Biology & Genomics

Call copy number variants from exome and genome data with CNVkit

Normalize read depth and segment copy ratios with CBS and HMM methods

Resolve focal amplifications and extrachromosomal DNA with AmpliconArchitect

Call somatic and germline copy number variants with GATK standard workflows

Find recurrent driver copy number alterations across a tumor cohort with GISTIC2

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

Design covalent inhibitors and warheads for cysteine and other residues

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

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

Filter, annotate and export DESeq2 and edgeR differential expression results

Plot DE diagnostics like MA plots, volcano plots and sample PCA from DESeq2

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

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

Find differential expression across time series with LRT and spline models

Detect differential alternative splicing between conditions with rMATS and MAJIQ

Mark and remove PCR and optical duplicates in alignments with samtools markdup

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

Find adaptive loci with genotype-environment association tests like LFMM2

Delimit species from molecular data with ASAP, mPTP and GMYC

Query the Ensembl REST API for genes, sequences, variant effects and orthologs

Fetch GenBank and GenPept records and summaries from NCBI with Biopython

Find cross-database links between NCBI records like genes, proteins and papers

Search NCBI databases with field-qualified queries and the history server

Find differential m6A methylation between conditions from MeRIP-seq data

Call m6A RNA methylation peaks from MeRIP-seq IP and input pairs

Detect m6A RNA modifications from Nanopore direct RNA sequencing with m6Anet

Align and QC MeRIP-seq IP and input libraries with replicate concordance checks

Plot RNA modification metagene profiles, peak heatmaps and browser tracks

Balance batches against biology so genomics experiments stay estimable

Control false discovery rates across thousands of genomic tests

Calculate power for high-dimensional genomics experiments with count models

Design genomics experiments with randomization, blocking and proper replication