Skills correspondant au nom, à la description ou à l’auteur GitHub.
Modify phylogenetic tree structure using Biopython Bio.Phylo. Use for rooting trees with outgroups or midpoint, pruning taxa, collapsing clades, ladderizing branches, and extracting subtrees.
Generate reverse complements and complements of DNA/RNA sequences using Biopython. Use when working with opposite strands, primer design, or converting between template and coding strands.
Find restriction enzyme cut sites in DNA sequences using Biopython Bio.Restriction. Search with single enzymes, batches of enzymes, or commercially available enzyme sets. Returns cut positions for linear or cir...
Write biological sequences to files (FASTA, FASTQ, GenBank, EMBL) using Biopython Bio.SeqIO. Use when saving sequences, creating new sequence files, or outputting modified records.
Read, write, and convert phylogenetic tree files using Biopython Bio.Phylo. Use for parsing Newick, Nexus, PhyloXML, and NeXML tree formats, converting between formats, and handling multiple trees in a single f...
Process multiple sequence files in batch using Biopython. Use when working with many files, merging/splitting sequences, or automating file operations across directories.
Visualize metagenomic profiles using R (phyloseq, microbiome) and Python (matplotlib, seaborn). Create stacked bar plots, heatmaps, PCA plots, and diversity analyses. Use when creating publication-quality figur...
Handle paired-end FASTQ files (R1/R2) using Biopython. Use when working with Illumina paired reads, synchronizing pairs, interleaving/deinterleaving, or filtering paired data.
Filter and select sequences by criteria (length, ID, GC content, patterns) using Biopython. Use when subsetting sequences, removing unwanted records, or selecting by specific criteria.
Select restriction enzymes by criteria using Biopython Bio.Restriction. Find enzymes that cut once, don't cut, produce specific overhangs, are commercially available, or have compatible ends for cloning.
Create and manipulate Seq, MutableSeq, and SeqRecord objects using Biopython. Use when creating sequences from strings, modifying sequence data in-place, or building annotated sequence records.
Build reproducible scientific documents, presentations, and websites with Quarto supporting R, Python, Julia, and Observable JS.
Find cross-references between NCBI databases using Biopython Bio.Entrez. Use for navigating from genes to proteins, sequences to publications, finding related records, and discovering database relationships.
Retrieve records from NCBI databases using Biopython Bio.Entrez. Use for downloading sequences, fetching GenBank records, getting document summaries, and parsing NCBI data into Biopython objects.
Search NCBI databases using Biopython Bio.Entrez. Use for finding records by keyword, building search queries, discovering database structure, and getting global query counts across databases.
Query NCBI Gene Expression Omnibus (GEO) for expression datasets using Biopython Bio.Entrez. Use for finding microarray/RNA-seq datasets, downloading expression data, and linking GEO to SRA.
Compute evolutionary distances and build phylogenetic trees using Biopython Bio.Phylo.TreeConstruction. Use for creating distance matrices from alignments, building NJ/UPGMA trees, parsimony analysis, and gener...
Analyze codon usage, calculate CAI (Codon Adaptation Index), and examine synonymous codon bias using Biopython. Use when analyzing coding sequences for expression optimization or evolutionary analysis.
Work with FASTQ quality scores using Biopython. Use when analyzing read quality, filtering by quality, trimming low-quality bases, or generating quality reports.
Perform pairwise sequence alignment using Biopython Bio.Align.PairwiseAligner. Use for comparing two sequences, finding optimal alignments, scoring similarity, and identifying local or global matches between DN...
Calculate sequence statistics (N50, length distribution, GC content, summary reports) using Biopython. Use when analyzing sequence datasets, generating QC reports, or comparing assemblies.
Analyze restriction digest fragments using Biopython Bio.Restriction. Predict fragment sizes, get fragment sequences, simulate gel electrophoresis patterns, and perform double digests.
Navigate protein structure hierarchy using Biopython Bio.PDB SMCRA model. Use for accessing models, chains, residues, and atoms, iterating over structure levels, extracting sequences, identifying residue types,...
Review Python code for quality, security, and best practices
Le classement utilise les étoiles du dépôt GitHub indexé. Plusieurs skills peuvent partager ce nombre : ce n’est ni un nombre d’installations ni une note de qualité.