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simpy
Process-based discrete-event simulation framework in Python. Use this skill when building simulations of systems with processes, queues, resources, and time-based events such as manufacturing systems, service o...
☆ 8,602查看技能
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biopython
Primary Python toolkit for molecular biology. Preferred for Python-based PubMed/NCBI queries (Bio.Entrez), sequence manipulation, file parsing (FASTA, GenBank, FASTQ, PDB), advanced BLAST workflows, structures,...
☆ 626查看技能
GitHub
bio-transcription-translation
Transcribe DNA to RNA and translate to protein using Biopython. Use when converting between DNA, RNA, and protein sequences, finding ORFs, or using alternative codon tables.
☆ 300查看技能
GitHub
bio-alignment-msa-parsing
Parse and analyze multiple sequence alignments using Biopython. Extract sequences, identify conserved regions, analyze gaps, work with annotations, and manipulate alignment data for downstream analysis.
☆ 300查看技能
GitHub
bio-single-cell-data-io
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 Seurat objects and AnnData objects, and...
☆ 300查看技能
GitHub
bio-single-cell-clustering
Dimensionality reduction and clustering for single-cell RNA-seq using Seurat (R) and Scanpy (Python). Use for running PCA, computing neighbors, clustering with Leiden/Louvain algorithms, generating UMAP/tSNE em...
☆ 300查看技能
GitHub
bio-restriction-mapping
Create restriction maps showing enzyme cut positions on DNA sequences using Biopython Bio.Restriction. Visualize cut sites, calculate distances between sites, and generate text or graphical maps.
☆ 300查看技能
GitHub
bio-blast-searches
Run remote BLAST searches against NCBI databases using Biopython Bio.Blast. Use for sequence similarity searches, identifying unknown sequences, finding homologs, and querying NCBI's nr/nt databases.
☆ 300查看技能
GitHub
bio-population-genetics-scikit-allel-analysis
Python population genetics with scikit-allel. Read VCF files, compute allele frequencies, calculate diversity statistics, perform PCA, and run selection scans using GenotypeArray and HaplotypeArray data structu...
☆ 300查看技能
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bio-pdb-geometric-analysis
Perform geometric calculations on protein structures using Biopython Bio.PDB. Use for measuring distances, angles, and dihedrals, finding neighbor atoms, superimposing structures, calculating RMSD, identifying...
☆ 300查看技能
GitHub
bio-sequence-properties
Calculate sequence properties like GC content, molecular weight, isoelectric point, and GC skew using Biopython. Use when analyzing sequence composition, computing physical properties, or comparing sequences.
☆ 300查看技能
GitHub
bio-motif-search
Find patterns, motifs, and subsequences in biological sequences using Biopython. Use when searching for transcription factor binding sites, regulatory elements, or any sequence pattern. For restriction enzyme a...
☆ 300查看技能
GitHub
bio-entrez-link
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.
☆ 299查看技能
GitHub
bio-entrez-fetch
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.
☆ 299查看技能
GitHub
bio-entrez-search
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.
☆ 299查看技能
GitHub
bio-geo-data
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.
☆ 299查看技能
GitHub
bio-phylo-distance-calculations
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...
☆ 299查看技能
GitHub
bio-codon-usage
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.
☆ 299查看技能
GitHub
bio-fastq-quality
Work with FASTQ quality scores using Biopython. Use when analyzing read quality, filtering by quality, trimming low-quality bases, or generating quality reports.
☆ 299查看技能
GitHub
bio-alignment-pairwise
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...
☆ 299查看技能
GitHub
bio-sequence-statistics
Calculate sequence statistics (N50, length distribution, GC content, summary reports) using Biopython. Use when analyzing sequence datasets, generating QC reports, or comparing assemblies.
☆ 299查看技能
GitHub
bio-restriction-fragment-analysis
Analyze restriction digest fragments using Biopython Bio.Restriction. Predict fragment sizes, get fragment sequences, simulate gel electrophoresis patterns, and perform double digests.
☆ 299查看技能
GitHub
bio-pdb-structure-navigation
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,...
☆ 299查看技能
GitHub
pycse
Python computations in science and engineering (pycse) - helps with scientific computing tasks including nonlinear regression, uncertainty quantification, design of experiments (DOE), Latin hypercube sampling,...
☆ 272查看技能
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