mskilab/bamUtils

Stars
3
Rank 3,963,521 (Top 79 %)
Language
R
Created over 8 years ago
Updated almost 2 years ago

mskilab/bamUtils

mskilab

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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

dryclean

Irons out wrinkles in noisy coverage data using robust PCA

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.

chromunity

Discovery of communities in Pore-C concatemers

gUtils

Utility functions to extend and optimize GenomicRanges functionality.

skitools

General purpose mskilab R tools

Ppurple

Probabilistic purity ploidy estimation

Jupyter Notebook

MuTrix

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

bambi

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

RSeqLib

R interface to SeqLib

loosends

Loose ends in cancer genome structure

pgv

Pan gGnome Viewer