Biology & Genomics

Validate protein designs and binder complexes with AlphaFold2 confidence scores

Fetch AlphaFold predicted protein structures by UniProt ID and read pLDDT scores

Work with AnnData objects and h5ad files for single-cell and omics data

Design protein binders with BindCraft and built in AlphaFold2 validation

Choose between BoltzGen, BindCraft and RFdiffusion for protein binder design

Plan SPR and BLI binding experiments and troubleshoot weak binding signals

Look up measured drug target binding affinities in BindingDB by target or compound

Predict ADMET properties and toxicity endpoints to filter drug candidates

Call open chromatin peaks from ATAC-seq alignments with MACS3

Check ATAC-seq library quality with TSS enrichment, FRiP and fragment sizes

Find differentially accessible chromatin regions between ATAC-seq conditions

Detect transcription factor footprints in ATAC-seq data with TOBIAS

Find transcription factor motifs with variable accessibility using chromVAR

Map nucleosome positions and nucleosome free regions from ATAC-seq fragments

Basecall raw Nanopore POD5 signal into reads with Dorado on a GPU

Process many sequence files in batch with Biopython, merging and splitting records

Test whether a GWAS and eQTL signal share one causal variant with coloc

Narrow GWAS loci to likely causal variants with SuSiE and FINEMAP

Estimate causal effects between traits with Mendelian randomization using TwoSampleMR

Preprocess cell free DNA reads with short fragment alignment and UMI dedup

Compare ChIP-seq binding between conditions with DiffBind and replicate samples

Find enriched transcription factor motifs in ChIP-seq peaks with HOMER and MEME

Annotate ChIP-seq peaks to promoters, introns and nearest genes with ChIPseeker

Call narrow and broad ChIP-seq peaks with MACS3 using input controls

Check ChIP-seq quality with FRiP, cross correlation and IDR replicate concordance

Identify super-enhancer domains from H3K27ac ChIP-seq with ROSE

Plot ChIP-seq signal heatmaps, profiles and genome browser tracks

Map rsIDs to genomic coordinates and pull dbSNP variant annotations

Check gnomAD population allele frequencies to judge how rare a variant is

Annotate variants with ClinVar, gnomAD, COSMIC and dbSNP data in one query

Extract mutational signatures from somatic variants with SigProfiler

Read and write gzip and BGZF compressed sequence files with Biopython

Build sample specific consensus FASTA sequences by applying VCF variants

Annotate copy number calls with affected genes, pathways and clinical notes

Plot genome wide copy number profiles and sample heatmaps for publication

Detect copy number variants from exome or panel data with CNVkit

Call somatic and germline copy number variants with the GATK workflow

Quantify base and prime editing outcomes, bystander edits and indel rates

Correct batch effects when combining pooled CRISPR screens across batches

Measure indel and HDR editing efficiency from amplicon sequencing with CRISPResso2

Call essential and resistance genes from CRISPR screen counts with MAGeCK and BAGEL2

Model sgRNA efficacy and gene essentiality across several CRISPR knockout screens

Design custom sgRNA libraries with selection, controls and oligo ordering

Rank genes in pooled CRISPR knockout screens with MAGeCK count analysis

Check library representation and replicate correlation before calling hits

Run differential expression on RNA-seq counts with DESeq2 in R

Run differential expression on RNA-seq counts with edgeR and quasi likelihood tests

Filter, annotate and export DESeq2 or edgeR differential expression results

Plot MA plots, dispersion estimates and sample heatmaps for DE results