Tagged bioinformatics

Annotate protein variants with ProtVar, ClinVar, gnomAD and CADD scores

Trace a variant through regulation, target genes, pathways and disease outcomes

Coach design thinking projects with method sequencing and deck workflows

Turn stories and characters into cinematic frames, storyboards and video prompts

Extract a design system from a screenshot or URL and rebuild it as portable JSON

Filter BAM alignments by flags, mapping quality and genomic region with samtools

Align two DNA, RNA or protein sequences with Biopython PairwiseAligner

Align protein structures with Foldseek, TM-align or US-align when sequences diverge

Detect allele-specific chromatin accessibility in ATAC-seq with WASP and ASEReadCounter

Call open chromatin peaks from ATAC-seq with MACS3, Genrich or HMMRATAC

Run ATAC-seq quality checks for TSS enrichment, FRiP and ENCODE thresholds

Link cis-regulatory peaks from scATAC-seq with Cicero, ArchR or SCENIC+

Build a stable consensus ATAC-seq peakset from replicate peaks for comparisons

Model base-level ATAC-seq accessibility and variant effects with chromBPNet

Find differentially accessible chromatin between ATAC-seq conditions with DiffBind

Link distal ATAC-seq enhancers to target genes with ABC and ENCODE-rE2G

Detect transcription factor footprints in ATAC-seq with TOBIAS and HINT-ATAC

Map nucleosome positions and fuzziness from ATAC-seq fragment sizes with NucleoATAC

Process single-cell ATAC data with Signac, ArchR or SnapATAC2 from QC to clusters

Map Ensembl IDs and pull gene coordinates and orthologs from BioMart in bulk

Test whether two traits share a causal variant using coloc and related methods

Map GWAS loci to candidate effector genes with L2G, MAGMA and PoPS

Narrow GWAS lead SNPs to credible causal variant sets with SuSiE and FINEMAP

Estimate genetic correlation between two traits from GWAS summary statistics

Fit structural equation models to GWAS summary statistics with GenomicSEM

Estimate SNP heritability and partition it across annotations with LDSC

Decompose exposure effects into direct and mediated paths for molecular mediators

Estimate causal effects from GWAS summary statistics with Mendelian randomization

Detect and correct horizontal pleiotropy in two-sample Mendelian randomization

Validate drug targets with cis-pQTL Mendelian randomization on proteome data

Run TWAS with FUSION, PrediXcan and FOCUS to find genes tied to GWAS signals

Detect allele-specific ChIP-seq binding from heterozygous variants with WASP

Train base-resolution deep learning models for ChIP-seq and CUT&RUN profiles with BPNet

Segment the genome into chromatin states from histone ChIP-seq with ChromHMM

Find differentially bound ChIP-seq regions with DiffBind, csaw and DESeq2

Discover de novo and known motifs in ChIP-seq peaks with HOMER and MEME

Annotate ChIP-seq peaks to genes and regulatory elements with ChIPseeker and GREAT

Call narrow and broad ChIP-seq peaks with MACS3, HOMER or SPP

Assess ChIP-seq quality with FRiP, NSC, RSC, library complexity and IDR

Normalize ChIP-seq data with Drosophila or E. coli spike-in controls

Identify super-enhancers from H3K27ac or BRD4 ChIP-seq with ROSE

Plot ChIP-seq coverage and heatmaps with deepTools, pyGenomeTracks and Gviz

Call HLA alleles from sequencing data for transplant and neoantigen work

Call microsatellite instability from exome, genome and panel data

Call star alleles and drug-gene phenotypes for pharmacogenomic reports

Assign COSMIC mutational signatures to tumor genomes to infer DNA damage causes

Rank rare-disease variants from family sequencing with phasing and phenotype scores

Annotate CLIP-seq binding sites to RNA features like UTRs, introns and ncRNAs

Align CLIP-seq reads to the genome with crosslink-preserving settings