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Operate Temps through the pinned `@temps-sdk/cli` package with bunx or npx. Use when the user mentions Temps CLI, `@temps-sdk/cli`, a CLI command, or asks to deploy, configure, inspect, automate, or administer Temps from a terminal. Covers contexts, projects, deployments, environments, services, domains, monitoring, backups, telemetry, browser Performance Insights/Core Web Vitals, Cloud, platform administration, and read-only managed-data browsing. Apply the target-context, secret-handling, confirmation, and verification rules for every agentic CLI operation.

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Design, build, test, and distribute external Temps plugins with TypeScript/Bun; provide development and local-testing guidance for existing Rust plugins. Use for creating a plugin, adding an embedded console UI or deployment-event automation, testing host permissions and AI, installing from GitHub, or submitting a plugin to the public catalog. End-to-end publishing covers TypeScript GitHub-source plugins, not Rust native-package releases or in-process TempsPlugin backend crates.

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Best practices for the Common utilities package in LlamaFarm. Covers HuggingFace Hub integration, GGUF model management, and shared utilities.

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Master orchestrator that generates all implementation specs (PRD, Architecture, UX, Implementation, Test, Release) from product plan. Use when generating complete specification package.

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Pathview is a stand-alone software package for pathway based data integration and visualization.

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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

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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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'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

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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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Tools for LiP peptide and protein significance analysis. Provides functions for summarization, estimation of LiP peptide abundance, and detection of changes across conditions. Utilizes functionality across the MSstats family of packages.

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This package provides a client for the Bioconductor AnnotationHub web resource. The AnnotationHub web resource provides a central location where genomic files (e.g., VCF, bed, wig) and other resources from standard locations (e.g., UCSC, En

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SpatialFeatureExperiment (SFE) is a new S4 class for working with spatial single-cell genomics data. The voyager package implements basic exploratory spatial data analysis (ESDA) methods for SFE. Univariate methods include univariate global spatial ESDA methods such as Moran's I, permutation testing for Moran's I, and correlograms. Bivariate methods include Lee's L and cross variogram. Multivariate methods include MULTISPATI PCA and multivariate local Geary's C recently developed by Anselin. The

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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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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 performs differential pattern analysis for Ribo-seq data. It identifies genes with significantly different patterns in the ribosome footprint between two conditions. RiboDiPA contains five major components including bam file processing, P-site mapping, data binning, differential pattern analysis and footprint visualization.

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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 quantitation, and supports novel splicing event identification. We introduce a novel visualization for AS using normalized coverage, thereby allowing visualization of differential AS across

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The package comprises a set of pretrained machine learning models to predict basic immune cell types. This enables all users to quickly get a first annotation of the cell types present in their dataset without requiring prior knowledge. scAnnotatR also allows users to train their own models to predict new cell types based on specific research needs.

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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.

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ProteoDisco is an R package to facilitate proteogenomics studies. It houses functions to create customized (variant) protein databases based on user-submitted genomic variants, splice-junctions, fusion genes and manual transcript sequences. The flexible workflow can be adopted to suit a myriad of research and experimental settings.

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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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NanoTube includes functions for the processing, quality control, analysis, and visualization of NanoString nCounter data. Analysis functions include differential analysis and gene set analysis methods, as well as postprocessing steps to help understand the results. Additional functions are included to enable interoperability with other Bioconductor NanoString data analysis packages.

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Classes and statistical methods for large SNP association studies. This extends the earlier snpMatrix package, allowing for uncertainty in genotypes.

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The package CellBarcode performs Cellular DNA Barcode analysis. It can handle all kinds of DNA barcodes, as long as the barcode is within a single sequencing read and has a pattern that can be matched by a regular expression. \code{CellBarcode} can handle barcodes with flexible lengths, with or without UMI (unique molecular identifier). This tool also can be used for pre-processing some amplicon data such as CRISPR gRNA screening, immune repertoire sequencing, and metagenome data.

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The epistack package main objective is the visualizations of stacks of genomic tracks (such as, but not restricted to, ChIP-seq, ATAC-seq, DNA methyation or genomic conservation data) centered at genomic regions of interest. epistack needs three different inputs: 1) a genomic score objects, such as ChIP-seq coverage or DNA methylation values, provided as a `GRanges` (easily obtained from `bigwig` or `bam` files). 2) a list of feature of interest, such as peaks or transcription start sites, provi

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