Curated, auto-synced collection of 2,000+ Claude Code & Codex skills for AI4Protein, bioinformatics, AI development, and academic paper writing. One curl command installs them all.
Skill Claude Code
Observe the user's screen via screenpipe, detect repeated research workflows, match them against existing scientific-agent-skills, and draft new skills (or composition recipes that chain existing ones) for the patterns not yet covered. Use when the user asks to analyze their recent work and propose skills based on…
Skill Claude CodeCodex
Audit and rewrite prose so it stops reading as machine-generated. Use this skill when asked to remove AI-isms, clean up AI writing, edit a draft for AI tells, audit a README, changelog, release note, PR description, or blog post for machine-sounding prose, or make text sound less like AI. Supports a detect-only mode…
Skill Claude CodeCodex
Backend architecture patterns, API design, database optimization, and server-side best practices for Node.js, Express, and Next.js API routes.
Skill Claude CodeCodex
Build robust backtesting systems for trading strategies with proper handling of look-ahead bias, survivorship bias, and transaction costs. Use when developing trading algorithms, validating strategies, or building backtesting infrastructure.
Skill Claude CodeCodex
Identifies essential genes from CRISPR-Cas9 fitness screens using BAGEL2 (Kim & Hart 2021 Genome Med), a Bayesian classifier scoring per-gene Bayes Factors via log-likelihood ratios over per-sgRNA fold changes, calibrated against CEGv2 core-essentials (Hart 2017 G3, 684 genes) and NEGv1 non-essentials (Hart 2014, 927…
Skill Claude CodeCodex
Annotate bacterial and archaeal genomes and plasmids with Bakta's Prodigal/HMM/diamond pipeline. Identifies CDS, ncRNA, tRNA, rRNA, tmRNA, sORFs, CRISPR arrays, oriC/oriV/oriT, and gaps against a curated UniRef-derived database. Produces NCBI-compatible GFF3, GenBank, EMBL, JSON, FASTA, TSV, and a circular genome…
Skill Claude CodeCodex
Generate alignment statistics using samtools flagstat, stats, depth, coverage, and mosdepth. Use when assessing alignment quality, calculating coverage, or generating QC reports.
Skill Claude CodeCodex
Analyzes base-editing screens for variant function. Covers library design (Hanna 2021 ClinVar-scale CBE screen benchmarked on BRCA1/2, Cuella-Martin 2021 DDR saturation), CBE vs ABE chemistry choice (BE3/BE4 vs ABE7.10/ABE8.20/ABE8e), editing-window math (positions 4-8 from PAM-distal end; 4-7 for ABE7.10)…
Skill Claude CodeCodex
Designs cytosine (CBE, C-to-T) and adenine (ABE, A-to-G) base-editor guides by positioning the target base at the activity-peak of the editing window (protospacer positions 5-7, PAM-distal numbering), minimizing bystander edits for product purity, reading dinucleotide context (APOBEC1 TC favored / GC disfavored), and…
Skill Claude CodeCodex
Basecalls raw Oxford Nanopore signal (POD5/FAST5) into reads with Dorado, choosing the chemistry-matched model and accuracy tier (fast/hac/sup), requesting modified bases (5mCG5hmCG, 6mA, m6A) at basecall time, and handling duplex, demultiplexing, trimming, and HERRO read correction. Covers why the model+version is an…
Skill Claude CodeCodex
Master defensive Bash programming techniques for production-grade scripts. Use when writing robust shell scripts, CI/CD pipelines, or system utilities requiring fault tolerance and safety.
Skill Claude CodeCodex
Batch effect correction for CRISPR screens covering ComBat empirical-Bayes, RUV, SVA, control-sgRNA normalization, and the model-based alternative of including batch as a covariate in MAGeCK MLE or Chronos. Covers screen-specific batch sources (passage cohort, library lot, infection day, sequencing run, Cas9 lot, FBS…
Skill Claude CodeCodex
Designs genomics experiments so technical nuisance variation (batch, lane, plate, flow cell, operator, reagent lot, processing day) is balanced against the biological variable of interest and therefore estimable rather than confounded, using constrained sample-to-batch assignment (designit, OSAT), the…
Skill Claude CodeCodex
Download large datasets from NCBI efficiently using EPost, history server, batching, rate limiting, and retry logic. Use when bulk-fetching tens of thousands of sequences, pulling all results of a large ESearch, designing reproducible pipelines, comparing E-utilities to NCBI Datasets v2 CLI, or implementing…
Skill Claude CodeCodex
Integrate multiple scRNA-seq samples or batches with Harmony, scVI/scANVI, Seurat (CCA/RPCA), fastMNN, Scanorama, or BBKNN. Resolves which method to use for the dataset size and design, how strongly to correct, when integration is the wrong move (confounded batch/biology), how to score integration with scIB metrics…
Skill Claude CodeCodex
Process many sequence files in batch (count, merge, split, convert, summarize) with memory-safe streaming and on-disk indexing using Biopython, pysam, or pyfastx. Use when iterating over a directory of FASTA/FASTQ files, merging or splitting datasets, building random access across many or huge files, or automating…
Skill Claude CodeCodex
Master Bash Automated Testing System (Bats) for comprehensive shell script testing. Use when writing tests for shell scripts, CI/CD pipelines, or requiring test-driven development of shell utilities.
Skill Claude CodeCodex
Frames Bayesian phylogenetics as approximating a posterior distribution over trees conditioned on data AND priors via an MCMC that must be proven to have converged, using MrBayes, BEAST2, RevBayes, and PhyloBayes-MPI. Covers why convergence (ESS, PSRF, ASDSF, topology vs scalar) is the load-bearing claim, why…
Skill Claude Code
Skill "bayesian-optimizer" from FridrichMethod/awesome-skills, covering copyright notice, copyright (c) 2026 md babu mia, phd, all rights reserved, this code is proprietary and confidential and provenance: authenticated by md babu mia.
Skill Claude CodeCodex
Designs Bayesian clinical trials including Phase I dose-finding (BOIN, CRM, EWOC, mTPI-2), meta-analytic-predictive (MAP) priors with robust mixtures for external data borrowing, EXNEX for basket trials, hierarchical models for safety AE (Berry-Berry), Bayesian platform trials (I-SPY 2, GBM AGILE, REMAP-CAP), and…
Skill Claude CodeCodex
Optimize Bazel builds for large-scale monorepos. Use when configuring Bazel, implementing remote execution, or optimizing build performance for enterprise codebases.
Skill Claude CodeCodex
CLI for VCF/BCF: filter, merge, annotate, query, normalize, compute stats. Core post-variant-calling: quality filtering, multi-sample merging, rsID annotation, genotype extraction. Samtools companion in HTSlib. Use GATK for complex indel realignment during calling; use VCFtools for population genetics stats.
Skill Claude CodeCodex
Bead-based signal normalization and cross-batch harmonization for CyTOF and high-parameter cytometry - EQ four-element bead normalization of instrument sensitivity drift (CATALYST normCytof, premessa), and reference-anchor cross-batch normalization (CytoNorm, per-cluster quantile splines). Covers the distinction…
Skill Claude CodeCodex
Handles BED-format genomic intervals (BED3 through BED12, narrowPeak/broadPeak) and the coordinate-system substrate the whole interval category rests on, with bedtools (CLI) and pybedtools/pyranges/pandas (Python). Covers the 0-based half-open vs 1-based-closed convention boundary and the start-1/end-unchanged…
At most 3 mods per repository are shown here, and a mod shipped inside a plugin is left to that plugin's page — the rest are on their repository pages: