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General
Installation
Tutorials
Getting started
Evaluating iterative algorithms
Best Practices
Diagnostics & Visualizations
Third-party models
Benchmarking mRNA’s mRFP-expression
Benchmarking antimicrobial peptides
Beyond proteins primary structure
API
Core
seqme.evaluate
seqme.Cache
seqme.Metric
seqme.MetricResult
seqme.combine
seqme.rank
seqme.extract_non_dominated
seqme.top_k
seqme.sort
seqme.strip
seqme.rename
seqme.show
seqme.plot_bar
seqme.plot_scatter
seqme.plot_parallel
seqme.plot_line
seqme.to_latex
seqme.to_pickle
seqme.read_pickle
seqme.to_fasta
seqme.read_fasta
Metrics
seqme.metrics.Diversity
seqme.metrics.Uniqueness
seqme.metrics.Novelty
seqme.metrics.NGramJaccardSimilarity
seqme.metrics.FBD
seqme.metrics.MMD
seqme.metrics.KID
seqme.metrics.Precision
seqme.metrics.Recall
seqme.metrics.ClippedDensity
seqme.metrics.ClippedCoverage
seqme.metrics.AuthPct
seqme.metrics.FKEA
seqme.metrics.ID
seqme.metrics.Threshold
seqme.metrics.HitRate
seqme.metrics.Hypervolume
seqme.metrics.ConformityScore
seqme.metrics.KLDivergence
seqme.metrics.Fold
seqme.metrics.Subset
seqme.metrics.Count
seqme.metrics.Length
Models
seqme.models.ESM2
seqme.models.ESMFold
seqme.models.ESMIF1
seqme.models.Hyformer
seqme.models.RNAFM
seqme.models.GENALM
seqme.models.KmerFrequencyEmbedding
seqme.models.AliphaticIndex
seqme.models.Aromaticity
seqme.models.BomanIndex
seqme.models.Charge
seqme.models.Gravy
seqme.models.Hydrophobicity
seqme.models.HydrophobicMoment
seqme.models.InstabilityIndex
seqme.models.IsoelectricPoint
seqme.models.ProteinWeight
seqme.models.LogP
seqme.models.QED
seqme.models.SAScore
seqme.models.ThirdPartyModel
seqme.models.PCA
seqme.models.Ensemble
Utils
seqme.utils.pca
seqme.utils.tsne
seqme.utils.umap
seqme.utils.plot_embeddings
seqme.utils.spearman_alignment_score
seqme.utils.knn_alignment_score
seqme.utils.plot_knn_alignment_score
seqme.utils.shuffle_characters
seqme.utils.subsample
Contributing guide
About
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GitHub
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