Results for “pydeseq2”

Differential gene expression analysis (Python DESeq2). Identify DE genes from bulk RNA-seq counts, Wald tests, FDR correction, volcano/MA plots, for RNA-seq analysis.

Differential gene expression analysis (Python DESeq2). Identify DE genes from bulk RNA-seq counts, Wald tests, FDR correction, volcano/MA plots, for RNA-seq analysis.

Create Pydantic models following the multi-model pattern with Base, Create, Update, Response, and InDB variants for clean API contracts in Python applications using Pydantic v2.

Orchestrates a complete bulk RNA-seq differential-expression study from raw FASTQ reads through QC, alignment, quantification, differential expression, pathway enrichment, and publication figures.

Inspects and debugs OAuth 2.0 authorization flows including PKCE, client credentials, and device code grants, validating tokens, decoding claims, and tracing redirect chains.

Dense, machine-readable API reference for PyFixest — high-dimensional fixed-effects OLS/WLS/IV and Poisson (feols, fepois, feglm), clustered/robust standard errors, R-style formula syntax, and post-estimation. Use when writing or debugging Python fixed-effects regressions with the pyfixest package.

Systematic audit and review by Referee 2. Two modes — "deck" reviews slide presentations for rhetoric, visual quality, and compile cleanliness; "code" performs cross-language replication and econometric audit of empirical pipelines. Use when reviewing slides, auditing code, or verifying replication.

Generate cinematic videos with Seedance 2.0 using director-level prompts, camera grammar, and multi-mode generation across Chinese, Global, and VIP tiers.

Performs differential expression analysis on bulk RNA-seq or pseudo-bulk count matrices with QC, PCA, and contrast testing.

Generate cinematic short-form video with ByteDance Seedance 2.0 Pro on RunComfy. Documents Seedance 2.0 Pro's strengths (multi-modal references — up to 9 images, 3 videos, 3 audio — synchronized in-pass audio with natural lip-sync, cinematic motion refinement), the 4–15s duration schema, and when to route to HappyHorse 1.0 / Wan 2.7 / Kling instead. Calls `runcomfy run bytedance/seedance-v2/pro` through the local RunComfy CLI. Triggers on "seedance", "seedance 2", "seedance v2", "seedance pro", "bytedance video", or any explicit ask to generate video with this model.

Adds PyTorch FSDP2 (fully_shard) to training scripts with correct init, sharding, mixed precision/offload config, and distributed checkpointing. Use when models exceed single-GPU memory or when you need DTensor-based sharding with DeviceMesh.

Adds PyTorch FSDP2 (fully_shard) to training scripts with correct init, sharding, mixed precision/offload config, and distributed checkpointing. Use when models exceed single-GPU memory or when you need DTensor-based sharding with DeviceMesh.

Generate cinematic short-form video with ByteDance Seedance 2.0 Pro on RunComfy. Documents Seedance 2.0 Pro's strengths (multi-modal references — up to 9 images, 3 videos, 3 audio — synchronized in-pass audio with natural lip-sync, cinematic motion refinement), the 4–15s duration schema, and when to route to HappyHorse 1.0 / Wan 2.7 / Kling instead. Calls `runcomfy run bytedance/seedance-v2/pro` through the local RunComfy CLI. Triggers on "seedance", "seedance 2", "seedance v2", "seedance pro", "bytedance video", or any explicit ask to generate video with this model.

Use when aligning short reads to a reference genome or indexed sequence database. Suitable for mapping FASTQ/FASTA reads in paired-end or single-end mode to produce SAM output.

Process and analyze physiological signals including ECG, EEG, EDA, RSP, PPG, EMG, and EOG using Python.

SENTINEL v2.0 — Quality Trader Convergence Scanner. Inverted pipeline: find ELITE/RELIABLE traders, see where they converge. When 5+ quality traders hold the same asset in the same direction, enter.

Use for writing, reviewing, debugging, migrating, or testing SQLAlchemy 2.x Core or ORM code involving Engine, Connection, Session, mapped models, select statements, transactions, pooling, results, loading, or AsyncSession. Do not use for raw database SQL with no SQLAlchemy boundary, Alembic migration design, DuckDB relations, or database administration.

Comprehensive biosignal processing toolkit for analyzing physiological data including ECG, EEG, EDA, RSP, PPG, EMG, and EOG signals. Use this skill when processing cardiovascular signals, brain activity, electrodermal responses, respiratory patterns, muscle activity, or eye movements. Applicable for heart rate variability analysis, event-related potentials, complexity measures, autonomic nervous system assessment, psychophysiology research, and multi-modal physiological signal integration.

Provides a command-line workflow for binary analysis with radare2, covering reconnaissance, disassembly, function analysis, string and import inspection, patching, binary diffing, and r2pipe scripting across PE, ELF, Mach-O, DEX, and WASM formats.

Takes pre-computed differential expression results from DESeq2, edgeR, limma, or PyDESeq2 and produces a structured, publication-ready summary with ranked gene lists, biological themes, and key observations.

Debug Python: pdb REPL + debugpy remote (DAP).

Use when working from the local Evo 2 repository for DNA-sequence scoring, embeddings, generation, or phage-genome design experiments.

Agent E2 - Qualitative Coding Specialist - Systematic coding and theme development. Covers codebook development, coding strategies, saturation assessment, and CAQDAS guidance.

TIGER v2 — Multi-scanner trading system for Hyperliquid perps via Senpi MCP. 5 signal patterns (BB compression breakout, BTC correlation lag, momentum breakout, mean reversion, funding rate arb), DSL v4 trailing stops, goal-based aggression engine, and risk guardrails. Configurable profit target over deadline. 12-cron architecture (10 TIGER + prescreener + ROAR meta-optimizer). Pure Python analysis. Requires Senpi MCP, python3, mcporter CLI, and OpenClaw cron system.

Adversarial dynamic e2e QA workflow - generate hostile scenarios, test, verify, fix, report, and clean up

Analyzes Zeek conn.log connection intervals using statistical methods to detect C2 beaconing patterns, flagging periodic connections with low jitter.

Use when aligning RNA-seq reads to a reference genome using graph-based indexing for fast and sensitive spliced alignment.

SQLAlchemy Python SQL toolkit and ORM with powerful query builder, relationship mapping, and database migrations via Alembic

Use when the user asks to run a full empirical / causal analysis in Python — by default in the style of an applied economics paper (AER / QJE / JPE / ReStud / AEJ) with DID / RD / IV / SCM / DML / matching, written-out estimating equation + identifying assumption, Table 1 / Table 2 / event-study figure / robustness gauntlet — OR in epidemiology / public health style (target-trial emulation, IPTW + g-formula + TMLE triplet, Mendelian randomization, KM/AFT survival, E-value sensitivity, STROBE/TRIPOD reporting) — OR in ML causal inference style (DML, S/T/X/R/DR meta-learners, causal forest, Dragonnet/TARNet/CEVAE, BCF, CATE distribution, policy learning, conformal causal, fairness audit, causal discovery) — OR in distributional / gap-decomposition style (Oaxaca–Blinder `sp.oaxaca`, Kitagawa `sp.kitagawa_decompose`, DiNardo–Fortin–Lemieux `sp.dfl_decompose`, Gelbach `sp.gelbach`, Fairlie `sp.fairlie`, RIF / FFL `sp.rif_decomposition`, all reachable through the `sp.decompose` dispatcher). Also covers exporting mu

Generate cinematic short-form video with ByteDance Seedance 2.0 Pro on RunComfy. Documents Seedance 2.0 Pro's strengths (multi-modal references — up to 9 images, 3 videos, 3 audio — synchronized in-pass audio with natural lip-sync, cinematic motion refinement), the 4–15s duration schema, and when to route to HappyHorse 1.0 / Wan 2.7 / Kling instead. Calls `runcomfy run bytedance/seedance-v2/pro` through the local RunComfy CLI. Triggers on "seedance", "seedance 2", "seedance v2", "seedance pro", "bytedance video", or any explicit ask to generate video with this model.

Comprehensive QA and testing skill for quality assurance, test automation, and testing strategies for ReactJS, NextJS, NodeJS applications. Includes test suite generation, coverage analysis, E2E testing setup, and quality metrics. Use when designing test strategies, writing test cases, implementing test automation, performing manual testing, or analyzing test coverage.

Assesses a project against all five SOC 2 Trust Service Criteria, producing a control-by-control PASS/PARTIAL/FAIL matrix with evidence references, remediation roadmap, and evidence collection checklist for audit readiness.

Debug Python with pdb, breakpoint(), post-mortem inspection, and debugpy remote attach.

Debug Python code interactively with pdb and debugpy, covering local breakpoints, post-mortem analysis, and remote attachment to running processes.