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2017-dibsi-metagenomics

2017 DIBSI Metagenomics Workshop

adas-cogmri-biomarker

This repository contains the R script files required for implementing the ADAS-CogMRI biomarker for use in clinical trials of Alzheimer's disease modifying treatments.

advanced-shiny

Shiny tips & tricks for improving your apps and solving common problems

algorithms-for-dna-sequencing

Codes from Coursera's course Algorithms for DNA sequencing, part of genomic data science specialization offered by Johns Hopkins University

algorithms-for-dna-sequencing-1

Coursera MOOC Algorithms for DNA Sequencing by Ben Langmead, PhD, Jacob Pritt

atlas

:earth_americas: ATLAS - workflows for assembly, annotation, and genomic binning of metagenomic and metatranscriptomic data.

biocasia2020

BiocAsia2020 repository

biocintegrativecancervis

biomarker-correlations

Analyze clinical trial data by examining subgroup correlations of biomarker parameters of interest

book

canopy

Accessing Intra-Tumor Heterogeneity and Tracking Longitudinal and Spatial Clonal Evolutionary History by Next-Generation Sequencing.

cell-free-dna-in-als

master lab notebook/code for cfDNA project in the Zaitlen lab

cell-free-dna-reading-list

Important papers relating to the biology of cell free DNA

celltypeinferencemethods

A public list of computational methods for cell type inference from genome-scale DNA methylation data

cfdna

cfdna-deconvolution

code for estimating tissue of origin proportion in cell-free DNA methylation data

cfdnamethy

Disease Prediction by Cell-Free DNA Methylation

cfwgbs-pipline

A comprehensive and rigid computational framework to identify reliable cfDNA methylation biomarkers from cfWGBS data

chameleon_cluster

A chameleon clustering algorithm implementation for PYTHON3.

clinical-trial-analysis

A R and Machine Learning NLP Project

clinical-trials

Extract data from clinicaltrials.gov and converts them to CSV

clinical_trials

Search clinical trials with Shiny app

clinical_trials_gov

Importing and processing trial data from ClinicalTrials.gov

clinicaltrials

Code used to retrieve and analyze clinical trial records from clinicaltrials.gov

clinicaltrialsapi

Access the NIH ClinicalTrials.gov REST API

clonevol

Inferring and visualizing clonal evolution in multi-sample cancer sequencing

clusterprofiler

:bar_chart:statistical analysis and visualization of functional profiles for genes and gene clusters

ctdna-pipeline

A simplified pipeline for ctDNA sequencing data analysis

ctdnasomaticvariantcall.jl

Somatic Variant Call for ctDNA

dna-seq-gatk-variant-calling

This Snakemake pipeline implements the GATK best-practices workflow