275 skills · sorted by relevance
Infrastructure to support 'views' used to classify Bioconductor packages. 'biocViews' are directed acyclic graphs of terms from a controlled vocabulary. There are three major classifications, corresponding to 'software', 'annotation', and '
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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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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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ChIPseeker is a Bioconductor package for annotating ChIP-seq data analysis. Peak Annotation is performed by the annotatePeak function. The position and strand information of nearest genes are reported, in addition to the distance from the p
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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.
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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Statial is a suite of functions for identifying changes in cell state. The functionality provided by Statial provides robust quantification of cell type localisation which are invariant to changes in tissue structure. In addition to this Statial uncovers changes in marker expression associated with varying levels of localisation. These features can be used to explore how the structure and function of different cell types may be altered by the agents they are surrounded with.
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SGC is a semi-supervised pipeline for gene clustering in gene co-expression networks. SGC consists of multiple novel steps that enable the computation of highly enriched modules in an unsupervised manner. But unlike all existing frameworks, it further incorporates a novel step that leverages Gene Ontology information in a semi-supervised clustering method that further improves the quality of the computed modules.
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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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Identification of differentially expressed genes and estimation of the False Discovery Rate (FDR) using both the Significance Analysis of Microarrays (SAM) and the Empirical Bayes Analyses of Microarrays (EBAM).
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sechm provides a simple interface between SummarizedExperiment objects and the ComplexHeatmap package. It enables plotting annotated heatmaps from SE objects, with easy access to rowData and colData columns, and implements a number of features to make the generation of heatmaps easier and more flexible. These functionalities used to be part of the SEtools package.
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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 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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Image segmentation is the process of identifying the borders of individual objects (in this case cells) within an image. This allows for the features of cells such as marker expression and morphology to be extracted, stored and analysed. simpleSeg provides functionality for user friendly, watershed based segmentation on multiplexed cellular images in R based on the intensity of user specified protein marker channels. simpleSeg can also be used for the normalization of single cell data obtained f
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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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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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Performs unbiased cell type recognition from single-cell RNA sequencing data, by leveraging reference transcriptomic datasets of pure cell types to infer the cell of origin of each single cell independently.
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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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Provides basic utility functions for performing single-cell analyses, focusing on simple normalization, quality control and data transformations. Also provides some helper functions to assist development of other packages.
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