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14810 skills availablespatial-deconvolution
Estimate cell type composition in spatial spots using scRNA-seq references. import scanpy as sc import anndata as ad imp...
spatial-communication
Analyze ligand-receptor interactions and cell-cell communication in spatial data. import squidpy as sq import scanpy as ...
image-analysis
Extract features and segment tissue images in spatial transcriptomics data. import squidpy as sq import scanpy as sc imp...
bio-phylo-tree-visualization
Draw phylogenetic trees using matplotlib integration. from Bio import Phylo import matplotlib.pyplot as plt tree = Phylo...
jaspar-database
JASPAR (https://jaspar.elixir.no/) is the gold-standard open-access database of curated, non-redundant transcription fac...
bio-ribo-seq-orf-detection
Reference examples tested with: BioPython 1.83+, DESeq2 1.42+, pandas 2.2+ Before using code patterns, verify installed ...
varCADD
Genome-wide pathogenicity prediction leveraging standing variation data to improve accuracy over traditional CADD scores...
bio-geo-data
Query and access Gene Expression Omnibus datasets using Biopython's Entrez module. from Bio import Entrez Entrez.email =...
bio-data-visualization-heatmaps-clustering
library(pheatmap) library(RColorBrewer) pheatmap(mat, scale = 'row', clusterrows = TRUE, clustercols = TRUE) annotationc...
bio-liquid-biopsy-pipeline
Complete workflow for cfDNA analysis from sequencing to clinical interpretation. Pre-analytical QC → cfDNA Preprocessing...
bio-reporting-automated-qc-reports
multiqc results/ -o qcreport/ multiqc results/ -n myprojectqc multiqc results/ --module fastqc --module star MultiQC rec...
bio-expression-matrix-metadata-joins
import pandas as pd metadata = pd.readcsv('sampleinfo.csv', indexcol=0) import pandas as pd counts = pd.readcsv('counts....
bio-atac-seq-motif-deviation
Reference examples tested with: ggplot2 3.5+, limma 3.58+ Before using code patterns, verify installed versions match. I...
dask
Dask is a Python library for parallel and distributed computing that enables three critical capabilities: Larger-than-me...
tooluniverse-drug-target-validation
Validate drug target hypotheses using multi-dimensional computational evidence before committing to wet-lab work. Produc...
biomni
Biomni is an open-source biomedical AI agent framework from Stanford's SNAP lab that autonomously executes complex resea...
deep-research
Autonomous multi-step research that searches multiple sources, reads full content, synthesizes findings, and produces a ...
bio-workflows-microbiome-pipeline
Paired-End FASTQ (16S V4) ┌──────────────────────────────────────────────────┐ │ microbiome-pipeline ...
bio-spatial-transcriptomics-spatial-deconvolution
Reference examples tested with: anndata 0.10+, matplotlib 3.8+, numpy 1.26+, pandas 2.2+, scanpy 1.10+ Before using code...
mrd-edge-detection-agent
The MRD-EDGE Detection Agent implements the MRD-EDGE (Enhanced Detection of ctDNA through Genomic Error suppression) dee...
scvi-tools
scvi-tools is a comprehensive Python framework for probabilistic models in single-cell genomics. Built on PyTorch and Py...
nk-cell-therapy-agent
The NK Cell Therapy Agent provides AI-driven design and optimization of natural killer cell therapies for cancer treatme...
gnomad-database
The Genome Aggregation Database (gnomAD) is the largest publicly available collection of human genetic variation, aggreg...
bio-workflow-management-snakemake-workflows
Compatible with Snakemake 7.x, 8.x, and 9.x. For Snakemake 8.0+, use --executor instead of --cluster. rule all: input: e...