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alzheimers_disease_analysis

This repo contains a data science project to identify patients at high-risk of Alzheimer's disease.

aneufinder

Find CNVs in single cell sequencing data.

atac-seq-pipeline

ENCODE ATAC-seq pipeline

awesome-expression-browser

😎 A curated list of software and resources for exploring and visualizing (browsing) expression data 😎

awesome-single-cell

Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

bcbio-nextgen

Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis

bic-variants_pipeline

BIC@MSKCC Variants Pipeline

bismark

A tool to map bisulfite converted sequence reads and determine cytosine methylation states

cancer-methylation

Cancer methylation study

cellannotationtutorial

Accompanying code for the tutorial: Annotating single cell transcriptomic maps using automated and manual methods

chip-seq-pipeline2

ENCODE ChIP-seq pipeline

common-workflow-language

Repository for the CWL standards. Use https://cwl.discourse.group/ for support 😊

comparative_snatac_snrna

comparativemetagenomics

cowplot

cowplot: Streamlined Plot Theme and Plot Annotations for ggplot2

cwas

data-analysis-with-r

Using gglot2, tidyr, dplyr, ggmap, choroplethr, shiny, logistic regression, clustering models and more

datascience

Grassroots Machine Learning with Python - examples and tutorials

deseq2

Differential gene expression analysis based on the negative binomial distribution

dplyr_tutorials

Repository for dplyr tutorials I made

duplex-seq-pipeline

A standalone end-to-end data analysis pipeline for Duplex Sequencing

e-mtab-6141

Data from Lewis, Barnes, Blighe et al., Cell Rep. 2019 Aug 27; 28(9): 2455–2470.e5.

empiricaldist

Python library that represents empirical distribution functions.

epigeneticclock

Calculate DNA methylation age using Horvath 2013 method

gat

Genomic Association Tester

gene_lists

List of gene lists for genomic analyses.

hands-on-machine-learning-for-algorithmic-trading

Hands-On Machine Learning for Algorithmic Trading, published by Packt

humandiseaseontology

Repository for the Human Disease Ontology.

illumina450k_filtering

A collection of resources to filter 'bad' probes from the Illumina 450k and EPIC methylation arrays

intro-to-rnaseq-hpc-o2

This repository has teaching materials for a 2 and 3-day Introduction to RNA-sequencing data analysis workshop using the O2 Cluster