Biology & Genomics

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

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

Annotate VCF variants with consequences and frequencies using VEP and SnpEff

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

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

Left-align, decompose and normalize indels and multiallelic variants with bcftools

View and query VCF and BCF files and read QUAL, GQ and genotype fields

Merge, split, intersect and subset VCF files with bcftools

Compute VCF quality metrics like Ti/Tv, missingness and HWE with bcftools stats

Run structure-based virtual screening with Vina, GNINA and DiffDock

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

Run biomarker discovery from expression data to validated panels end to end

Run post-GWAS causal inference from heritability to Mendelian randomization

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

Run the full CLIP-seq pipeline from FASTQ to binding sites and motifs

Run copy-number pipelines from BAM to segmented, annotated CNV calls

Plan CRISPR editing experiments from guide design to validated constructs

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

Run cytometry analysis from FCS files to differentially abundant populations

Run eDNA metabarcoding from raw amplicons to community ecology results

Run pipeline from differential expression to pathway enrichment and plots

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 GWAS from genotype QC and imputation to association results

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

Run imaging mass cytometry from raw MCD files to spatial patient analysis

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

Run MeRIP-seq m6A analysis from FASTQ to differential methylation peaks

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

Run untargeted LC-MS metabolomics from feature extraction to pathway mapping

Run shotgun metagenomics from FASTQ to taxonomic and functional profiles

Run bisulfite and EM-seq methylation analysis from FASTQ to DMRs

Run 16S and ITS amplicon analysis from FASTQ to differential abundance

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

Rank neoantigen vaccine candidates from somatic variants with pVACseq and HLA typing

Trace pathogen outbreaks from isolate genomes to transmission networks

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

Run ribo-seq analysis from FASTQ to ORF calling and translation efficiency

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

Call somatic SNVs and indels from tumor-normal pairs with GATK Mutect2

Analyze spatial transcriptomics from Visium, Xenium or MERFISH to spatial domains