其他技能

Sort alignment files by coordinate or read name using samtools and pysam. Use when preparing BAM files for indexing, variant calling, or paired-end analysis.

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Analyze TF motif accessibility variability across samples or single cells using chromVAR. Use when identifying TF motifs whose accessibility correlates with conditions, computing per-sample motif z-scores after matched background correction, comparing to ArchR / Signac equivalents, or distinguishing motif-accessibility signal from per-site footprinting.

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Trim multiple sequence alignments using ClipKIT, trimAl, BMGE, Divvier, or HMMcleaner with mode selection guidance per downstream goal. Use when removing unreliable columns or contaminating residues before phylogenetic inference, HMM building, or selection analysis.

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Map nucleosome center positions, occupancy, and fuzziness from ATAC-seq fragment-size patterns using NucleoATAC, ATACseqQC, DANPOS3, or scprinter. Use when characterizing nucleosome organization at promoters and enhancers, calling +1/-1 nucleosomes flanking NFRs, generating V-plots for chromatin structure visualization, or comparing nucleosome positioning between conditions.

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Creates sashimi-style plots showing RNA-seq read coverage and splice junction counts using ggsashimi (general-purpose, condition-grouped overlays), rmats2sashimiplot (rMATS-output-aware), MAJIQ-VOILA (LSV posteriors interactive HTML), leafviz (leafcutter clusters Shiny), Jutils (tool-agnostic heatmaps and sashimi for rMATS/leafcutter/MntJULiP/MAJIQ output), or pyGenomeTracks (multi-track publication figures). Tool choice depends on the upstream differential-splicing tool's output format and the publication vs interactive use case. Use when visualizing specific splicing events, validating differential splicing calls, or producing publication-quality figures.

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Quantifies alternative splicing as PSI (percent spliced in) from RNA-seq using rMATS-turbo (BAM-based event), SUPPA2 (TPM-based event), MAJIQ V3 (LSV-based Bayesian), leafcutter (annotation-free intron clusters), VAST-TOOLS (cross-species with microexon support), Shiba (junction-imbalance-corrected, 2025 SOTA at low coverage), or IRFinder-S (intron retention coverage-aware). Distinguishes the five canonical event classes (SE, A5SS, A3SS, MXE, RI), special classes (microexons, exitrons, AFE/ALE), intron retention subtypes (canonical RI vs detained introns), and applies effective-length normalization. Use when measuring splice-site usage or isoform inclusion ratios from short-read RNA-seq.

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Mark and remove PCR/optical duplicates using samtools fixmate and markdup. Use when preparing alignments for variant calling or when duplicate reads would bias analysis.

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Identify differentially accessible chromatin regions across conditions using DiffBind, csaw, DESeq2, or edgeR. Use when comparing ATAC-seq accessibility between treatment groups, choosing between consensus-peak vs sliding-window approaches, picking the correct normalization (full library vs reads-in-peaks), correcting batch with SVA/RUVseq, or interpreting log2FC and FDR thresholds in a chromatin context.

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Detect and adjust for horizontal pleiotropy in two-sample Mendelian randomization by distinguishing uncorrelated (UHP) from correlated (CHP) pleiotropy and choosing among Egger, MR-PRESSO, MR-RAPS, CAUSE, LHC-MR, LCV, MR-Clust, MR-Mix, and contamination-mixture methods. Use when validating an MR causal claim, running the STROBE-MR sensitivity battery, suspecting a shared heritable confounder, working under weak-instrument or polygenic-exposure regimes, or reconciling discordant estimates across robust methods.

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View, convert, and understand SAM/BAM/CRAM alignment files using samtools and pysam. Use when inspecting alignments, converting between formats, or understanding alignment file structure.

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Align protein structures using Foldseek 3Di, TM-align, US-align, DALI, or Foldmason for structural MSA. Predict, score, and superpose backbone coordinates when sequence identity is below the twilight zone or remote-homology detection is required. Use when sequence MSA fails (<25% identity), when the dark proteome is the target, when AlphaFoldDB / ESM Atlas search is needed, or when structural superposition is the goal.

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Use when accepting ANY real-world payment — Apple Pay, Wallet passes, Tap to Pay, Orders in Wallet. NOT in-app purchase / digital content (use axiom-integration). Covers entitlements, certs, signing, App Review payment rules.

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Use when the user mentions App Store screenshot validation, screenshot review, checking screenshots before submission, or verifying screenshot dimensions and content.

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Use when the user mentions slow builds, build performance, or build time optimization.

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Use when the user wants to triage a CORPUS of production crashes/hangs from an aggregator (Sentry, App Store Connect) — grouped, counted issues — rather than a single crash file.

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Use when working with ANY GPU rendering, Metal, OpenGL migration, shaders, 3D content, RealityKit, AR, USD/USDZ files, or display performance. Covers Metal migration, shader conversion, RealityKit ECS, RealityView, USDKit, ProMotion.

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Use when the user wants to add in-app purchases, implement StoreKit 2, or set up subscriptions.

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Use when the user has a crash log (.ips, MetricKit JSON, legacy .crash text, .xccrashpoint bundle, or pasted text) that needs analysis.

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Create child communication safety experiences using PermissionKit to request parental permission for children. Use when building apps that involve child-to-contact communication, need to check communication limits, request parent/guardian approval, or handle permission responses for minors.

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Implement, review, or improve WidgetKit widgets and controls. Use when building Home Screen, Lock Screen, StandBy, or CarPlay widgets with timeline providers; configurable widgets with AppIntentTimelineProvider; interactive widgets or Control Center controls with Button/Toggle wiring; WidgetKit push reloads, refresh budgets, deep links, Smart Stack relevance, Liquid Glass/accented rendering, widget extension setup, WidgetBundle, App Groups, and entitlements.

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Build alternative browser engines using BrowserEngineKit. Use when developing a non-WebKit browser engine for iOS/iPadOS in supported regions, managing web content/rendering/networking extension processes, configuring GPU and networking process capabilities, checking alternative-engine device eligibility, or reviewing BrowserEngineKit entitlements and Info.plist setup.

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Read and write NFC tags using CoreNFC. Use when scanning NDEF tags, reading ISO7816/ISO15693/FeliCa/MIFARE tags, writing NDEF messages, handling NFC session lifecycle, configuring NFC entitlements, or implementing background tag reading in iOS apps.

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Query grid electricity forecasts and submit load events using EnergyKit to help users optimize home electricity usage. Use when building smart home apps, EV charger controls, HVAC scheduling, or energy management dashboards that guide users to use power during cleaner or cheaper grid periods.

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Discover and configure Bluetooth and Wi-Fi accessories using AccessorySetupKit. Use when presenting a privacy-preserving accessory picker, defining discovery descriptors for BLE or Wi-Fi devices, handling accessory session events, migrating from CoreBluetooth permission-based scanning, or setting up accessories without requiring broad Bluetooth permissions.

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