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The ggbio package extends and specializes the grammar of graphics for biological data. The graphics are designed to answer common scientific questions, in particular those often asked of high throughput genomics data. All core Bioconductor
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Extract the genomic locations of genes, transcripts, exons, introns, and CDS, for the gene models stored in a TxDb object. A TxDb object is a small database that contains the gene models of a given organism/assembly. Bioconductor provides a
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This package provides a client for the Bioconductor ExperimentHub web resource. ExperimentHub provides a central location where curated data from experiments, publications or training courses can be accessed. Each resource has associated me
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Harmonize data management of multiple experimental assays performed on an overlapping set of specimens. It provides a familiar Bioconductor user experience by extending concepts from SummarizedExperiment, supporting an open-ended mix of st
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Expert-level condensed matter physics knowledge. Use when working with crystal structure, band theory, semiconductors, superconductivity, magnetism, phase transitions, Fermi liquids, topological materials, or strongly correlated systems. Also use when the user mentions 'band gap', 'Fermi energy', 'semiconductor', 'superconductor', 'phonon', 'crystal lattice', 'Brillouin zone', 'Bloch theorem', 'Hall effect', 'magnetism', 'phase transition', or 'topological insulator'.
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Explore UN Comtrade data for strategic commodities such as oil, gas, gold, and semiconductors. Filter by country or product to identify trading partners, compare trade values and weights, and flag sharp year-over-year changes.
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Initialize project with Conductor artifacts (product definition, tech stack, workflow, style guides)
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Validates Conductor project artifacts for completeness, consistency, and correctness. Use after setup, when diagnosing issues, or before implementation to verify project context.
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Dielectric substrates, metal conductors, multi-layer stackups, and loss models (FR4, Rogers, Teflon) for RF PCB simulation. TRIGGER: user asks to set up a substrate, define dielectric properties, create a stackup, select a PCB material (FR4, Rogers, Teflon, etc.), or configure metal conductors. Invoke BEFORE writing dielectric() or metal() code — the API for named vs custom materials differs significantly. SKIP: PCB layout assembly (use matlab-assemble-pcb-layout), transmission line design (use matlab-design-pcb-transmission-line), EM analysis (use matlab-analyze-em), importing a PCB file (use matlab-read-pcb-layout).
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Expert blueprint for rhythm games including audio synchronization (BPM conductor, latency compensation with AudioServer.get_time_since_last_mix), note highways (scroll speed, timing windows), judgment systems (Perfect/Great/Good/Bad/Miss), scoring with combo multipliers, input processing (lane-based, hold note detection), and chart/beatmap loading. Based on DDR/osu!/Beat Saber research. Trigger keywords: rhythm_game, audio_sync, timing_judgment, note_highway, combo_system, BPM_conductor, latency_compensation.
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Expert blueprint for rhythm games including audio synchronization (BPM conductor, latency compensation with AudioServer.get_time_since_last_mix), note highways (scroll speed, timing windows), judgment systems (Perfect/Great/Good/Bad/Miss), scoring with combo multipliers, input processing (lane-based, hold note detection), and chart/beatmap loading. Based on DDR/osu!/Beat Saber research. Trigger keywords: rhythm_game, audio_sync, timing_judgment, note_highway, combo_system, BPM_conductor, latency_compensation.
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Variance-stabilizing transformations help with the analysis of heteroskedastic data (i.e., data where the variance is not constant, like count data). This package provide two types of variance stabilizing transformations: (1) methods based on the delta method (e.g., 'acosh', 'log(x+1)'), (2) model residual based (Pearson and randomized quantile residuals).
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Annotate variants, compute amino acid coding changes, predict coding outcomes.
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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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This package implements a suite of methods to preprocess data from PTR-TOF-MS instruments (HDF5 format) and generates the 'sample by features' table of peak intensities in addition to the sample and feature metadata (as a single ExpressionSet object for subsequent statistical analysis). This package also permit usefull tools for cohorts management as analyzing data progressively, visualization tools and quality control. The steps include calibration, expiration detection, peak detection and qua
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Current version only works in 'merge' mode: A single table of gene summarizations is generated with one column for each sample file.
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treekoR is a novel framework that aims to utilise the hierarchical nature of single cell cytometry data to find robust and interpretable associations between cell subsets and patient clinical end points. These associations are aimed to recapitulate the nested proportions prevalent in workflows inovlving manual gating, which are often overlooked in workflows using automatic clustering to identify cell populations. We developed treekoR to: Derive a hierarchical tree structure of cell clusters; qua
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SimBu can be used to simulate bulk RNA-seq datasets with known cell type fractions. You can either use your own single-cell study for the simulation or the sfaira database. Different pre-defined simulation scenarios exist, as are options to run custom simulations. Additionally, expression values can be adapted by adding an mRNA bias, which produces more biologically relevant simulations.
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This is an advanced version of TDbasedUFE, which is a comprehensive package to perform Tensor decomposition based unsupervised feature extraction. In contrast to TDbasedUFE which can perform simple the feature selection and the multiomics analyses, this package can perform more complicated and advanced features, but they are not so popularly required. Only users who require more specific features can make use of its functionality.
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Monocle performs differential expression and time-series analysis for single-cell expression experiments. It orders individual cells according to progress through a biological process, without knowing ahead of time which genes define progre
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Offers functions for plotting split (or implicit) networks (unrooted, undirected) and explicit networks (rooted, directed) with reticulations extending. 'ggtree' and using functions from 'ape' and 'phangorn'. It extends the 'ggtree' package [@Yu2017] to allow the visualization of phylogenetic networks using the 'ggplot2' syntax. It offers an alternative to the plot functions already available in 'ape' Paradis and Schliep (2019) <doi:10.1093/bioinformatics/bty633> and 'phangorn' Schliep (2011) <d
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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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omicsViewer visualizes ExpressionSet (or SummarizedExperiment) in an interactive way. The omicsViewer has a separate back- and front-end. In the back-end, users need to prepare an ExpressionSet that contains all the necessary information for the downstream data interpretation. Some extra requirements on the headers of phenotype data or feature data are imposed so that the provided information can be clearly recognized by the front-end, at the same time, keep a minimum modification on the existin
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The sva package contains functions for removing batch effects and other unwanted variation in high-throughput experiment. Specifically, the sva package contains functions for the identifying and building surrogate variables for high-dimensi
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