Biology & Genomics

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

Analyze CUT&RUN and CUT&Tag data with SEACR, MACS2 and spike-in controls

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

Resolve dbSNP rsIDs, merge histories and variant notation like HGVS and VCF

Query gnomAD allele frequencies, constraint scores and rare variant filters

Annotate variant lists in batch from ClinVar, gnomAD, dbNSFP and CADD

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

Identify direct miRNA targets from AGO and chimeric CLIP-seq reads

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

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

Predict RNA-binding protein sites from sequence with deep learning models

Discover RNA-binding protein motifs from CLIP peaks and crosslink sites

Call RNA-binding sites from CLIP-seq data with CLIPper, PureCLIP and CTK

Preprocess CLIP-seq FASTQ with UMI extraction, trimming and duplicate collapse

Run quality control on CLIP-seq libraries for complexity, FRiP and reproducibility

Detect single-nucleotide crosslink sites from truncations and mutations in CLIP

Find differentially bound RNA-binding regions between CLIP-seq conditions

Map m6A RNA methylation at single-nucleotide resolution with miCLIP and GLORI

Profile RNA-binding protein targets without antibodies using STAMP and TRIBE

Calculate codon adaptation index and optimize coding sequences for expression

Reconstruct ancestral sequences and traits across a phylogenetic tree

Project gene annotations between genomes with TOGA, CESAR and LiftOff

Model gene family gains and losses across species with CAFE5

Reconcile gene trees with species trees for duplication, transfer and loss

Compute genome distances and assign species with ANI, AAI and GTDB-Tk

Detect horizontal gene transfer from composition and phylogenetic conflicts

Detect introgression between populations with D-statistics and TreeMix

Infer orthologs and gene families across species with OrthoFinder

Build and analyze pangenomes for core and accessory gene content

Detect positive selection in codon data with PAML and HyPhy site models

Find syntenic blocks and rearrangements between genomes with MCScanX and SyRI

Build whole-genome alignments with Cactus, LASTZ and minimap2

Date whole-genome duplication events and trace their ancestry with wgd

Read and index gzip, bzip2 and BGZF sequence files with Biopython and samtools

Generate 3D conformer ensembles with RDKit ETKDG and force-field refinement

Generate consensus FASTA sequences by applying VCF variants with bcftools consensus

Infer tumor purity, ploidy and allele-specific copy number with ASCAT and FACETS

Annotate copy number segments with genes, dosage scores and cancer drivers