Tagged bioinformatics

Discover RNA-binding protein motifs from CLIP peaks and crosslink sites

Call RNA-binding sites from CLIP-seq data with CLIPper, PureCLIP and CTK

Find differentially bound RNA-binding regions between CLIP-seq conditions

Map m6A RNA methylation at single-nucleotide resolution with miCLIP and GLORI

Profile RNA-binding protein targets without antibodies using STAMP and TRIBE

Reconstruct ancestral sequences and traits across a phylogenetic tree

Project gene annotations between genomes with TOGA, CESAR and LiftOff

Model gene family gains and losses across species with CAFE5

Reconcile gene trees with species trees for duplication, transfer and loss

Compute genome distances and assign species with ANI, AAI and GTDB-Tk

Detect horizontal gene transfer from composition and phylogenetic conflicts

Detect introgression between populations with D-statistics and TreeMix

Infer orthologs and gene families across species with OrthoFinder

Build and analyze pangenomes for core and accessory gene content

Detect positive selection in codon data with PAML and HyPhy site models

Find syntenic blocks and rearrangements between genomes with MCScanX and SyRI

Build whole-genome alignments with Cactus, LASTZ and minimap2

Date whole-genome duplication events and trace their ancestry with wgd

Annotate copy number segments with genes, dosage scores and cancer drivers

Call copy number variants from exome and genome data with CNVkit

Resolve focal amplifications and extrachromosomal DNA with AmpliconArchitect

Score homologous recombination deficiency from tumor scar metrics with scarHRD

Resolve subclonal copy number and whole-genome doubling with Battenberg and MEDICC2

Identify essential genes from CRISPR knockout screens with BAGEL2

Analyze base-editing screens for variant function with editing window math

Correct batch effects in CRISPR screens with ComBat, RUV and SVA

Design and analyze paired and multiplex combinatorial CRISPR screens

Correct copy-number artifacts that make amplified loci look essential in CRISPR screens

Quantify CRISPR editing outcomes from amplicon reads with CRISPResso2

Find synthetic-lethal and resistance genes in CRISPR drug screens with drugZ

Pick hit-calling methods for pooled CRISPR screens and reconcile disagreements

Design and analyze in vivo CRISPR screens in tumor models and organoids

Run JACKS to separate gene essentiality from guide efficacy in CRISPR screens

Design pooled sgRNA libraries for knockout, CRISPRi, CRISPRa and base editor screens

Analyze pooled CRISPR screens with MAGeCK RRA and MLE workflows

Analyze Perturb-seq and CROP-seq screens linking guides to single-cell readouts

Design and analyze pooled prime editing screens with pegRNA efficiency models

Check pooled CRISPR screen quality with library representation and replicates

Build circular genome plots with circlize, pyCirclize or Circos

Build genome browser style multi-track figures with coverage, peaks and genes

Plot mutation positions on protein domain maps as lollipop charts

Build volcano and MA plots with LFC shrinkage and FDR thresholds

Correct batch effects in bulk RNA-seq with design matrices, ComBat and RUVSeq

Run bulk RNA-seq differential expression with DESeq2 and LFC shrinkage

Run bulk RNA-seq differential expression with edgeR quasi-likelihood tests

Measure biodiversity with Hill numbers, rarefaction and turnover metrics

Analyze species-environment links with constrained ordination and PERMANOVA

Estimate effective population size and inbreeding for conservation genetics

Turn eDNA metabarcoding reads into species tables with DADA2 and OBITools