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Implements low-level utilities for single-cell trajectory analysis, primarily intended for re-use inside higher-level packages. Include a function to create a cluster-level minimum spanning tree and data structures to hold pseudotime infere

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The package implements a method for normalising microarray intensities from single- and multiple-color arrays. It can also be used for data from other technologies, as long as they have similar format. The method uses a robust variant of th

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Methods to infer clonal tree configuration for a population of cells using single-cell RNA-seq data (scRNA-seq), and possibly other data modalities. Methods are also provided to assign cells to inferred clones and explore differences in gene expression between clones. These methods can flexibly integrate information from imperfect clonal trees inferred based on bulk exome-seq data, and sparse variant alleles expressed in scRNA-seq data. A flexible beta-binomial error model that accounts for stoc

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Provides a comprehensive suite of functions to design and annotate CRISPR guide RNA (gRNAs) sequences. This includes on- and off-target search, on-target efficiency scoring, off-target scoring, full gene and TSS contextual annotations, and SNP annotation (human only). It currently support five types of CRISPR modalities (modes of perturbations): CRISPR knockout, CRISPR activation, CRISPR inhibition, CRISPR base editing, and CRISPR knockdown. All types of CRISPR nucleases are supported, including

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Provides functionalities to visualize and contextualize CRISPR guide RNAs (gRNAs) on genomic tracks across nucleases and applications. Works in conjunction with the crisprBase and crisprDesign Bioconductor packages. Plots are produced using the Gviz framework.

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The creation of effective visualizations is a fundamental component of data analysis. In biomedical research, new challenges are emerging to visualize multi-dimensional data in a 2D space, but current data visualization tools have limited capabilities. To address this problem, we leverage Gestalt principles to improve the design and interpretability of multi-dimensional data in 2D data visualizations, layering aesthetics to display multiple variables. The proposed visualization can be applied to

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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.

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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.

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Multivariate methods are well suited to large omics data sets where the number of variables (e.g. genes, proteins, metabolites) is much larger than the number of samples (patients, cells, mice). They have the appealing properties of reducin

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The semantic comparisons of Gene Ontology (GO) annotations provide quantitative ways to compute similarities between genes and gene groups, and have became important basis for many bioinformatics analysis approaches. GOSemSim is an R packag

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Utilities for microbiome analysis.

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cogeqc aims to facilitate systematic quality checks on standard comparative genomics analyses to help researchers detect issues and select the most suitable parameters for each data set. cogeqc can be used to asses: i. genome assembly and annotation quality with BUSCOs and comparisons of statistics with publicly available genomes on the NCBI; ii. orthogroup inference using a protein domain-based approach and; iii. synteny detection using synteny network properties. There are also data visualizat

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This package builds on existing tools and adds some simple but extremely useful capabilities for working wth ChIP-Seq data. The focus is on detecting differential binding windows/regions. One set of functions focusses on set-operations retaining mcols for GRanges objects, whilst another group of functions are to aid visualisation of results. Coercion to tibble objects is also implemented.

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BEER implements a Bayesian model for analyzing phage-immunoprecipitation sequencing (PhIP-seq) data. Given a PhIPData object, BEER returns posterior probabilities of enriched antibody responses, point estimates for the relative fold-change in comparison to negative control samples, and more. Additionally, BEER provides a convenient implementation for using edgeR to identify enriched antibody responses.

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epigraHMM provides a set of tools for the analysis of epigenomic data based on hidden Markov Models. It contains two separate peak callers, one for consensus peaks from biological or technical replicates, and one for differential peaks from multi-replicate multi-condition experiments. In differential peak calling, epigraHMM provides window-specific posterior probabilities associated with every possible combinatorial pattern of read enrichment across conditions.

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The biovizBase package is designed to provide a set of utilities, color schemes and conventions for genomic data. It serves as the base for various high-level packages for biological data visualization. This saves development effort and enc

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topGO package provides tools for testing GO terms while accounting for the topology of the GO graph. Different test statistics and different methods for eliminating local similarities and dependencies between GO terms can be implemented and

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This package implements five methods proposed by Resnik, Schlicker, Jiang, Lin and Wang respectively for measuring semantic similarities among DO terms and gene products. Enrichment analyses including hypergeometric model and gene set enric

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Memory efficient string containers, string matching algorithms, and other utilities, for fast manipulation of large biological sequences or sets of sequences.

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Expert knowledge for Azure Network Function Manager development including security, and configuration. Use when setting up NF Manager prerequisites, resource groups, managed identities, role assignments, or secure NF access, and other Azure Network Function Manager related development tasks. Not for Azure Firewall Manager (use azure-firewall-manager), Azure Virtual Network Manager (use azure-virtual-network-manager), Azure Virtual Network (use azure-virtual-network), Azure Virtual WAN (use azure-virtual-wan).

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Expert knowledge for Azure Managed Applications development including limits & quotas, security, configuration, and deployment. Use when designing createUiDefinition UIs, JIT access, managed identities, StorageAccountSelector, or Bicep-based catalog publishing, and other Azure Managed Applications related development tasks. Not for Azure Blueprints (use azure-blueprints), Azure Resource Manager (use azure-resource-manager), Azure Lighthouse (use azure-lighthouse), Azure Partner Solutions (use azure-partner-solutions).

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Expert knowledge for Azure AI Document Intelligence development including troubleshooting, best practices, decision making, limits & quotas, security, configuration, integrations & coding patterns, and deployment. Use when using AnalyzeDocument APIs, custom/classification models, containers, managed identities, or v4.0 migrations, and other Azure AI Document Intelligence related development tasks. Not for Azure AI Search (use azure-cognitive-search), Azure AI Vision (use azure-ai-vision), Azure AI Custom Vision (use azure-custom-vision), Azure AI Video Indexer (use azure-video-indexer).

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Expert knowledge for Azure Database for PostgreSQL development including troubleshooting, best practices, decision making, architecture & design patterns, limits & quotas, security, configuration, integrations & coding patterns, and deployment. Use when using Flexible Server, pgvector search, managed identities, Private Link/TLS, or PITR/geo-restore, and other Azure Database for PostgreSQL related development tasks. Not for Azure SQL Database (use azure-sql-database), Azure SQL Managed Instance (use azure-sql-managed-instance), SQL Server on Azure Virtual Machines (use azure-sql-virtual-machines), Azure Database for MySQL (use azure-database-mysql).

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Expert knowledge for Azure Automation development including troubleshooting, best practices, decision making, limits & quotas, security, configuration, integrations & coding patterns, and deployment. Use when building runbooks, DSC configs, Hybrid Runbook Workers, managed identities, or Automation deployments, and other Azure Automation related development tasks. Not for Azure Functions (use azure-functions), Azure Logic Apps (use azure-logic-apps), Azure DevOps (use azure-devops), Azure DevTest Labs (use azure-devtest-labs).

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