mdhewei

Downstream analysis of ATAC-seq or ChIP-seq peak files. Annotates peaks to genomic features, computes signal summaries, finds diff...

Route to the correct publication-quality plot sub-skill for volcano plots, heatmaps, box/violin plots, scatter plots, bar charts, ...

Cluster samples or features in omics data using K-means, hierarchical agglomerative clustering, DBSCAN, or consensus clustering. E...

Co-expression in PATIENT SAMPLES (TCGA tumors / GTEx normal tissues). NOT for cell lines — use depmap_coexpression.py for DepMap c...

Run Cox proportional hazards regression on clinical and molecular data. Fits univariate and multivariate Cox models, computes haza...

Design a pooled CRISPR sgRNA library for a list of target genes. Designs sgRNAs for each gene, selects top guides based on predict...

Analyze CRISPR pooled screens using MAGeCK. Accepts a raw count table or FASTQ files. Runs MAGeCK RRA (pairwise test) or MAGeCK ML...

Quality control analysis for pooled CRISPR screens. Accepts a sgRNA read count matrix (guides × samples) and computes library repr...

Curate literature-backed gene or protein lists for a requested function, pathway, molecular class, or regulator type, then normali...

DepMap analysis for a gene across CANCER CELL LINES (NOT patient samples). Modules: expression, mutation, copy number, essentialit...

Design base editor sgRNAs for a given gene. Fetches exonic sequence from Ensembl, scans for all NGG (or NG/NGA) PAM sites, filters...

Use when the user wants to retrieve CRISPR sgRNA candidates for one gene or a gene list from the GuidePro genome-wide reference ta...

Correlate gene expression or dependency scores with drug sensitivity data from PRISM (DepMap). Identifies drugs whose sensitivity ...

Retrieve and summarize normal tissue expression for a single human gene using GTEx, including full tissue-level expression, public...

Use when the user wants comprehensive annotation for one gene or a gene list, including gene identifiers, protein information, con...

Compare 2 to 6 gene lists for overlap and enrichment. Computes pairwise Jaccard similarity, overlap coefficients, and Fisher's exa...

Use when the user wants to run enrichment analysis from a gene list and generate publication-quality bubble plots for Gene Ontolog...

Download GTEx v8/v10 gene expression data (bulk RNA-seq TPMs, read counts, or median expression per tissue) from the GTEx Portal A...

Retrieve and summarize normal tissue expression for a single human gene using GTEx, including full tissue-level expression, public...

Train and evaluate machine learning classifiers on omics data (gene expression, mutation scores, copy number, or any numeric featu...

mdhewei/bioinfor-claw

mdhewei/bioinfor-claw

mdhewei/bioinfor-claw

mdhewei/bioinfor-claw

mdhewei/bioinfor-claw

Generate publication-quality Kaplan-Meier survival curves from time-to-event data. Supports multiple groups, log-rank test, Wilcox...

mdhewei/bioinfor-claw

Search and track recent preprints from bioRxiv and medRxiv on a given topic. Retrieves preprint metadata, abstracts, and author in...

mdhewei/bioinfor-claw

Retrieve protein structure and domain information for a single gene. Resolves the gene to a UniProt accession, fetches domain/feat...