tgen/ppmi-rnaseq-wb-paper tgen/ppmi-rnaseq-wb-paper

  • Stars
    star
    2
  • Language
    R
  • Created almost 4 years ago
  • Updated almost 4 years ago
Twitter logo Share LinkedIn logo Share Facebook logo Share
tgen/ppmi-rnaseq-wb-paper
github

tgen

Reviews

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

Repository Details

code used to generate figures for the ppmi whole blood rnaseq paper

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

MMRF_CoMMpass

A collection of scripts used to recreate files and graphs used in the MMRF CoMMpass analysis.
Shell
18
star
4

bisbee

alternative splicing analysis pipeline
Python
17
star
5

phoenix

Jetstream compatible workflow template supporting comprehensive analysis of human sequencing data against GRCh38
EJS
17
star
6

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
7

LumosVar

MATLAB
11
star
8

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
9

vcfMerger2

Dynamic vcfMerger for 2 to N somatic variants vcf files
Python
5
star
10

tCoNuT

TGen Copy Number Tool
MATLAB
4
star
11

Institutional_Instructions

Description of institutional rules and regulations regarding the usage of github, plus usage guidelines
Shell
3
star
12

jetstream_resources

Collection of scripts and README files tracking the source and generation of reference genomes and annotation files
Shell
3
star
13

gvm

Replacement for LumosVar preprocess step
C
2
star
14

ppmi-qc-wt-paper

QC of whole blood whole transcriptome for PPMI
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