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chromosomemappings

This repository contains chromosome/contig name mappings between UCSC <-> Ensembl <-> Gencode for a variety of genomes.

cite-seq-count

A tool that allows to get UMI counts from a single cell protein assay

cite-seq_optimization

Code and results from TotalSeqC antibody titration and pipeline benchmarking for CITE-seq experiments

clinicalgradednaseq

Automated next generation DNA sequencing analysis pipeline suited for clinical tests, with >99.9% sensitivity to Sanger sequencing at read-depth>18

clinvar-miner

Website to analyze conflicting assertions in ClinVar

coda

Coda: a convolutional denoising algorithm for genome-wide ChIP-seq data

conda

OS-agnostic, system-level binary package manager and ecosystem

continuous_analysis

Computational reproducibility using Continuous Integration to produce verifiable end-to-end runs of scientific analysis.

continuous_analysis_rnaseq

Example of how continuous analysis can be used for RNA-Seq differential expression.

countclust

A R package for Grade of Membership model and Visualization of counts data:

cpython

The Python programming language

cruk-summer-school-2017

Analysis of Cancer Genomes; 2017 edition

csv-to-fcs

A short script for converting .csv file data into an .fcs file, and vise versa.

cytof-workflow-v3

CyTOF workflow. Version 3.

cytotools

Useful small scripts for cytometry data management

data-science--cheat-sheet

Cheat Sheets

deep-learning-with-python-notebooks

Jupyter notebooks for the code samples of the book "Deep Learning with Python"

deep-review

A collaboratively written review paper on deep learning, genomics, and precision medicine

deeplearning-biology

A list of deep learning implementations in biology

demo-pipeline

disgenenet

dog_days

Using AWS RDS and S3 to store data about my dogs' vaccination and medical records. Creating an R shiny app to keep track of and share records with vets. :dog: :dog:

dpr

latent Dirichlet Process Regression for Genetic Prediction

dragmap

DRAGEN open-source mapper

edirectcookbook

encode-data-usage-examples

encoded

Metadata database for ENCODE project

eqtl

eQTL analysis pipeline

fastqtl

Enhanced version of the FastQTL QTL mapper

forked_repo