Instructions file CodexOpenCode
Instructions for PKU-YuanGroup/OpenAI4S, a project described as: 9.9 元豆包 API 复刻 Claude Science.
373 2d ago A 4 tokens
copy · 100% MIT
Instructions file
Instructions for PKU-YuanGroup/OpenAI4S, covering claude.md / agents.md, what this is, commands, the dual loop (the central architecture) and where things live.
373 2d ago A 7,047 tokens
original MIT
Skill Claude CodeCodex
ADMET-guided genetic molecule optimization workflow from seed SMILES; use when the agent needs to build or run an RDKit/SA-Score/ADMET-AI GA pipeline for molecule optimization, enforce molecule lineage logs, render optimization-history HTML dashboards, and write candidate triage reports.
373 2d ago A 63 tokens
original MIT
alphafold2
04Skill Claude CodeCodex
Predict protein structure for monomers and multimers with AlphaFold2 via the ColabFold runner (Mirdita et al. 2022, github.com/sokrypton/ColabFold; AlphaFold2 Jumper et al. 2021). Reach for this skill to fold a sequence or complex with the AF2/AF2-Multimer evoformer, to validate designed sequences by self-consistency…
373 2d ago A 117 tokens
original MIT
Skill Claude CodeCodex
Audit tabular datasets before analysis or training for schema drift, missing values, duplicate rows or IDs, target imbalance, and entity or group leakage across splits using pure-stdlib helpers.
373 2d ago A 40 tokens
original MIT
bioprobench
06Skill Claude CodeCodex
Score an LLM's biological-protocol reasoning on the BioProBench benchmark: protocol QA, step ordering, error detection, protocol generation, and LLM-judged error reasoning; or generate the responses.
373 2d ago A 46 tokens
original MIT
Skill Claude CodeCodex
Read, write, and convert multiple sequence alignment files using Biopython Bio.AlignIO. Supports Clustal, PHYLIP, Stockholm, FASTA, Nexus, and other alignment formats for phylogenetics and conservation analysis. Use when reading, writing, or converting alignment file formats.
373 2d ago A 64 tokens
copy · 95% MIT
Skill Claude CodeCodex
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.
373 2d ago A 60 tokens
copy · 97% MIT
Skill Claude CodeCodex
Trim PCR primers from aligned reads in amplicon-panel BAMs using samtools ampliconclip. Use when processing SARS-CoV-2 ARTIC, hereditary cancer panels, ctDNA hot-spot panels, or any amplicon assay where primer-derived bases would falsely confirm reference at primer footprints.
373 2d ago A 71 tokens
copy · 95% MIT
Skill Claude CodeCodex
Filter alignments by flags, mapping quality, and regions using samtools view and pysam. Use when extracting specific reads, removing low-quality alignments, or subsetting to target regions.
373 2d ago A 44 tokens
copy · 98% MIT
Skill Claude CodeCodex
Create and use BAI/CSI indices for BAM/CRAM files using samtools and pysam. Use when enabling random access to alignment files or fetching specific genomic regions.
373 2d ago A 41 tokens
copy · 95% MIT
Skill Claude CodeCodex
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.
373 2d ago A 37 tokens
copy · 97% MIT
Skill Claude CodeCodex
Validate alignment quality with insert size distribution, proper pairing rates, GC bias, strand balance, and other post-alignment metrics. Use when verifying alignment data quality before variant calling or quantification.
373 2d ago A 43 tokens
copy · 92% MIT
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.
373 2d ago A 39 tokens
copy · 95% MIT
Skill Claude CodeCodex
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.
373 2d ago A 39 tokens
copy · 98% MIT
Skill Claude CodeCodex
Generate pileup data for variant calling using samtools mpileup and pysam. Use when preparing data for variant calling, analyzing per-position read data, or calculating allele frequencies.
373 2d ago A 42 tokens
copy · 97% MIT
Skill Claude CodeCodex
Generate consensus sequences and manage reference files using samtools. Use when creating consensus from alignments, indexing references, or creating sequence dictionaries.
373 2d ago A 32 tokens
copy · 94% MIT
Skill Claude CodeCodex
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.
373 2d ago A 45 tokens
copy · 95% MIT
Skill Claude CodeCodex
Parse and analyze multiple sequence alignments using Biopython. Extract sequences, identify conserved regions, analyze gaps, work with annotations, and manipulate alignment data for downstream analysis. Use when parsing or manipulating multiple sequence alignments.
373 2d ago A 52 tokens
copy · 86% MIT
Skill Claude CodeCodex
Calculate alignment statistics including sequence identity, conservation scores, substitution matrices, and similarity metrics. Use when comparing alignment quality, measuring sequence divergence, and analyzing evolutionary patterns.
373 2d ago A 40 tokens
copy · 95% MIT
Skill Claude CodeCodex
Perform multiple sequence alignment using MAFFT, MUSCLE5, ClustalOmega, or T-Coffee. Guides tool and algorithm selection based on dataset size, sequence divergence, and downstream application. Use when aligning three or more homologous sequences for phylogenetics, conservation analysis, or evolutionary studies.
373 2d ago A 66 tokens
copy · 100% MIT
Skill Claude CodeCodex
Perform pairwise sequence alignment using Biopython Bio.Align.PairwiseAligner. Use when comparing two sequences, finding optimal alignments, scoring similarity, and identifying local or global matches between DNA, RNA, or protein sequences.
373 2d ago A 52 tokens
copy · 97% MIT
Skill Claude CodeCodex
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…
373 2d ago A 102 tokens
copy · 98% MIT
Skill Claude CodeCodex
Detects differential alternative splicing between conditions using rMATS-turbo (binomial LRT on junction counts), leafcutter (Dirichlet-multinomial GLM on intron clusters), MAJIQ V3 deltapsi/HET (Bayesian posterior on LSVs), SUPPA2 (empirical-null on TPM-derived PSI), or Shiba (junction-imbalance-corrected, 2025 SOTA…
373 2d ago A 146 tokens
copy · 94% MIT