Biology & Genomics

Import count matrices from featureCounts, STAR, Salmon and 10X into R or Python

Map gene IDs across Ensembl, Entrez, HGNC, UniProt and RefSeq systems

Join sample metadata to count matrices and build correct design matrices

Normalize and transform RNA-seq counts with TMM, VST and log-CPM

Store and operate on sparse single-cell expression matrices efficiently

Work with FASTQ quality scores and convert Phred encodings with Biopython

Filter FASTA and FASTQ records by length, GC content, motifs and IDs

Normalize CyTOF bead signal drift and harmonize cytometry batches

Cluster flow and mass cytometry cells into types with FlowSOM and PhenoGraph

Correct fluorophore spillover and apply logicle or arcsinh transforms to cytometry

Run flow and mass cytometry quality control for anomalies, drift and dead cells

Test which cell populations shift in abundance or marker levels with diffcyt

Detect and remove doublets from flow and mass cytometry data

Read and write FCS files and parse FlowJo, Cytobank and Diva workspaces

Define cell populations with manual and automated gating in cytometry data

Convert sequence files between FASTA, FASTQ, GenBank and EMBL formats

Run relative and absolute binding free energy calculations with OpenFE and FEP

Call germline variants with GATK HaplotypeCaller and GVCF joint genotyping

Build weighted gene co-expression networks to find modules and hub genes

Compare gene networks between conditions to find rewired gene relationships

Infer gene regulatory networks with ARACNe, GENIE3 and VIPER activity

Build enhancer-driven gene regulatory networks from scRNA-seq and ATAC-seq

Simulate transcription factor knockdowns in silico and predict perturbation responses

Infer single-cell transcription factor regulons and activity with pySCENIC

Design novel molecules with REINVENT and diffusion models for multi-goal optimization

Score genome annotation completeness with BUSCO, OMArk and CheckM2

Transfer gene annotations between genome assemblies with liftover and Liftoff

Predict eukaryotic gene structures with BRAKER3, GALBA and Helixer

Assign GO terms, protein domains and KEGG orthologs to predicted proteins

Find noncoding RNAs like tRNA, rRNA and riboswitches with Infernal and tRNAscan

Annotate bacterial genomes and plasmids with Bakta or Prokka for submission

Mask and classify repeats and transposable elements with RepeatModeler2 and EDTA

Polish draft genome assemblies with Racon, medaka and Polypolish to raise accuracy

Assess genome assembly contiguity, completeness and correctness with BUSCO and Merqury

Find and remove foreign sequence contamination in genome assemblies with FCS-GX

Estimate genome size, heterozygosity and ploidy from reads with GenomeScope2

Assemble haplotype-resolved and T2T genomes from PacBio HiFi reads with hifiasm

Assemble genomes from noisy Nanopore or PacBio CLR reads with Flye and Canu

Assemble metagenomes into MAGs from long or short reads with metaFlye and MEGAHIT

Scaffold contigs into chromosome-scale sequences with Hi-C data using YaHS

Assemble genomes from Illumina short reads with SPAdes, MEGAHIT and Unicycler

Design base editor guides with the target base set inside the editing window

Design and rank CRISPR guide RNAs for knockout with PAM scanning and filters

Design donor templates for precise CRISPR knock-ins with homology arms and blocking edits

Predict CRISPR off-target sites genome-wide with CFD scores and variant screening

Design pegRNAs and nicking guides for prime editing with PBS and RTT tuning

Read and convert BED interval files with coordinate conventions handled

Generate and normalize bedGraph coverage tracks with bedtools and deepTools

Read and write bigWig signal tracks with pyBigWig and UCSC tools