BioMate-KB Bioconductor Skills — 200 packages (top 100 by downloads + 100 rising stars) as vignette-grounded Claude/agent skills, with per-package workflow recipes
bioMate-AI/biomate-bioconductor-kb
Skill Claude Code
The scDblFinder package gathers various methods for the detection and handling of doublets/multiplets in single-cell sequencing data (i.e. multiple cells captured within the same droplet or reaction volume). It includes methods formerly fou.
bioMate-AI/biomate-bioconductor-kb
Skill Claude Code
We present a statistical simulator, scDesign3, to generate realistic single-cell and spatial omics data, including various cell states, experimental designs, and feature modalities, by learning interpretable parameters from real data. Using a unified probabilistic model for single-cell and spatial omics data…
bioMate-AI/biomate-bioconductor-kb
Skill Claude Code
Implements miscellaneous functions for interpretation of single-cell RNA-seq data. Methods are provided for assignment of cell cycle phase, detection of highly variable and significantly correlated genes, identification of marker genes, and.
bioMate-AI/biomate-bioconductor-kb
Skill Claude Code
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.
bioMate-AI/biomate-bioconductor-kb
Skill Claude Code
Skill "bioconductor-sechm" from bioMate-AI/biomate-bioconductor-kb, covering sechm, workflows, standard workflow, load example data and 1. basic scaled heatmap of top variable genes.
bioMate-AI/biomate-bioconductor-kb
Skill Claude Code
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…
bioMate-AI/biomate-bioconductor-kb
Skill Claude Code
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).
bioMate-AI/biomate-bioconductor-kb
Skill Claude Code
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…
bioMate-AI/biomate-bioconductor-kb
Skill Claude Code
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…
bioMate-AI/biomate-bioconductor-kb
Skill Claude Code
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.
bioMate-AI/biomate-bioconductor-kb
Skill Claude Code
SpatialDE is a method to find spatially variable genes (SVG) from spatial transcriptomics data. This package provides wrappers to use the Python SpatialDE library in R, using reticulate and basilisk.
bioMate-AI/biomate-bioconductor-kb
Skill Claude Code
Defines an S4 class for storing data from spatial -omics experiments. The class extends SingleCellExperiment to support storage and retrieval of additional information from spot-based and molecule-based platforms, including spatial coordina.
bioMate-AI/biomate-bioconductor-kb
Skill Claude Code
The analysis and visualization of alternative splicing (AS) events from RNA sequencing data remains challenging. SpliceWiz is a user-friendly and performance-optimized R package for AS analysis, by processing alignment BAM files to quantify read counts across splice junctions, IRFinder-based intron retention…
bioMate-AI/biomate-bioconductor-kb
Skill Claude Code
SpotClean is a computational method to adjust for spot swapping in spatial transcriptomics data. Recent spatial transcriptomics experiments utilize slides containing thousands of spots with spot-specific barcodes that bind mRNA. Ideally, unique molecular identifiers at a spot measure spot-specific expression, but this…
bioMate-AI/biomate-bioconductor-kb
Skill Claude Code
Spatially-aware quality control (QC) software for both spot-level and artifact-level QC in spot-based spatial transcripomics, such as 10x Visium. These methods calculate local (nearest-neighbors) mean and variance of standard QC metrics (library size, unique genes, and mitochondrial percentage) to identify outliers…
bioMate-AI/biomate-bioconductor-kb
Skill Claude Code
Perform quality control, TMM normalization, and RUV4 batch correction on NanoString GeoMx DSP data.
bioMate-AI/biomate-bioconductor-kb
Skill Claude Code
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…
bioMate-AI/biomate-bioconductor-kb
Skill Claude Code
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.
bioMate-AI/biomate-bioconductor-kb
Skill Claude Code
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…
bioMate-AI/biomate-bioconductor-kb
Skill Claude Code
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…
bioMate-AI/biomate-bioconductor-kb
Skill Claude Code
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.
bioMate-AI/biomate-bioconductor-kb
Skill Claude Code
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…
bioMate-AI/biomate-bioconductor-kb
Skill Claude Code
'treeio' is an R package to make it easier to import and store phylogenetic tree with associated data; and to link external data from different sources to phylogeny. It also supports exporting phylogenetic tree with heterogeneous associated.
bioMate-AI/biomate-bioconductor-kb
Skill Claude Code
Identify robust associations between hierarchical cell subsets and clinical outcomes from single-cell cytometry data.
At most 3 mods per repository are shown here, and a mod shipped inside a plugin is left to that plugin's page — the rest are on their repository pages: