jaechang-hits
Publisher on askill
Pythonic wrapper around RDKit with simplified interface and sensible defaults for drug discovery cheminformatics. Use for SMILES parsing, molecular standardization, descriptor computation, fingerprint...
Fast short-read DNA aligner for whole-genome, whole-exome, and ChIP-seq alignment to a reference genome. BWA-MEM2 is the 2× faster successor to BWA-MEM; outputs SAM/BAM with read group headers require...
Query Ensembl REST API for gene/transcript/variant annotations across 300+ species. Retrieve gene info by symbol/ID, sequence, cross-references (HGNC, RefSeq, UniProt), variants, regulatory features,...
OMERO is an open-source platform for biological image data management. Use the omero-py Python client to connect to an OMERO server, search and retrieve images as numpy arrays, annotate images with ta...
Parse and create FCS (Flow Cytometry Standard) files v2.0-3.1. Read event data as NumPy arrays, extract channel metadata, handle multi-dataset files, export to CSV/FCS. For advanced gating and compens...
Bulk RNA-seq differential expression analysis with PyDESeq2. Load count matrices, normalize, fit negative binomial models, Wald test with BH-FDR correction, LFC shrinkage, volcano/MA plots. Use for tw...
Parse and query DrugBank local XML database for drug information, interactions, targets, and chemical properties. Search drugs by ID/name/CAS, extract drug-drug interactions with severity, map targets...
Query Metabolomics Workbench REST API (4,200+ studies, NIH-funded) for metabolite identification, study discovery, RefMet name standardization, MS m/z precursor ion searches, MetStat study filtering,...
Python library for biological data analysis covering sequence manipulation (DNA, RNA, protein), pairwise/multiple alignment, phylogenetic tree construction (NJ, UPGMA), diversity metrics (alpha: Shann...
Deep learning cell and nucleus segmentation from fluorescence and brightfield microscopy images. Uses pre-trained models (cyto3, nuclei, tissuenet) and a generalist flow-based algorithm that segments...
Dataflow-based scientific workflow engine for scalable bioinformatics pipelines. Nextflow defines processes (containerized tasks) connected by channels (data queues); supports local, HPC (SLURM/SGE),...
Query ClinicalTrials.gov API v2 for clinical study data. Search trials by condition, drug/intervention, location, sponsor, or phase. Retrieve detailed study information by NCT ID. Filter by recruitmen...
Create professional research posters in LaTeX using beamerposter, tikzposter, or baposter. Layout design, typography, color schemes, figure integration, accessibility, and quality control for conferen...
Cheminformatics toolkit for molecular analysis and virtual screening. Use for SMILES/SDF parsing, molecular descriptor calculation (MW, LogP, TPSA), fingerprint generation (Morgan/ECFP, MACCS, RDKit),...
Toolkit for genomic interval operations on BED, BAM, GFF, VCF files. Find overlapping regions, merge adjacent intervals, calculate coverage depth, extract FASTA sequences, find nearest features, and m...
Whole slide image processing for digital pathology. Tissue detection, tile extraction (random, grid, score-based), filter pipelines for H&E/IHC preprocessing. Use for dataset preparation, tile-based d...
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