Biology & Genomics

Plan iPSC and organoid models with pluripotency markers and differentiation pathways

Combine PDB, AlphaFold, GPCRdb and binding data to validate drug targets

Look up promoters, terminators and reporters in SynBioHub and the iGEM Registry

Run multi-database pathway enrichment across Reactome, KEGG and WikiPathways

Profile a drug target across expression, pathways, variants and druggability

Assess drug and chemical toxicity from adverse outcome pathways and FAERS signals

Predict MHC epitopes and HLA coverage for multi-epitope vaccine candidates

Parse and annotate VCF files and convert SPDI, HGVS, VCF and rsID notation

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

Benchmark variant effect predictors against deep mutational scanning data

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

Predict ADMET properties like hERG, CYP and Ames risk with ADMETlab and chemprop

Trim PCR primers from amplicon BAM files with samtools ampliconclip

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

Build BAI and CSI indexes for BAM and CRAM files for fast region lookup

Read, write and convert multiple sequence alignment files with Biopython

Parse and manipulate multiple sequence alignments with Biopython

Calculate identity, conservation and divergence statistics for sequence alignments

Run multiple sequence alignment with MAFFT, MUSCLE5 or Clustal Omega

Align two DNA, RNA or protein sequences with Biopython PairwiseAligner

Sort BAM files by coordinate or read name with samtools and pysam

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

Trim unreliable columns from multiple sequence alignments with ClipKIT or trimAl

Check alignment quality via insert sizes, pairing, GC bias and strand balance

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

Score transcription factor motif accessibility across samples with chromVAR

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

Compute BAM coverage and QC statistics with samtools flagstat, stats and mosdepth

Bulk-download NCBI sequences and search results with E-utilities and retries

Process many FASTA and FASTQ files in batch with streaming and on-disk indexes

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

Run remote BLAST searches against NCBI with Biopython and read E-values

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