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bindingdb-database
BindingDB (https://www.bindingdb.org/) is the primary public database of measured drug-protein binding affinities. It contains over 3 million binding ...
bio-workflows-cnv-pipeline
Complete workflow for detecting copy number variants from exome or targeted sequencing data. BAM files (tumor/normal or germline) [1. Target Preparati...
claw-metagenomics
Comprehensive shotgun metagenomics analysis combining taxonomic classification, antimicrobial resistance gene detection, and functional pathway profil...
statsmodels
Statsmodels is Python's premier library for statistical modeling, providing tools for estimation, inference, and diagnostics across a wide range of st...
networkx
NetworkX is a Python package for creating, manipulating, and analyzing complex networks and graphs. Use this skill when working with network or graph ...
bio-data-visualization-volcano-customization
library(ggplot2) library(ggrepel) df$significance <- casewhen( df$padj < 0.05 & df$log2FoldChange > 1 'Up', df$padj < 0.05 & df$log2FoldChange < -1 ...
executing-plans
Load plan, review critically, execute tasks in batches, report for review between batches. Core principle: Batch execution with checkpoints for archit...
scientific-problem-selection
A conversational framework for systematic scientific problem selection based on Fischbach & Walsh's "Problem choice and decision trees in science and ...
bio-workflows-methylation-pipeline
Complete workflow from bisulfite sequencing FASTQ to differentially methylated regions. FASTQ files [1. QC & Trimming] -----> fastp/Trim Galore [2. Al...
protein-structure-prediction
The Protein Structure Prediction Skill provides an interface to state-of-the-art folding models. It takes an amino acid sequence and returns a PDB fil...
open-notebook
Open Notebook is an open-source, self-hosted alternative to Google's NotebookLM that enables researchers to organize materials, generate AI-powered in...
recovery-community-moderator
Trauma-informed AI moderator for addiction recovery communities. Applies harm reduction principles, honors 12-step traditions, and distinguishes betwe...