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eacon

Easy Copy Number !

edit_efficiency_correction

Project of Wang Lab in IBMS: Identification of LOF variants using base editing screens with editing efficiency correction

epimogrify_np

framework

Open-source opinionated Galaxy-based framework for microbiota analysis

fraser

fraser-analysis

Accompanying analysis code for the FRASER manuscript

fuseq_wes

galaxy

Data intensive science for everyone.

galaxy-rna-workbench

Galaxy RNA workbench

galaxy_papaa

This repository is for installing and running a docker galaxy instance with pancancer aberrant pathway activity analysis (PAPAA) tools

genepattern-notebook

Platform for integrating genomic analysis with Jupyter Notebooks.

hlatyping

Precision HLA typing from next-generation sequencing data

hrd_genomic_scar_score

hrdetect-pipeline

isocor

IsoCor: Isotope Correction for mass spectrometry labeling experiments

jetstreamapitutorial_pearc19

knowledge-repo

A next-generation curated knowledge sharing platform for data scientists and other technical professions.

mageri

MAGERI - Assemble, align and call variants for targeted genome re-sequencing with unique molecular identifiers

marianas

Software for processing molecular barcoding (UMI)-based NGS data

mutect-nf

Mutect pipeline with Nextflow

mynotebook

nbtools

A framework for creating user-friendly widgets and tools in Jupyter Notebook.

ovahrdscar

R package to quantify allelic imbalances associated with homologous recombination deficiency in ovarian cancer. Use as input a list of segments per samples as those generated by ASCAT.

padua

Proteomic Data Analysis with Python (pandas, scikit-learn, numpy, scipy)

pancancer

Building classifiers using cancer transcriptomes across 33 different cancer-types

papaa

pdaug

penncnv

Copy number vaiation detection from SNP arrays

phantompeakqualtools

This package computes informative enrichment and quality measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data. It can also be used to obtain robust estimates of the predominant fragment length or characteristic tag shift values in these assays.

phosmap

A Comprehensive R Package For Analyzing Quantitative Phosphoproteomics Data