• Stars
    star
    18
  • Rank 1,208,065 (Top 24 %)
  • Language
    Shell
  • License
    MIT License
  • Created over 7 years ago
  • Updated over 1 year ago

Reviews

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

Repository Details

A collection of scripts used to recreate files and graphs used in the MMRF CoMMpass analysis.

More Repositories

1

banovichlab

Public code repository for the Banovich Lab at the Translational Genomics Research Institute (TGen).
R
40
star
2

CovGen

Creates a target specific exome_full192.coverage.txt file required by MutSig
Python
20
star
3

bisbee

alternative splicing analysis pipeline
Python
17
star
4

phoenix

Jetstream compatible workflow template supporting comprehensive analysis of human sequencing data against GRCh38
EJS
17
star
5

jetstream

Workflow management system written as a pure Python package and command-line utility. It supports complex workflows modeled as directed- acyclic graphs (DAGs), and execution on batch schedulers
Python
16
star
6

LumosVar

MATLAB
11
star
7

lumosVar2

Calls somatic SNVs, indels, and allelic copy number jointly across multiple samples from the same patient. These can be standard tumor/normal pair, longitudinal samples, primary/met, etc. Can also be used for tumor only calling, ideally with a high tumor content and a low tumor content sample.
MATLAB
10
star
8

vcfMerger2

Dynamic vcfMerger for 2 to N somatic variants vcf files
Python
5
star
9

tCoNuT

TGen Copy Number Tool
MATLAB
4
star
10

Institutional_Instructions

Description of institutional rules and regulations regarding the usage of github, plus usage guidelines
Shell
3
star
11

jetstream_resources

Collection of scripts and README files tracking the source and generation of reference genomes and annotation files
Shell
3
star
12

gvm

Replacement for LumosVar preprocess step
C
2
star
13

ppmi-qc-wt-paper

QC of whole blood whole transcriptome for PPMI
R
2
star
14

ppmi-rnaseq-wb-paper

code used to generate figures for the ppmi whole blood rnaseq paper
R
2
star
15

Post_Medusa_Processing

Shell
1
star
16

pegasusPipe

Shell
1
star
17

tempe

A container focused and streamlined iteration of the Phoenix pipeline
Jinja
1
star
18

seurat

Tumor-Normal Variant Caller
1
star
19

coyote

EJS
1
star
20

medusaPipe

Shell
1
star
21

GemDb

GemDb mongo variants/annotations hub
Python
1
star
22

Neoantigen-pred

Python
1
star