getzlab/PhylogicNDTReviewer getzlab/PhylogicNDTReviewer

  • Stars
    star
    1
  • Language
    Jupyter Notebook
  • License
    MIT License
  • Created about 2 years ago
  • Updated 4 months ago
Twitter logo Share LinkedIn logo Share Facebook logo Share
getzlab/PhylogicNDTReviewer
github

getzlab

Reviews

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

Repository Details

Interactive app to review Phylogic solutions and data.

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

ABSOLUTE

ABSOLUTE source code that works with allelic copy ratio on both hg19 and hg38
R
6
star
12

canine

A modular, high-performance computing solution to run jobs using SLURM
Python
6
star
13

AnnoMate

Review anything (purities, mutations, etc) within a jupyter notebook with plotly dash and jupyter widgets
Python
6
star
14

Boiarsky-etal-2022

Code to reproduce methods & results from Boiarsky et. al., Nature Communications 2022
Jupyter Notebook
6
star
15

igv_remote

A Python interface for interacting with IGV desktop over a port using IGV batch commands
Python
5
star
16

SMM_clustering_2020

Repo for analysis of SMM DNA + RNA data.
Jupyter Notebook
3
star
17

LUAD_subtypes

HTML
3
star
18

CApy

Cancer Analysis tools in Python
Python
3
star
19

CLUMPS

Python
3
star
20

rnaseqc2-paper

RNA-SeQC 2 manuscript materials
Jupyter Notebook
3
star
21

pathway_based_biomarker

MATLAB
3
star
22

CLUMPS2

Re-factored code for CLUMPS.
Python
2
star
23

mudi

A collection of downstream python single-cell utilities.
Python
2
star
24

mutect-benchmark

Code repo for master thesis
Jupyter Notebook
2
star
25

MSMuTect2

Accurate detection of somatic MS (microsatellite) indels.
Python
2
star
26

CLLmap

R
2
star
27

PurityReviewer

Suite of purity reviewers and review components
Python
2
star
28

igv_gdc_buddy

stream & update gdc signed url to IGV
Python
2
star
29

gbm_icb_manuscript

Code for reproducing the figures in the Ghannam et al. GBM ICB manuscript
Jupyter Notebook
1
star
30

GISTIC2_postprocessing

The repo contains codes (in matlab) to force call GISTIC2 driver events at sample level
MATLAB
1
star
31

lapdog

A python module, CLI, and browser-based UI to run jobs outside of Firecloud
Python
1
star
32

MSMuTect1

Shell
1
star
33

MSMuTect

Calling indels in microsatellite loci
1
star
34

REBC_tools

Repo for code & tasks used for REBC analysis
MATLAB
1
star
35

AsymTools2

AsymTools is a package for analyzing transcriptional and replicative mutational strand asymmetries in cancer sequencing datasets.
MATLAB
1
star
36

MSMutSig

Detects loci with a significantly higher-than-expected frequency of somatic MS (microsatellite) indels.
R
1
star
37

bladder_cancer_classifier

R
1
star
38

DLBclass-tool

Jupyter Notebook
1
star