Results for “pydeseq2”

21 skills

Perform differential gene expression analysis for bulk RNA-seq data using PyDESeq2, supporting formulaic designs, Wald tests, FDR correction, LFC shrinkage, and result visualization.

30.2k · bundle

alterlab-pydeseq2

Run differential gene expression analysis on bulk RNA-seq count matrices with PyDESeq2, the Python port of DESeq2 — size-factor normalization, dispersion estimation, Wald tests, FDR (Benjamini-Hochberg) correction, and volcano/MA plots. Use when identifying differentially expressed genes between conditions from raw bulk RNA-seq counts. Part of the AlterLab Academic Skills suite.

More results

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.

metinduraktr-44

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.

pydantic-models-py

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.

muapi-seedance-2

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

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.

orchestra-research

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.

10.4k · bundle

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.

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.

12.8k · bundle

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.

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

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.

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.

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.

fabric-extract-v2

Parallel Fabric Workspace Metadata Extraction

stable-baselines3

Train reinforcement learning agents using PPO, SAC, DQN, TD3, DDPG, and A2C algorithms with a scikit-learn-like API. Supports custom Gymnasium environments, vectorized environments, callbacks, and model persistence.

30.2k · bundle

Use when extracting INSDSeq XML feature tables into tab-delimited text for downstream parsing or annotation review.

pixel-art-scaler

Deterministic pixel art upscaling using EPX/Scale2x, hq2x/hq4x, and xBR algorithms that add valid sub-pixels through pattern recognition. Activate on 'pixel art scaling', 'EPX', 'Scale2x', 'hq2x', 'hq4x', 'xBR', 'retro game upscaling'. NOT for AI/ML upscaling, photo enlargement, or simple nearest-neighbor.