Biology & Genomics

Filter imputed variants with quality metrics like R2, INFO and DR2

Choose and prepare reference panels for phasing and imputation by ancestry

Run Bayesian phylogenetics with MrBayes and BEAST2 and check convergence

Build model-corrected distance matrices and distance trees with Biopython and ape

Estimate divergence times with molecular clocks, calibrations and BEAST2

Infer maximum-likelihood trees with IQ-TREE 2 and model selection

Estimate species trees from gene trees with ASTRAL under coalescent models

Read, write and convert phylogenetic tree files while keeping annotations

Edit tree structure and root phylogenies with Biopython Bio.Phylo

Draw and export phylogenetic trees with matplotlib, ggtree and iTOL

Generate samtools mpileup data for variant calling and allele frequencies

Run single-variant GWAS with plink2, GEMMA, BOLT-LMM, SAIGE and regenie

Compute linkage disequilibrium, prune variants and clump GWAS hits

Convert and QC PLINK genotype filesets for missingness, MAF and HWE

Infer population structure with PCA, ADMIXTURE and FST statistics

Test rare variants by gene with burden, SKAT and ACAT aggregation tests

Analyze population genetics in Python with scikit-allel diversity and FST statistics

Scan genomes for selection with SFS tests, iHS, XP-EHH and FST statistics

Check docked protein-ligand poses for physical validity with PoseBusters

Design and rank PCR primer pairs for a template with primer3-py

Check whether PCR primer pairs amplify only the intended genome target

Check primers for hairpins, dimers and 3-prime end stability with primer3-py

Design qPCR primers and TaqMan probes with primer3-py internal oligo settings

Design PROTACs and molecular glues with ligase choice, linkers and ternary models

Load mass spec data and remove decoys, contaminants and ambiguous protein IDs

Analyze DIA proteomics with DIA-NN, Spectronaut and OpenSWATH peak scoring

Test differentially abundant proteins with limma, DEqMS and MSstats

Match MS/MS spectra to peptides with target-decoy FDR control

Group proteins from peptide evidence and control protein-level FDR

Run quality control on bottom-up proteomics data from raw signal to replicates

Analyze phosphoproteomics and PTM sites with localization control and MSstatsPTM

Quantify protein abundance from label-free, TMT and SILAC mass spec data

Build DIA spectral libraries from DDA, chromatograms and predicted spectra

Build QSAR models with applicability domain checks and scaffold-balanced splits

Enumerate virtual compound libraries from reaction SMARTS with RDKit

Align DNA short reads with Bowtie2 end-to-end or local mode for ChIP-seq

Align DNA reads to a reference with bwa-mem2 for variant calling pipelines

Align RNA-seq reads with HISAT2 for splice-aware, low-memory mapping

Align RNA-seq reads with STAR using splice junction databases and two-pass mode

Remove sequencing adapters and primers from FASTQ reads with Cutadapt

Detect cross-species, vector and cross-sample contamination in sequencing reads

Preprocess Illumina FASTQ in one pass with fastp adapter, quality and poly-G trimming

Filter reads by quality, length, N content and complexity with Trimmomatic and fastp

Generate FASTQ quality reports with FastQC and MultiQC across many samples

Run RNA-seq post-alignment QC for strandedness, coverage bias and rRNA contamination

Collapse UMI reads to molecules with umi_tools and fgbio consensus calling

Read FASTA, FASTQ, GenBank and ABI sequence files with Biopython SeqIO

Build consensus sequences and index reference files with samtools

Detect distant protein homologs with profile and structure methods beyond BLAST