stjude/sjcb_python_utils

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Created over 4 years ago
Updated over 4 years ago

stjude/sjcb_python_utils

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St Jude Computational Biology Python utility functions

learngenomics.dev

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

ROSE

ROSE: RANK ORDERING OF SUPER-ENHANCERS

CICERO

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

ChIPseqSpikeInFree

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

RNAIndel

Somatic indel discovery tool for tumor RNA-Seq data.

fqlib

Library for manipulating Illumina generated FastQ files

cis-x

Search for activating regulatory variants in the tumor genome

proteinpaint

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

indelPost

Python library for simple and complex indels.

PrimerTK

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

punctatools

Detection, colocalization, and quantification of spots / puncta

Jupyter Notebook

Episomizer

Constuct Extrachromosomal Circular DNA using Whole Genome Sequencing Data

DeepBrainIPP

Automated Brain Structures Segmentation Framework

fuzzion2

fuzzy fusion finder

seaseq

Abraham's lab - ChipSeq Pipeline

XenoCP

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

teltale

Compute telomeric read fractions in a BAM file.

RNApeg

RNA junction finder

sjcloud-data-transfer-app

Application to securely upload data to and download data from St. Jude Cloud Platform.

TALL-example

ChIP-Seq

doCNA

WARDEN

Source code for the WARDEN DNAnexus apps