stjude Goto Github PK

am_utils

Some useful functions

bam2gff

BAMtoGFF, matrix density, plot visualizations

chip-seq

chipseqspikeinfree

A Spike-in Free ChIP-Seq Normalization Approach for Detecting Global Changes in Histone Modifications

cicero

CICERO: a versatile method for detecting complex and diverse driver fusions using cancer RNA sequencing data.

cis-x

Search for activating regulatory variants in the tumor genome

cosima

csp

validation and detection of heteroresistance in staphylococci and related features using cumulative survival profiling

dab_detector

Scripts and classes for DAB plaque detection

deepbrainipp

Automated Brain Structures Segmentation Framework

deepmrirec

Deep learning based pipeline for MRI reconstruction

docna

dowen_fan

Abraham lab ChIA-PET analysis pipeline

episomizer

Constuct Extrachromosomal Circular DNA using Whole Genome Sequencing Data

explore-r

exploreapi

R package for accessing explore.pediatriccancergenomeproject.org data programatically through R

fuzzion

Fuzzy fusion finder for next generation sequencing data.

fuzzion2

fuzzy fusion finder

gpfscode

Data mining and analysis of GPFS client metrics.

indelpost

Python library for simple and complex indels.

intake_io

Image-focused IO for Python using intake and xarray

learngenomics.dev

A guided, intuitive introduction to genomics for software engineers. Curated by the community.

lsfcode

Software for managing HPC infrastructure via LSF

mouse_survival

phoenix

Phoenix job manager

primertk

A toolkit to design standard primers, multiplexed primers, and primers around SV's

proteinpaint

Data visualization and analysis framework focused on phenotype-molecular data integration at cohort level.

punctatools

Detection, colocalization, and quantification of spots / puncta

rnaindel

Somatic indel discovery tool for tumor RNA-Seq data.

rnapeg

RNA junction finder