Tagged bioinformatics

Predict protein and complex structures with ESMFold, AlphaFold and Boltz

Transform, renumber and clean protein structures in place with Bio.PDB

Prepare protein structures for docking and MD with hydrogens and protonation

Judge protein model reliability from resolution, B-factors and MolProbity scores

Run flux balance analysis and flux variability on genome-scale metabolic models

Predict gene essentiality and synthetic lethality in metabolic models with COBRApy

Build draft genome-scale metabolic models from genomes with CarveMe and gapseq

Validate and gap-fill genome-scale metabolic models with memote and COBRApy

Assemble TCR and BCR clonotypes from V(D)J reads with MiXCR presets

Integrate single-cell TCR and BCR data with gene expression using scirpy

Test rhythmicity at 24-hour period in time-series omics with cosinor and JTK

Compare how rhythms change between conditions in circadian and time-series omics

Discover periodic signals of unknown period in irregular omics time series

Cluster temporally variable genes by trajectory shape with Mfuzz and tslearn

Infer time-delayed gene regulatory edges from bulk time-series expression

Model smooth and abrupt temporal trajectories in time-resolved omics data

Translate DNA to protein with NCBI codon tables and find six-frame ORFs

Estimate ctDNA tumor fraction from shallow whole-genome sequencing with ichorCNA

Query UniProt for protein sequences, annotations, GO terms and ID mappings

Call germline variants from BAM files with bcftools and choose a caller

Classify variant pathogenicity with ACMG AMP germline and somatic tier guidance

Call SNPs and indels with Google DeepVariant CNN models for many platforms

Filter variant callsets with VQSR, hard filters and Ti/Tv quality checks

Joint genotype per-sample gVCFs into a cohort callset with GATK or GLnexus

Call structural variants from short and long reads with Manta, DELLY and GRIDSS

Author portable bioinformatics pipelines in CWL with cwltool

Run the bulk ATAC-seq pipeline from FASTQ to differential accessibility

Run post-GWAS causal inference from heritability to Mendelian randomization

Run the ChIP-seq pipeline from FASTQ to blacklist-filtered annotated peaks

Plan CRISPR editing experiments from guide design to validated constructs

Run pooled and single-cell CRISPR screen analysis from FASTQ to hit genes

Run germline variant calling from FASTQ to filtered, benchmarked VCF

Run genome annotation from assembled contigs to functional annotation

Run de novo genome assembly from profiling and QC to scaffolded assemblies

Run gene regulatory network inference from single-cell data to perturbations

Run Hi-C analysis from FASTQ to compartments, TADs and chromatin loops

Run cell-free DNA pipelines from plasma sequencing to tumor monitoring

Run long-read structural variant calling and benchmarking end to end

Run genome-scale metabolic modeling from protein FASTA to flux predictions

Integrate RNA, protein and methylation data from the same samples with MOFA2 or DIABLO

Process 10x Multiome RNA and ATAC data from Cell Ranger ARC to an annotated object

Trace pathogen outbreaks from isolate genomes to transmission networks

Turn MaxQuant, FragPipe or DIA-NN output into differential protein abundance results

Run bulk RNA-seq differential expression from FASTQ to an annotated gene table

Run single-cell RNA-seq from Cell Ranger output to annotated cell types

Run small RNA-seq from FASTQ to differential miRNA and target analysis

Find differential alternative splicing in bulk RNA-seq with rMATS and leafcutter

Build TCR clonotypes, diversity and lineages from repertoire FASTQ with MiXCR

Find temporal gene modules and pathway enrichment in bulk time-course data