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azimuth

Python 3 version of https://github.com/MicrosoftResearch/Azimuth for use by Prime Medicine (updated dependencies)

configs

Config files used to define parameters specific to compute environments at different Institutions

crispresso2

Analysis of deep sequencing data for rapid and intuitive interpretation of genome editing experiments

deepprime

Source codes and examples for DeepPrime

forgi

An RNA manipulation library.

nf-core-crisprvar

Run CRISPResso on genome editing experiments

nf-nanoseq

Nanopore demultiplexing, QC and alignment pipeline

pridict

Prime editing guide RNA prediction

pridict2

sarek

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

sigprofilerextractor

SigProfilerExtractor allows de novo extraction of mutational signatures from data generated in a matrix format. The tool identifies the number of operative mutational signatures, their activities in each sample, and the probability for each signature to cause a specific mutation type in a cancer sample.

sigprofilerplotting

SigProfilerPlotting provides a standard tool for displaying all types of mutational signatures as well as all types of mutational patterns in cancer genomes. The tool seamlessly integrates with other SigProfiler tools.

sv-callers

Snakemake-based workflow for detecting structural variants in genomic data