scikit-bio
Biological data toolkit. Sequence analysis, alignments, phylogenetic trees, diversity metrics (alpha/beta, UniFrac), ordination (PCoA), PERMANOVA, FASTA/Newick I/O, for microbiome analysis.
72
66%
Does it follow best practices?
Impact
73%
2.21xAverage score across 6 eval scenarios
Passed
No known issues
Optimize this skill with Tessl
npx tessl skill review --optimize ./scientific-skills/scikit-bio/SKILL.mdEvaluation results
65%
28%Gut Microbiome Diversity Analysis: Healthy vs IBD Patients
Diversity analysis best practices
Integer counts
100%
100%
Faith's PD tree param
50%
50%
UniFrac tree param
0%
0%
PERMANOVA permutations
0%
100%
PERMDISP alongside PERMANOVA
0%
0%
PCoA on distance matrix
100%
100%
partial_beta_diversity for pairs
0%
100%
Alpha result as Series
100%
100%
Beta result as DistanceMatrix
100%
100%
uv install command
0%
0%
Permutation test 999+
0%
100%
36%
26%Gene Characterization: Alignment and Translation Pipeline
Sequence class selection and alignment methods
DNA class usage
0%
100%
RNA class for transcription
0%
100%
Protein class for translation
0%
100%
FASTQ quality via positional_metadata
0%
100%
local_pairwise_align_ssw for DNA
0%
0%
StripedSmithWaterman for protein
0%
0%
Affine gap penalties
100%
0%
Degap before realignment
0%
0%
Generator-based FASTQ reading
0%
0%
uv install command
0%
0%
95%
74%Comparative Phylogenetic Analysis of Bacterial Isolates
Phylogenetic tree construction methods
nj() for neighbor joining
0%
100%
upgma() for UPGMA
0%
100%
GME/BME scalability note
0%
100%
DistanceMatrix class
0%
100%
Patristic distances
50%
70%
Cophenetic matrix
0%
75%
Robinson-Foulds distance
41%
100%
PCoA on distance matrix
30%
100%
Newick output
100%
100%
uv install command
0%
100%
82%
30%River Microbiome Environmental Drivers Analysis
Constrained ordination with environmental variables
CCA function used
0%
100%
CCA sample_ids param
0%
0%
CCA species_ids param
0%
0%
Biplot scores extracted
66%
100%
CCA axis coordinates saved
75%
100%
Ordination results persisted
100%
100%
PCoA for unconstrained comparison
100%
100%
DistanceMatrix class
100%
75%
Proportion explained reported
100%
100%
Environmental DataFrame
60%
100%
uv install command
0%
100%
88%
16%Isolation by Distance in Coastal Microbiome Study
BIOM table processing and Mantel test
BIOM HDF5 format
0%
0%
axis='sample' for sample IDs
100%
100%
axis='observation' for feature IDs
100%
100%
Mantel test called
100%
100%
Mantel permutations >= 999
100%
100%
Mantel method specified
100%
100%
DistanceMatrix for community distances
100%
100%
DistanceMatrix for geographic distances
100%
100%
Integer counts for diversity
0%
100%
Mantel results reported
100%
100%
uv install command
0%
100%
76%
68%Amplicon Sequencing QC, Rarefaction, and Alignment Curation
Rarefaction, format conversion, and MSA processing
Generator-based FASTQ reading
0%
83%
positional_metadata quality access
0%
100%
subsample_counts for rarefaction
0%
100%
Rarefaction to consistent depth
100%
100%
TabularMSA for MSA storage
0%
100%
omit_gap_positions used
0%
0%
MSA consensus method
0%
100%
FASTA output from generator
0%
0%
DNA class for sequences
0%
100%
uv install command
0%
100%
- Repository
- K-Dense-AI/claude-scientific-skills
- Commit
25e1c0f
- Evaluated
- Agent
- Claude Code
- Model
- Claude Sonnet 4.6
Table of Contents
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