Tagged bioinformatics

Integrate scRNA-seq batches with Harmony, scVI and fastMNN while keeping biology

Label single cell types automatically with CellTypist, SingleR and Azimuth

Infer ligand receptor cell communication networks with CellChat and LIANA

Cluster single cell data with PCA, Leiden and UMAP in Seurat or Scanpy

Load 10X data and convert between h5ad, RDS, Seurat and AnnData objects

Remove doublet cells from scRNA-seq data with Scrublet and scDblFinder

Reconstruct cell lineage trees from CRISPR barcodes or mitochondrial mutations

Find cluster marker genes and assign cell type labels in Seurat or Scanpy

Infer metabolite mediated signaling between cell types from scRNA-seq with MeboCost

Analyze CITE-seq, Multiome and other multi modal single cell datasets

Analyze Perturb-seq and CROP-seq pooled CRISPR screens with single cell RNA

Filter, normalize and select genes for single cell RNA-seq in Seurat or Scanpy

Analyze single cell ATAC-seq with Signac or ArchR including peaks and motifs

Analyze alternative splicing per cell with BRIE2 or leafcutter2

Infer developmental trajectories and RNA velocity from single cell data

Plot gene expression and clusters over histology images for spatial data

Check RNA-seq data quality for splicing with junction saturation and RSeQC

Quantify splicing PSI values from RNA-seq with SUPPA2 or rMATS-turbo

Predict protein and complex structures with AlphaFold3, ESMFold, Chai-1 and Boltz

Combine single cell TCR and BCR data with gene expression using scirpy

Estimate circulating tumor DNA fraction from shallow whole genome sequencing

Call SNPs and indels from aligned reads with bcftools mpileup and call

Interpret variant pathogenicity with ClinVar and ACMG guidelines for diagnostics

Call germline variants with the DeepVariant deep learning caller

Filter SNP and indel calls with VQSR, hard filters and bcftools expressions

Jointly genotype GVCFs across cohorts with GATK CombineGVCFs and GenotypeGVCFs

Call structural variants from short reads with Manta, Delly and LUMPY

Dock compound libraries into a protein site with AutoDock Vina and rank them

Run multi step biomedical research tasks across genomics and drug discovery

Predict protein complex and protein ligand structures with the open Boltz model

Design all atom protein binders around ligands with the BoltzGen diffusion model

Remove batch effects from merged bulk RNA-seq cohorts with pyComBat

Estimate cell fractions in bulk RNA-seq and generate synthetic single cell data

Run PyDESeq2 differential expression with ID mapping and fold change filters

Run bulk RNA-seq differential expression and enrichment in omicverse

Build co-expression modules and hub genes from expression matrices with WGCNA

Fill gaps in single cell trajectories by generating cells from bulk RNA-seq

Query cBioPortal for cancer mutations, copy number, expression and survival data

Optimize cell free protein synthesis yield and troubleshoot aggregation

Query CELLxGENE Census single cell data by cell type, tissue and disease

Predict protein complex and ligand structures with the Chai-1 model

Run SRA download, FASTQ QC, STAR alignment and kallisto quantification pipelines

Search protein structures by 3D similarity in PDB and AlphaFold databases with Foldseek

Run quick BLAST and gene lookups across Ensembl, AlphaFold and Enrichr with gget

Load pathway gene sets correctly and run GSEA enrichment in OmicVerse

Query GTEx for tissue expression, eQTLs and sQTLs to link variants to genes

Search nine genomic databases for variant associations across GWAS and eQTL sources

Query InterPro for protein domain, family and functional site annotations

Rank protein binder designs from AlphaFold, Boltz and BindCraft outputs by ipSAE