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MSA2dist calculates pairwise distances between all sequences of a DNAStringSet or a AAStringSet using a custom score matrix and conducts codon based analysis. It uses scoring matrices to be used in these pairwise distance calcualtions which can be adapted to any scoring for DNA or AA characters. E.g. by using literal distances MSA2dist calculates pairwise IUPAC distances.

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mzR provides a unified API to the common file formats and parsers available for mass spectrometry data. It comes with a subset of the proteowizard library for mzXML, mzML and mzIdentML. The netCDF reading code has previously been used in XC

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Manhattan plot and QQ Plot are commonly used to visualize the end result of Genome Wide Association Study. The "ggmanh" package aims to keep the generation of these plots simple while maintaining customizability. Main functions include manhattan_plot, qqunif, and thinPoints.

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syntenet can be used to infer synteny networks from whole-genome protein sequences and analyze them. Anchor pairs are detected with the MCScanX algorithm, which was ported to this package with the Rcpp framework for R and C++ integration. Anchor pairs from synteny analyses are treated as an undirected unweighted graph (i.e., a synteny network), and users can perform: i. network clustering; ii. phylogenomic profiling (by identifying which species contain which clusters) and; iii. microsynteny-bas

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lisaClust provides a series of functions to identify and visualise regions of tissue where spatial associations between cell-types is similar. This package can be used to provide a high-level summary of cell-type colocalization in multiplexed imaging data that has been segmented at a single-cell resolution.

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The Model-based Analysis of ChIP-Seq (MACS) is a widely used toolkit for identifying transcript factor binding sites. This package is an R wrapper of the lastest MACS3.

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Microbiome time series simulation with generalized Lotka-Volterra model, Self-Organized Instability (SOI), and other models. Hubbell's Neutral model is used to determine the abundance matrix. The resulting abundance matrix is applied to (Tree)SummarizedExperiment objects.

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The FDA Adverse Event Reporting System (FAERS) is a database used for the spontaneous reporting of adverse events and medication errors related to human drugs and therapeutic biological products. faers pacakge serves as the interface between the FAERS database and R. Furthermore, faers pacakge offers a standardized approach for performing pharmacovigilance analysis.

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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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Installs a self-contained conda instance that is managed by the R/Bioconductor installation machinery. This aims to provide a consistent Python environment that can be used reliably by Bioconductor packages. Functions are also provided to e

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This package is a implementation of biclustering ensemble method MoSBi (Molecular signature Identification from Biclustering). MoSBi provides standardized interfaces for biclustering results and can combine their results with a multi-algorithm ensemble approach to compute robust ensemble biclusters on molecular omics data. This is done by computing similarity networks of biclusters and filtering for overlaps using a custom error model. After that, the louvain modularity it used to extract biclus

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Provides Bayesian PCA, Probabilistic PCA, Nipals PCA, Inverse Non-Linear PCA and the conventional SVD PCA. A cluster based method for missing value estimation is included for comparison. BPCA, PPCA and NipalsPCA may be used to perform PCA o

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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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Manage paid ads on AdManage.ai from declarative config - default schedules launches across Meta/TikTok/Snapchat/Pinterest/LinkedIn (always PAUSED); create provisions Meta campaigns and ad sets.

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Monitor external web and social mentions of the operator's active projects - surface what people are discovering, where they're confused, and where to engage

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Provides guidance for writing, optimizing, and benchmarking Triton kernels for Intel XPU GPUs (Battlemage/Arc Pro B50) using the Xe-Forge optimization framework. Includes an LLM-driven trial-loop workflow (analyze, validate, benchmark, profile, finalize), XPU-specific patterns (tensor descriptors, GRF mode, tile swizzling), KernelBench fused kernels, and Flash Attention.

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Build prospect lists where the prospect is already one hop from the client, and write the line that says so. Seven members, each with its own source. Current-customer alumni is the priority member - everyone who ever worked at one of the client's customers or case-study companies and has since moved on. Triggers on "warm intro", "who do we know at that account", "they used to work at our customer", "alumni of our case study company", "shared investor angle", "who is in the same city as our rep", "did they visit our site". Outputs warm_intro_line plus a per-member evidence column.

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Smartlead API endpoint reference and patterns. Use for any Smartlead campaign, lead, email account, analytics, or inbox operation. Covers auth, rate limiting, and all commonly used endpoints.

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This skill should be used when searching for people/leads using the Prospeo Search Person API. It provides the correct API format, filter types, rate limiting patterns, and state-by-state crawling techniques to overcome the 25K result limit. Use when building lead lists, searching by job title/industry/location, or integrating with Prospeo.

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Amazon product listing image strategy and optimization. Comprehensive shot planning, infographic design, lifestyle photography, mobile optimization, and conversion-focused visual content. Use when the user asks about Amazon images, product photography, visual optimization, or listing conversion.

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Find and remove unreachable/unused code safely. Use during cleanup or before a refactor.

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Read one conversation window and return every independently mutable claim it states, one record each, with who or what it is about, whether it happened or stands, and the words that carry its time. Used by the memory extraction model on every conversation window; the engine resolves dates, validates keys, and repairs format.

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Scaffold your own focused AI agent harness — pick host (Claude Code, Codex, pi.dev, Hermes), template, agents, skills, and ship a npm-publishable harness with its own npx CLI. Use when a user asks to "create my own agent harness", "scaffold a harness", "make a custom Claude Code plugin like ruflo", or "build a vertical AI assistant for X".

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GCP Secret Manager integration: validate setup, fetch values, or confirm an NPM_TOKEN is non-revoked via `npm whoami`. Used for publish-time token rotation without long-lived keys in CI.

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