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Performs proximity operations on genomic intervals with bedtools (closest, window, flank, slop) and pybedtools - nearest-feature queries with signed/strand-aware distance, fixed-radius window searches, strand-aware promoter construction, and interval extension. Covers the closest -d/-D a/b/ref/-t/-k/-io/-iu/-id flags, the -D ref strand sign-flip, silent chromosome-end clipping in slop/flank, -t all tie double-counting, and the critical distinction between a geometry answer (nearest TSS) and a biology answer (which gene an element regulates). Use when assigning peaks or variants to genes, defining promoters from a gene model, building distance-to-TSS distributions, finding features within a window, or extending intervals - and when deciding whether nearest-gene is a fair prior (GWAS locus) or a trap (distal enhancer).

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Detects focal chromatin loops (point interactions / corner-dots) in balanced Hi-C and Micro-C contact maps and aggregates/validates a loop set. Covers de-novo calling with cooltools dots (HiCCUPS-style 4-background local enrichment with lambda-chunked FDR), chromosight (template-correlation), and Mustache (scale-space blob detection); aggregate peak analysis (APA) via cooltools pileup for confirmation; the depth/resolution prerequisite (de-novo needs ~5-10kb resolution = hundreds of millions to billions of valid pairs); consensus across callers and convergent-CTCF support as validation; and differential loops via union anchors plus chromosight quantify. Use when calling chromatin loops or dots from a cooler, deciding whether a map is deep enough to call de-novo vs running APA on known CTCF/cohesin anchors, building an aggregate peak pileup, comparing loops across conditions, or validating loop calls. For HiChIP/PLAC-seq/PCHi-C protein-anchored data use FitHiChIP/MAPS, not dots.

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Reads, queries, and writes bigWig indexed binary signal tracks (coverage, fold-change, conservation, methylation-rate) with pyBigWig (Python) and the UCSC Kent tools (bedGraphToBigWig, bigWigToBedGraph, bigWigInfo, bigWigSummary, bigWigAverageOverBed) and deepTools (multiBigwigSummary, computeMatrix, bigwigCompare). Covers the central trap that a wide query returns a precomputed zoom-level summary (by default the mean, which annihilates narrow peaks) not per-base data, when exact=True/values() is mandatory, the NaN-not-zero gap-handling fork, choosing mean vs max vs sum vs coverage by biological question, and the sorted-bedGraph plus chrom.sizes build requirement. Use when extracting signal at regions, computing mean signal per gene/peak, building a browser track from bedGraph, comparing tracks, or building TSS/gene-body metaprofiles.

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Performs set operations on genomic intervals - intersect (-wa/-wb/-wo/-wao/-loj/-c/-v/-u), subtract (-A), merge (-d, -c/-o), complement, cluster, multiinter, unionbedg, map, and groupby - with bedtools (CLI) and pybedtools/pyranges/bioframe (Python). Covers the sorted-input contract and the -sorted chromosome-order footgun, reciprocal/fractional overlap (-f/-F/-r/-e) and the A-vs-B asymmetry, -split for spliced/BED12/BAM features, and jaccard/fisher as mechanics only. Use when finding overlapping or unique regions between BED/peak/feature files, building consensus peaksets, removing blacklisted regions, transferring annotation values onto intervals, or computing interval-set similarity; route overlap-significance testing to overlap-significance.

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Aligns and QCs methylated-RNA-immunoprecipitation (MeRIP / m6A-seq) IP and input libraries using STAR or HISAT2 splice-aware mapping, samtools sort/index, IP/input matched-pair tracking, antibody-lot metadata recording, replicate concordance via deepTools multiBamSummary + plotCorrelation, IP enrichment QC via plotFingerprint and per-transcript IP/input ratio distributions, library-complexity saturation curves via PreSeq, and the explicit do-NOT-deduplicate convention for standard non-UMI MeRIP. Use when preparing paired IP and input BAM files for exomePeak2 / MeTPeak / MACS3 peak calling, evaluating MeRIP replicate concordance and IP enrichment, deciding whether to deduplicate (standard MeRIP typically NOT), choosing genome-vs-transcriptome alignment for downstream peak vs m6Anet workflows, recording antibody clone and lot metadata for cross-batch reconciliation, detecting failed IPs via saturation curves and IP/input distribution shape, or generating IP-over-Input bigWig tracks for visualisation.

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Processes eDNA metabarcoding from raw paired-end reads to species tables, navigating ASV (DADA2, UNOISE3) vs OTU (swarm v2) decision (Callahan 2017 vs Schloss multi-copy-16S critique), marker/primer choice (Leray COI, MiFish 12S, 515F/806R 16S, ITS2) with primer-specific bias, OBITools3 v3 command-name break (obi stats plural; .tar.gz taxonomy), tag-jumping with dual-indexing (Schnell 2015; NovaSeq 10x MiSeq), decontam as screening-not-classifier (Davis 2018), read-counts-not-abundance critique (Lamb 2019), site-occupancy modeling (Ficetola 2015), Naive-Bayes calibration limits (Bokulich 2018), and eDNA decay (Strickler 2015). Use when going from raw eDNA FASTQ to species tables, picking marker + denoising pipeline, deciding whether read counts represent abundance, applying occupancy modeling, configuring OBITools3 v3, or interpreting decontam output. Not for clinical 16S microbiome (see microbiome/amplicon-processing).

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Reconstruct ancestral states at internal phylogenetic nodes for sequences (PAML codeml, IQ-TREE --ancestral, GRASP, FastML), discrete traits (corHMM hidden-rate Markov, ape::ace, phytools::make.simmap stochastic mapping, BayesTraits), and continuous traits (phytools::fastAnc, geiger Brownian/OU, RPANDA). Use when designing constructs for ancestral protein resurrection, tracing trait evolution along a tree, performing stochastic character mapping, testing models of trait evolution (BM vs OU vs EB), inferring ancestral genome content via Dollo or DTL reconciliation, or quantifying ancestral-state uncertainty for downstream comparative analyses.

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Annotate copy number variant segments with overlapping genes, dosage-sensitivity scores, cancer driver databases, population frequencies, and clinical-variant content. Covers bedtools/pybedtools interval intersection, AnnotSV comprehensive annotation and ranking, ClinGen haploinsufficiency/triplosensitivity scoring, gnomAD-SV/DGV frequency filtering, COSMIC Cancer Gene Census, and ClinVar overlap. Use when interpreting which genes a CNV affects, distinguishing the driver gene of a focal event from passengers, filtering against population CNVs, separating whole-gene from partial-gene overlap, or preparing CNVs for clinical classification.

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Assesses ChIP-seq quality across antibody specificity, fragmentation, enrichment, replicate concordance, and library complexity. Computes FRiP, NSC/RSC (phantompeakqualtools), library complexity (NRF/PBC1/PBC2), deepTools plotFingerprint (JS distance, AUC, synthetic JS), ChIPQC, IDR with ENCODE Nself/Nt rules, and detects hyper-ChIPable artifacts. Use when validating an antibody, diagnosing failed peak calls, deciding whether to proceed with downstream analysis, grading against ENCODE thresholds, or auditing replicate concordance.

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Build and validate experimental WebMCP tools for an existing web page. Use when an agent needs to expose a site's real workflows as page tools, create webmcp.init.js, define deterministic checks, or compare WebMCP with accessibility-tree automation.

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Build machine vision inspection systems with MATLAB Visual Inspection Toolbox. Covers the full arc from problem selection through deployment: anomaly detection (Student-Teacher, PatchCore, FastFlow, FCDD), object detection (YOLOX), counting (CounTR, shape matching), gauging and measurement (caliper, fitcircle, fitangle), blob analysis (regionprops, calibrated measurement), shape matching for fixturing and localization, synthetic data generation for training augmentation, and deployment to standalone apps, embedded C/C++, NVIDIA GPUs (TensorRT), NPUs (ONNX), and Beckhoff PLCs. Routes to rule-based tools when problems are geometric and deterministic, AI-based tools when defect appearance varies, and hybrid pipelines combining both.

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Build MCP servers in Python with FastMCP. Define tools / resources / prompts, build the server, test locally, deploy to FastMCP Cloud or Docker. Use whenever the user mentions building an MCP server, exposing tools to LLMs, FastMCP, building a Claude integration, or troubleshooting FastMCP module-level server, storage, lifespan, middleware, OAuth, or deployment errors.

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Post project updates to team chat, gather feedback, triage responses, and plan next steps. Adapts to available tools (chat, git, issues, tasks). First run discovers tools and saves a playbook; subsequent runs execute from the playbook. Trigger with 'team update', 'post update', 'sync with team', 'standup', 'check team chat', 'feedback loop', 'project update', 'what did the team say'.

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Use when skinning a character in Maya ("bind skin", "fix the weights", weight painting, Skin Tools or ngSkinTools layers), when deformation looks wrong (pinching, candy-wrapper wrist, collapsing elbow or shoulder, volume loss, clothes poking through), when mirroring, copying or capping skin weights for Unreal or Unity, building blend shapes, corrective shapes or pose space deformation (Pose Editor on IK-driven joints), a face rig with shapes or joints, multiple skinClusters, Delta Mush or the ML Deformer, or running a range-of-motion deformation test.

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chrome-devtools-mcp launcher — a single bash script that resolves Playwright's bundled Chrome-for-Testing and Node.js directly through Nix. See repo README for usage, override mechanisms, and version compatibility.

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kubectl-mcp-server CLI commands for tool discovery, direct invocation, and diagnostics. Use when exploring available tools, calling tools from command line, or checking server health.

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Help the user turn their Retentioneering ideas, friction reports, bug findings, or feature needs into high-quality upstream contributions: from capturing and validating the idea, through minimal reproductions and issue drafts, to preparing, testing, and submitting a pull request that follows this repository's conventions. Use when the user says they found a bug, wants a feature, wrote a workaround worth upstreaming, or asks how to contribute, open an issue, or make a PR to retentioneering-tools.

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Tools for deep-sequencing data analysis and visualization

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Free tool marketing strategy covering idea evaluation, tool design, lead capture architecture, SEO landing pages, launch playbook, and ROI measurement for calculators, generators, checkers, graders, and interactive tools.

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Configure Temps as an MCP (Model Context Protocol) server so AI assistants can interact with a Temps instance directly -- listing/inspecting projects and deployments, and (when write mode is enabled) triggering deployments with human confirmation. Use when the user wants to: (1) Set up the Temps MCP server, (2) Connect Claude Code/Desktop, Codex, Cursor, VS Code, Windsurf, or Zed to Temps, (3) Add Temps tools to an AI assistant, (4) Test the MCP wizard locally, (5) Manage multiple Temps MCP connections (dev, staging, prod, or several local dev slots) side by side. Triggers: "temps mcp", "configure temps tools", "add temps to claude", "temps ai assistant", "mcp server setup", "mcp add", "test the mcp wizard".

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Universal MCP client for connecting to any MCP server with progressive disclosure. Wraps MCP servers as skills to avoid context window bloat from tool definitions. Use when interacting with external MCP servers (Zapier, Sequential Thinking, GitHub, filesystem, etc.), listing available tools, or executing MCP tool calls. Triggers on requests like "connect to Zapier", "use MCP server", "list MCP tools", "call Zapier action", "use sequential thinking", or any MCP server interaction.

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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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TFBSTools is a package for the analysis and manipulation of transcription factor binding sites. It includes matrices conversion between Position Frequency Matirx (PFM), Position Weight Matirx (PWM) and Information Content Matrix (ICM). It c

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A set of tools for making TxDb objects from genomic annotations from various sources (e.g. UCSC, Ensembl, and GFF files). These tools allow the user to download the genomic locations of transcripts, exons, and CDS, for a given assembly, and

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