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awesome-nextflow

A curated list of nextflow based pipelines

aws-genomics-workflows

Genomics Workflows on AWS

caas_1

Chromosome arm aneuploidies in cancer

cancer_notes

A continually expanding collection of cancer genomics notes and data

colorednoise

Python package to generate Gaussian (1/f)**beta noise (e.g. pink noise)

covid_19_analysis

Analyzing RNA-Sequencing Datasets for COVID19 Collaboration

crispr-mageck-nf

Analyze CRISPR and shRNA functional genetic screening data

datahub

A centralized location for storing curated data ready for inclusion in cBioPortal.

deep-learning-predicts-chromosomal-instability-from-histopathology-images

Deep learning predicts chromosomal instability from histopathology images

dge_workshop

enrichr

An R interface to enrichR

epigenetic-factor-tnbc

Assessing and prioritizing epigenetic factors in TNBC Patients

genomics

A collection of scripts and notes related to genomics and bioinformatics

mutect-nf

Mutect pipeline with Nextflow

nutrient_calculator

Code for a shinyapp that calculates nutrition values for food and recipes

rnaseq

RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.

rnaseq-based-xbp1s-detection-

IRE1-XBP1s

rnaseq-encode-nf

An example RNA-seq pipeline with Nextflow and using public ENCODE data

sarek

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

shiny-gallery

Code and other documentation for apps in the Shiny Gallery ✨

smurff

Bayesian Factorization with Side Information in C++ with Python wrapper

streamlit-example

Example Streamlit app that you can fork to test out share.streamlit.io

tcrp

Few shot learning for cancer

telomerehunter-docker

Repository to generate docker image for telomerehunter

test-datasets

Test data to be used for automated testing with the nf-core pipelines

transcriptional-signature-survival-analysis

Associating transcriptional signature with survival data

unet

Generic U-Net Tensorflow 2 implementation for semantic segmentation

unet-1

this is a simple demo for image segmentation.----unet网络进行语义分割的demo，用的数据集是KITTI

visualizing-drug-enzyme-mapping

Drug enzyme mapping visualizing using hadoop workflow