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adtex

Create docker image for adtex tool

alignqc

Long read alignment analysis. Generate a reports on sequence alignments for mappability vs read sizes, error patterns, annotations and rarefraction curve analysis. The most basic analysis only requires a BAM file, and outputs a web browser compatible xhtml to visualize/share/store/extract analysis results.

ark-analysis

Integrated pipeline for multiplexed image analysis

ascat

ASCAT copy number R package

ascatngs

Somatic copy number analysis using paired end wholegenome sequencing

au-public

Helpful tools from the Au lab, shared with everyone.

azure-vault-loader

A tool for loading secrets from azure key vault secrets onto remote machines holding proper credentials.

baffle

Add fake data with substructure to your real data to prevent online tools from scraping your data.

bioc-favorites

Dockerfile for putting together an R working environment.

bioformats2raw

Bio-Formats image file format to raw format converter

biofx

Bioinformatics tools to share with everyone

bms038_analysis

Code and additional processed data for manuscript "Tumor and Microenvironment Evolution during Immunotherapy with Nivolumab"; see for manuscript https://doi.org/10.1016/j.cell.2017.09.028 See also http://www.ioexplorer.org for interactive visuallization

cibersort

A shell to facilitate loading / running CIBERSORT software in structured environments

cidc-pipeline-prototype

A placeholder pipeline written in Snakemake.

cio-mass-cytometry

cio-wdl-16s-microbiome

A workflow for executing a microbiome workflow

cytof-wdl

A CyTOF analysis pipeline

cytofcore

R package for working with CyToF data

deepcell-tf

Deep Learning Library for Single Cell Analysis

epoch

Fast minimal hooks into resources.

facets

Algorithm to implement Fraction and Copy number Estimate from Tumor/normal Sequencing.

fasta.io

A static blog from a person.

fcs-io

FCS file handling

gatk

Official code repository for GATK versions 4 and up

gonk-diffusers-api

Python API for transforming text into vivid images using Stable Diffusion, with GPU support and concurrency control.

good-neighbors

Identify neighborhoods based on local cell populations.

gsva

A command-line interface and python module for R's GSVA bioconductor package

hello-world-snakemake

histomicstk

A Python and REST API for Histopathology Image Analysis

hla-polysolver

Fork of the Polysolver project