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bambi

indexed file format for barcoded BAMs with API for converting and accessing alignment records

bamutils

case-report

Genomic case report

case-report-api

The API service to facilitate the case-report frontend application

casereport

Genome graph based case reports

chromunity

Discovery of communities in Pore-C concatemers

dryclean

Irons out wrinkles in noisy coverage data using robust PCA

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.

fishhook

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

flow

R-based genomics workflow management

flowexample

Using Flow within NYGC Mskilab

fragcounter

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

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.

ggnome

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

ggnome.js

ggsim

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

gtrack

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

gutils

Utility functions to extend and optimize GenomicRanges functionality.

gxg

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

homeology

jabba

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

loosends

Loose ends in cancer genome structure

mutrax

R visualization package for plotting human mutation data on a UniProt model along with other event and patient level tracks.

mutrix

R package for visualizing matrices of mutations and other patient level features across patient sets

nf-casereports

End to end cancer genomics pipeline

nf-jabba

pgv

Pan gGnome Viewer

pgv-api

The API service to facilitate the pgv frontend application

ppurple

Probabilistic purity ploidy estimation