St. Jude Children's Research Hospital

Finding Cures, Saving Children.

Pinned Repositories

ChIPseqSpikeInFree
A Spike-in Free ChIP-Seq Normalization Approach for Detecting Global Changes in Histone Modifications
Language:R30 2 813
CICERO
CICERO: a versatile method for detecting complex and diverse driver fusions using cancer RNA sequencing data.
Language:Perl35 5 4820
cis-x
Search for activating regulatory variants in the tumor genome
Language:Perl14 3 68
indelPost
Python library for simple and complex indels.
Language:C13 3 43
learngenomics.dev
A guided, intuitive introduction to genomics for software engineers. Curated by the community.
Language:JavaScript348 7 1231
PrimerTK
A toolkit to design standard primers, multiplexed primers, and primers around SV's
Language:Python11 4 104
proteinpaint
Data visualization and analysis framework focused on phenotype-molecular data integration at cohort level.
Language:JavaScript17 4 4645
punctatools
Detection, colocalization, and quantification of spots / puncta
Language:Jupyter Notebook10 5 127
RNAIndel
Somatic indel discovery tool for tumor RNA-Seq data.
Language:Python21 10 89
ROSE
ROSE: RANK ORDERING OF SUPER-ENHANCERS
Language:Python41 2 2512

St. Jude Children's Research Hospital's Repositories

stjude/learngenomics.dev
A guided, intuitive introduction to genomics for software engineers. Curated by the community.
Language:JavaScript348 7 1231
stjude/ROSE
ROSE: RANK ORDERING OF SUPER-ENHANCERS
Language:Python41 2 2512
stjude/CICERO
CICERO: a versatile method for detecting complex and diverse driver fusions using cancer RNA sequencing data.
Language:Perl35 5 4820
stjude/ChIPseqSpikeInFree
A Spike-in Free ChIP-Seq Normalization Approach for Detecting Global Changes in Histone Modifications
Language:R30 2 813
stjude/RNAIndel
Somatic indel discovery tool for tumor RNA-Seq data.
Language:Python21 10 89
stjude/proteinpaint
Data visualization and analysis framework focused on phenotype-molecular data integration at cohort level.
Language:JavaScript17 4 4645
stjude/indelPost
Python library for simple and complex indels.
Language:C13 3 43
stjude/PrimerTK
A toolkit to design standard primers, multiplexed primers, and primers around SV's
Language:Python11 4 104
stjude/punctatools
Detection, colocalization, and quantification of spots / puncta
Language:Jupyter Notebook10 5 127
stjude/DeepBrainIPP
Automated Brain Structures Segmentation Framework
Language:Python7 4 03
stjude/fuzzion2
fuzzy fusion finder
Language:C++6 4 02
stjude/seaseq
Abraham's lab - ChipSeq Pipeline
Language:WDL6 3 15
stjude/XenoCP
A cloud-based tool for mouse read cleansing in xenograft samples
Language:Shell5 4 203
stjude/BAM2GFF
BAMtoGFF, matrix density, plot visualizations
Language:Python4 1 01
stjude/RNApeg
RNA junction finder
Language:Perl3 2 72
stjude/teltale
Compute telomeric read fractions in a BAM file.
Language:C++3 2 11
stjude/doCNA
Language:Python2 0 141
stjude/TALL-example
Language:R2 1 00
stjude/DeepMRIRec
Deep learning based pipeline for MRI reconstruction
Language:Jupyter Notebook1 2 02
stjude/WARDEN
Source code for the WARDEN DNAnexus apps
Language:Python1 3 0
stjude/Semisupervised_Learning
Development of an approach using semisupervised learning and multinomial logistic regression to label methylation samples to boost
Language:Jupyter Notebook0 1 00
stjude/am_utils
Some useful functions
stjude/BOUQUET
Language:R
stjude/cosima
Language:Python2 0
stjude/dab_detector
Scripts and classes for DAB plaque detection
Language:MATLAB
stjude/Dowen_Fan
Abraham lab ChIA-PET analysis pipeline
Language:Shell1 0
stjude/intake_io
Image-focused IO for Python using intake and xarray
Language:Python0 0
stjude/Mouse_Survival
Language:Jupyter Notebook2 1
stjude/SICER2
sicer2
Language:Python2 31
stjude/SVIndelGenotyper
Analysis of error profiles of Indels and structural variants in deep sequencing data
Language:Python2 0