Compute evolutionary distances and build phylogenetic trees using Biopython Bio.Phylo.TreeConstruction.
Build maximum likelihood phylogenetic trees using IQ-TREE2 and RAxML-NG with expert model selection, branch support assessment, and topology testing.
Read, write, and convert phylogenetic tree files using Biopython Bio.Phylo. Use when parsing Newick, Nexus, PhyloXML, or NeXML tree formats, converting between formats, o — from…
Modify phylogenetic tree structure using Biopython Bio.Phylo. Use when rooting trees with outgroups, midpoint, or MAD methods, pruning taxa, collapsing clades, ladderizin — from…
Draw and export phylogenetic trees using Biopython Bio.Phylo with matplotlib and modern alternatives.
Genome-wide association studies (GWAS) with PLINK. Perform case-control and quantitative trait association testing using logistic/linear regression with covariates, gener — from…
Read biological sequence files (FASTA, FASTQ, GenBank, EMBL, ABI, SFF) using Biopython Bio.SeqIO. Use when parsing sequence files, iterating multi-sequence files, random — from…
Read biological sequence files (FASTA, FASTQ, GenBank, EMBL, ABI, SFF) using Biopython Bio.SeqIO. Use when parsing sequence files, iterating multi-sequence files, random — from…
Build reproducible scientific documents, presentations, and websites with Quarto supporting R, Python, Julia, and Observable JS.
Select restriction enzymes by criteria using Biopython Bio.Restriction. Find enzymes that cut once, don't cut, produce specific overhangs, are commercially available, or — from…
Predict restriction digest fragment sizes and gel patterns using Biopython Bio.Restriction. Computes fragment lengths and sequences for single and double digests on linear or…
Design and validate Type IIS scarless DNA assembly (Golden Gate, MoClo) using Biopython Bio.Restriction.
Create restriction maps showing enzyme cut positions on DNA sequences using Biopython Bio.Restriction.
Find restriction enzyme cut sites in DNA sequences using Biopython Bio.Restriction. Search with single enzymes, batches of enzymes, or commercially available enzyme sets — from…
Generate reverse complements and complements of DNA/RNA sequences using Biopython. Use when working with opposite strands, primer design, or converting between template a — from…
Create and manipulate Seq, MutableSeq, and SeqRecord objects using Biopython. Use when creating sequences from strings, modifying sequence data in-place, or building anno — from…
Slice, extract, and concatenate biological sequences using Biopython. Use when extracting subsequences, joining sequences, or manipulating sequence regions by position.
Dimensionality reduction and clustering for single-cell RNA-seq using Seurat (R) and Scanpy (Python).
Dimensionality reduction and clustering for single-cell RNA-seq using Seurat (R) and Scanpy (Python).
Read, write, and create single-cell data objects using Seurat (R) and Scanpy (Python). Use for loading 10X Genomics data, importing/exporting h5ad and RDS files, creating — from…
Read, write, and create single-cell data objects using Seurat (R) and Scanpy (Python). Use for loading 10X Genomics data, importing/exporting h5ad and RDS files, creating — from…
Test whether cell-type proportions or composition changed between conditions in single-cell data using Milo (miloR), scCODA, sccomp, and propeller.
Detect and remove doublets (multiple cells captured in one droplet) from single-cell RNA-seq data. Uses Scrublet (Python), DoubletFinder (R), and scDblFinder (R).
Detect and remove doublets (two or more cells in one droplet) from single-cell RNA-seq using scDblFinder (R), Scrublet (Python), and DoubletFinder (R).
Find marker genes and annotate cell types in single-cell RNA-seq using Seurat (R) and Scanpy (Python).
Find marker genes and annotate cell types in single-cell RNA-seq using Seurat (R) and Scanpy (Python).
Quality control, filtering, and normalization for single-cell RNA-seq using Seurat (R) and Scanpy (Python).
Quality control, filtering, and normalization for single-cell RNA-seq using Seurat (R) and Scanpy (Python).
Profiles non-miRNA small RNAs - tRNA-derived fragments (tRFs/tsRNAs), piRNAs, and rRNA/snoRNA-derived species - with MINTmap, unitas, SPORTS, and proTRAC.
Compares how a rhythm CHANGES between conditions, genotypes, treatments, tissues, or ages (differential rhythmicity), classifying each feature as gain-of-rhythm, loss-of-rhythm,…
Discovers periodic signals of unknown period in time-series omics data using Lomb-Scargle periodograms (scipy), autocorrelation, and wavelet time-frequency decomposition (pywt).
End-to-end 16S amplicon workflow from FASTQ reads to differential abundance. Orchestrates DADA2 ASV inference, taxonomy assignment, diversity analysis, and compositional — from…
Write biological sequences to files (FASTA, FASTQ, GenBank, EMBL) using Biopython Bio.SeqIO. Use when saving sequences, creating new sequence files, or outputting modifie — from…
Write biological sequences to files (FASTA, FASTQ, GenBank, EMBL) using Biopython Bio.SeqIO. Use when saving sequences, creating new sequence files, or outputting modifie — from…
Use when you have identified a package available in the Bioconda channel (indicated by a conda version badge or Bioconda recipe URL) and need to verify that installation succeeds…
Use when applying Biome's linting capabilities, rule categories, and code quality enforcement to JavaScript/TypeScript projects.
Generate and analyze DNA sequences using NVIDIA's Evo 2 BioNeMo NIM microservice. Use for Evo2/Evo 2, DNA generation, genomic sequence generation, hosted generation, local Docker…
Check progress for a detached KERMT run (pretrain, finetune, or any kermt_run_detached invocation). Reads run.json, queries docker for container state, tails the pretrain/finetune…
Pretrain a fresh KERMT model from scratch on a user-provided corpus. Builds a new vocabulary from the corpus, instantiates the model architecture from defaults, and launches…
Bootstrap the KERMT agent environment — verify host docker + nvidia-container-toolkit, build the kermt:latest image from the repo's Dockerfile if it doesn't yet exist, and run a…
Generate multiple sequence alignments (MSAs) for protein sequences using the ColabFold MSA-Search NIM.
Run ProteinMPNN inverse folding via NVIDIA NIM to design protein sequences for a target backbone. Sends user-provided PDB files and design parameters to NVIDIA's hosted API,…
Run RFDiffusion protein backbone design via NVIDIA NIM. Use for de novo protein backbones, motif scaffolding, binder design, hotspot residues, contigs syntax, diffusion steps,…
Biopython is a comprehensive set of freely available Python tools for biological computation. It provides functionality for sequence manipulation, file I/O, database access,…
Comprehensive molecular biology toolkit. Use for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez) — from…
Advanced Biopython modules for motifs, population genetics, sequence utilities, restriction analysis, clustering, and GenomeDiagram visualization; use when you need extended…
Sequence alignment and alignment file processing with Biopython (Bio.Align/Bio.AlignIO), triggered when you need global/local pairwise alignment, MSA read/write/format conversion,…
Use Bio.Entrez to access NCBI databases (e.g., PubMed/GenBank) for searching, fetching summaries, and downloading records when your workflow needs to call the NCBI E-utilities API…
Use Bio.Phylo to read/write phylogenetic trees and perform visualization and statistics; use when tree parsing/conversion, pruning/rerooting, distance calculation, or plotting is…
Primary Python toolkit for molecular biology. Preferred for Python-based PubMed/NCBI queries (Bio.Entrez), sequence manipulation, file parsing (FASTA, GenBank, FASTQ, PDB),…
Biopython sequence analysis: parse FASTA/FASTQ/GenBank/GFF (SeqIO), NCBI Entrez (esearch/efetch/elink), remote/local BLAST, pairwise/MSA alignment (PairwiseAligner,…
Use Biopython to read/write/convert biological sequence files (FASTA/GenBank/FASTQ, etc.) and perform basic sequence operations; use when you need reliable sequence I/O,…
Use Bio.PDB to parse and analyze protein structures (PDB/mmCIF) for structural bioinformatics tasks; use when you need structure parsing, geometry calculations, or structural…
Submit compact BioStudies and ArrayExpress API requests for free-text search and accession-based study retrieval.
Philippine BIR tax compliance skill for Pulser Finance (Tax Guru agent). Generates BIR 2307 / 2550M / 2550Q / SAWT / QAP / SLSP DAT files and PDFs via Foundry Code Interpreter;…
Organize X/Twitter bookmark folders (collections) via GraphQL with Chrome cookie auth. Actions: list folders, list folder contents, add/remove/move a bookmark between folders,…
Generate professional printable birth-chart PDF packets (natal and synastry) from birth data, using the birth-charts pipeline repo.
Receive and verify Bitbucket Cloud webhooks. Use when setting up Bitbucket webhook handlers, debugging X-Hub-Signature verification, or handling repository and pull request events…
Покрывает кеширование в Bitrix — Cache (неуправляемый), ManagedCache, TaggedCache, автокеш ORM, кеш компонентов через startResultCache/endResultCache, композитный сайт, настройка…
Interacts with the BitSkins REST API V2 and WebSocket API for CS2/Dota 2 skin trading. Supports account management, market search, buying, selling, listing, delisting, relisting,…