mskilab-org

JaBbA

MIP based joint inference of copy number and rearrangement state in cancer whole genome sequence data.

gGnome

R API for browsing, analyzing, and manipulating reference-aligned genome graphs in a GenomicRanges framework

fishHook

R package for applying Gamma-Poisson regression to identify statistical enrichment or depletion of somatic mutations in regions after correcting for genomic covariates.

gGnome.js

gTrack

R package for visualizing complex and multi-track 1D and 2D genomic data in GenomicRanges framework

nf-jabba

dryclean

Irons out wrinkles in noisy coverage data using robust PCA

chromunity

Discovery of communities in Pore-C concatemers

pgv

Pan gGnome Viewer

gUtils

Utility functions to extend and optimize GenomicRanges functionality.

Flow

R-based genomics workflow management

fragCounter

GC and mappability corrected fragment coverage for paired end whole genome sequencing

GxG

Scalable GenomicRanges based class for storing, manipulating, and querying genomic matrices and pairwise features.

skitools

General purpose mskilab R tools

bamUtils

loosends

Loose ends in cancer genome structure

casereport

Genome graph based case reports

readsupport

Computes read support for arbitrary junctions and contigs for single, paired-end, and linked reads

skidb

Reference data utilities for mskilab

skilift

An R interface for loading and modifying PGV datafiles

.github

case-report

Genomic case report

case-report-api

The API service to facilitate the case-report frontend application

ffTrack

GenomicRanges based R class for fast, out-of-core memory access and storage of numeric and character data that is a function of genomic position.

FlowExample

Using Flow within NYGC Mskilab

gChain

R class for representing composable syntenic mappings between coordinates of 'omes and allowing nimble lift-over of genomic features and signals through these mappings within a GenomicRanges based framework.

ggSim

comprehensive simulation of whole-genome graphs (coverage, junctions, allelic and SNP phasing)

homeology

nf-casereports

End to end cancer genomics pipeline

pgv-api

The API service to facilitate the pgv frontend application