• Stars
    star
    6
  • Rank 2,539,965 (Top 51 %)
  • Language
    R
  • License
    BSD 3-Clause "New...
  • Created over 3 years ago
  • Updated 3 months ago

Reviews

There are no reviews yet. Be the first to send feedback to the community and the maintainers!

Repository Details

ABSOLUTE source code that works with allelic copy ratio on both hg19 and hg38

More Repositories

1

rnaseqc

Fast, efficient RNA-Seq metrics for quality control and process optimization
C++
146
star
2

SignatureAnalyzer

Updated SignatureAnalyzer-GPU with mutational spectra & RNA expression compatibility.
Python
71
star
3

deTiN

DeTiN is designed to measure tumor-in-normal contamination and improve somatic variant detection sensitivity when using a contaminated matched control.
Jupyter Notebook
49
star
4

MutSig2CV

MutSig2CV from Lawrence et al. 2014
MATLAB
30
star
5

dalmatian

dalmatian is a collection of high-level companion functions for Firecloud and FISS.
Python
18
star
6

CPTAC_PanCan_PTM_2023

Jupyter Notebook
14
star
7

scrinvex

Single Cell RNA Intron-Exon counting
C++
11
star
8

Haradhvala_et_al_2022

Jupyter Notebook
8
star
9

10x-cd45-isoform-quantification

Jupyter Notebook
8
star
10

CLUMPS-PTM

CLUMPS adapted to post-translational modifications.
Python
7
star
11

canine

A modular, high-performance computing solution to run jobs using SLURM
Python
6
star
12

AnnoMate

Review anything (purities, mutations, etc) within a jupyter notebook with plotly dash and jupyter widgets
Python
6
star
13

Boiarsky-etal-2022

Code to reproduce methods & results from Boiarsky et. al., Nature Communications 2022
Jupyter Notebook
6
star
14

igv_remote

A Python interface for interacting with IGV desktop over a port using IGV batch commands
Python
5
star
15

SMM_clustering_2020

Repo for analysis of SMM DNA + RNA data.
Jupyter Notebook
3
star
16

LUAD_subtypes

HTML
3
star
17

CApy

Cancer Analysis tools in Python
Python
3
star
18

CLUMPS

Python
3
star
19

rnaseqc2-paper

RNA-SeQC 2 manuscript materials
Jupyter Notebook
3
star
20

pathway_based_biomarker

MATLAB
3
star
21

CLUMPS2

Re-factored code for CLUMPS.
Python
2
star
22

mudi

A collection of downstream python single-cell utilities.
Python
2
star
23

mutect-benchmark

Code repo for master thesis
Jupyter Notebook
2
star
24

MSMuTect2

Accurate detection of somatic MS (microsatellite) indels.
Python
2
star
25

CLLmap

R
2
star
26

PurityReviewer

Suite of purity reviewers and review components
Python
2
star
27

igv_gdc_buddy

stream & update gdc signed url to IGV
Python
2
star
28

gbm_icb_manuscript

Code for reproducing the figures in the Ghannam et al. GBM ICB manuscript
Jupyter Notebook
1
star
29

GISTIC2_postprocessing

The repo contains codes (in matlab) to force call GISTIC2 driver events at sample level
MATLAB
1
star
30

lapdog

A python module, CLI, and browser-based UI to run jobs outside of Firecloud
Python
1
star
31

MSMuTect1

Shell
1
star
32

MSMuTect

Calling indels in microsatellite loci
1
star
33

REBC_tools

Repo for code & tasks used for REBC analysis
MATLAB
1
star
34

AsymTools2

AsymTools is a package for analyzing transcriptional and replicative mutational strand asymmetries in cancer sequencing datasets.
MATLAB
1
star
35

MSMutSig

Detects loci with a significantly higher-than-expected frequency of somatic MS (microsatellite) indels.
R
1
star
36

PhylogicNDTReviewer

Interactive app to review Phylogic solutions and data.
Jupyter Notebook
1
star
37

bladder_cancer_classifier

R
1
star
38

DLBclass-tool

Jupyter Notebook
1
star