BioTender-max/awesome-bio-agent-skills
Skill Claude CodeCodex
Workflow for gene and transcript quantification from RNA-seq reads using alignment-based or alignment-free tools.
not rated 178
+6 2mo ago A 25 tokens
178Stars on the repository
200Mods indexed here, across every type
2mo agoLast push, which is what freshness is scored on
customA LICENSE file GitHub cannot name, so bodies are not copied
BioTender-max/awesome-bio-agent-skills
Skill Claude CodeCodex
Workflow for foundational sequence parsing, conversion, compression handling, and interval-aware file validation.
not rated 178
+6 2mo ago A 23 tokens
BioTender-max/awesome-bio-agent-skills
Skill Claude CodeCodex
Workflow for small RNA and miRNA preprocessing, quantification, differential analysis, and target-oriented interpretation.
not rated 178
+6 2mo ago A 26 tokens
BioTender-max/awesome-bio-agent-skills
Skill Claude CodeCodex
Workflow for spatial transcriptomics preprocessing, domain detection, deconvolution, neighborhood analysis, and publication-ready maps.
not rated 178
+6 2mo ago A 28 tokens
BioTender-max/awesome-bio-agent-skills
Skill Claude CodeCodex
SPR and BLI assay planning, kinetic interpretation, and troubleshooting guidance. Use when: (1) Planning binding kinetics experiments, (2) Troubleshooting poor/no binding signal, (3) Interpreting kinetic data artifacts, (4) Choosing between SPR vs BLI platforms.
not rated 178
+6 2mo ago A 63 tokens
systems-biology
102BioTender-max/awesome-bio-agent-skills
Skill Claude CodeCodex
Workflow for constraint-based metabolic modeling, context-specific models, gene essentiality, and systems-level interpretation.
not rated 178
+6 2mo ago A 24 tokens
BioTender-max/awesome-bio-agent-skills
Skill Claude CodeCodex
Workflow for pseudotime, lineage branching, and state-transition analysis in single-cell data.
not rated 178
+6 2mo ago A 22 tokens
variant-calling
104BioTender-max/awesome-bio-agent-skills
Skill Claude CodeCodex
Workflow for small-variant and structural-variant discovery, filtering, annotation, and interpretation from sequencing data.
not rated 178
+6 2mo ago A 25 tokens
BioTender-max/awesome-bio-agent-skills
Skill Claude CodeCodex
Workflow for orchestrating reproducible omics pipelines with workflow engines and clear execution provenance.
not rated 178
+6 2mo ago A 20 tokens
BioTender-max/awesome-bio-agent-skills
Skill Claude CodeCodex
Species abundance estimation using Bracken with Kraken2 output. Redistributes reads from higher taxonomic levels to species for more accurate estimates. Use when accurate species-level abundances are needed from Kraken2 classification output.
not rated 178
+6 2mo ago A 48 tokens
BioTender-max/awesome-bio-agent-skills
Skill Claude CodeCodex
Applies ACMG/AMP 2015 framework with ClinGen SVI specifications, Tavtigian 2018/2020 Bayesian point system, Abou Tayoun 2018 PVS1 decision tree, Pejaver 2022 calibrated PP3/BP4 thresholds for REVEL/BayesDel/AlphaMissense, Brnich 2020 PS3/BS3 OddsPath, Walker 2023 SpliceAI splicing framework, and AMP/ASCO/CAP 2017…
not rated 178
+6 2mo ago A 161 tokens
BioTender-max/awesome-bio-agent-skills
Skill Claude CodeCodex
Remove sequencing adapters from FASTQ files using Cutadapt and Trimmomatic. Supports single-end and paired-end reads, Illumina TruSeq, Nextera, and custom adapter sequences. Use when FastQC shows adapter contamination or before alignment of short reads.
not rated 178
+6 2mo ago A 60 tokens
BioTender-max/awesome-bio-agent-skills
Skill Claude CodeCodex
Designs adaptive clinical trials including group-sequential (O'Brien-Fleming, Pocock, Lan-DeMets spending), sample-size re-estimation (blinded Friede-Kieser, unblinded Cui-Hung-Wang, Mehta-Pocock promising zone), seamless Phase 2/3 with treatment-arm selection, population enrichment, and response-adaptive…
not rated 178
+6 2mo ago A 147 tokens
BioTender-max/awesome-bio-agent-skills
Skill Claude CodeCodex
Predicts ADMET properties using ADMETlab 3.0 (119 endpoints with uncertainty), ADMET-AI, DeepChem MolNet, and chemprop D-MPNN with explicit handling of OECD QSAR principles, applicability domain assessment, calibration, hERG/CYP/AMES gold-standard endpoints, and PAINS / Lipinski / Ro5 / Veber / BBB druglikeness…
not rated 178
+6 2mo ago A 115 tokens
BioTender-max/awesome-bio-agent-skills
Skill Claude CodeCodex
Identify direct miRNA-target interactions from AGO HITS-CLIP, AGO-CLEAR-CLIP (chimeric reads), HEAP (Halo-Ago2 mouse), chimeric eCLIP / miR-eCLIP (deep miRNA-target profiling), or CLASH using chimeric-read processing pipelines, seed-pairing analysis, and 3' auxiliary pairing rules. Use when distinguishing direct miRNA…
not rated 178
+6 2mo ago A 152 tokens
BioTender-max/awesome-bio-agent-skills
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.
not rated 178
+6 2mo ago A 71 tokens
BioTender-max/awesome-bio-agent-skills
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.
not rated 178
+6 2mo ago A 44 tokens
BioTender-max/awesome-bio-agent-skills
Skill Claude CodeCodex
Quantify transcript expression using pseudo-alignment with Salmon or kallisto. Use when quantifying transcripts with Salmon or kallisto.
not rated 178
+6 2mo ago A 37 tokens
BioTender-max/awesome-bio-agent-skills
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.
not rated 178
+6 2mo ago A 41 tokens
bio-alignment-io
116BioTender-max/awesome-bio-agent-skills
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.
not rated 178
+6 2mo ago A 64 tokens
BioTender-max/awesome-bio-agent-skills
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.
not rated 178
+6 2mo ago A 37 tokens
BioTender-max/awesome-bio-agent-skills
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.
not rated 178
+6 2mo ago A 60 tokens
BioTender-max/awesome-bio-agent-skills
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.
not rated 178
+6 2mo ago A 43 tokens
BioTender-max/awesome-bio-agent-skills
Skill Claude CodeCodex
Detect allele-specific chromatin accessibility from ATAC-seq using WASP, GATK ASEReadCounter, or RASQUAL. Use when mapping cis-regulatory genetic variants from heterozygous SNPs, separating cis from trans regulation, building chromatin QTL (caQTL) maps, validating GWAS variant function with allelic imbalance, or…
not rated 178
+6 2mo ago A 93 tokens
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