St. Jude Children's Research Hospital

St. Jude Children's Research Hospital's repositories

learngenomics.dev

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

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ROSE

ROSE: RANK ORDERING OF SUPER-ENHANCERS

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CICERO

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

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ChIPseqSpikeInFree

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

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RNAIndel

Somatic indel discovery tool for tumor RNA-Seq data.

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proteinpaint

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

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indelPost

Python library for simple and complex indels.

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PrimerTK

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

Language:PythonApache-2.011 4 10

punctatools

Detection, colocalization, and quantification of spots / puncta

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DeepBrainIPP

Automated Brain Structures Segmentation Framework

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fuzzion2

fuzzy fusion finder

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seaseq

Abraham's lab - ChipSeq Pipeline

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XenoCP

A cloud-based tool for mouse read cleansing in xenograft samples

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BAM2GFF

BAMtoGFF, matrix density, plot visualizations

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RNApeg

RNA junction finder

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teltale

Compute telomeric read fractions in a BAM file.

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ChIP-Seq

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doCNA

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TALL-example

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DeepMRIRec

Deep learning based pipeline for MRI reconstruction

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WARDEN

Source code for the WARDEN DNAnexus apps

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Semisupervised_Learning

Development of an approach using semisupervised learning and multinomial logistic regression to label methylation samples to boost

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am_utils

Some useful functions

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cosima

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dab_detector

Scripts and classes for DAB plaque detection

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Dowen_Fan

Abraham lab ChIA-PET analysis pipeline

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intake_io

Image-focused IO for Python using intake and xarray

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Mouse_Survival

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SICER2

sicer2

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SVIndelGenotyper

Analysis of error profiles of Indels and structural variants in deep sequencing data

Language:PythonApache-2.0020