of comprehensive, interactive HTML reports with interesting findings about your samples.

The BIOM file format is designed to be a general-use format for representing counts of observations e.g. operational taxonomic units, KEGG orthology groups or lipid types, in one or more biological samples e.g. microbiome samples, genomes, metagenomes.

This package provides data for the SeuratExtend tool.

This package provides several programs that perform operations on SAM/BAM files. All of these programs are built into a single executable called bam.

This package contains the Battenberg R package for subclonal copy number estimation, as described by Nik-Zainal et al.

This package is used for cell type identification in spatial transcriptomics. It also handles cell type-specific differential expression.

Roary is a high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by the Prokka program) and calculates the pan genome. Using a standard desktop PC, it can analyse datasets with thousands of samples, without compromising the quality of the results. 128 samples can be analysed in under 1 hour using 1 GB of RAM and a single processor. Roary is not intended for metagenomics or for comparing extremely diverse sets of genomes.

CD-HIT is a program for clustering and comparing protein or nucleotide sequences. CD-HIT is designed to be fast and handle extremely large databases.

Trim Galore! is a wrapper script to automate quality and adapter trimming as well as quality control, with some added functionality to remove biased methylation positions for RRBS sequence files.

This package is a set of R functions for generating precise figures. This tool helps you to create clean markdown reports about what you just discovered with your analysis script.

Biosoup is a C++ collection of header-only data structures used for storage and logging in bioinformatics tools.

ImageArray provides a framework for on-disk and in-memory image arrays, specifically for pyramidal images stored in HDF5, Zarr and life sciences image file formats (OME Bio-Formats).

This package provides data for the book "Computational Genomics with R".

This package provides a lightweight interface to Stan <https://mc-stan.org>. The CmdStanR interface is an alternative to RStan that calls the command line interface for compilation and running algorithms instead of interfacing with C++ via Rcpp'.

This package implements the method csSAM that computes cell-specific differential expression from measured cell proportions using SAM.

The loom file format is an efficient format for very large omics datasets, consisting of a main matrix, optional additional layers, a variable number of row and column annotations. Loom also supports sparse graphs. This library makes it easy to work with .loom files for single-cell RNA-seq data.