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bioinf

work related

biotools

A list of useful bioinformatics resources

burden-pipeline

cis-x

Search for activating regulatory variants in the tumor genome

cwas

deep-learning

Repo for the Deep Learning Nanodegree Foundations program.

deepsea

DeepSEA in TensorFlow

denovogear

A program to detect denovo-variants using next-generation sequencing data.

dragonstar2019

easyamplicon

Easy Amplicon data analysis pipeline

evalsvcallers

Evaluate the performances (precision and recall) of structural variation (SV) callers

expansionhunterdenovo

A suite of tools for detecting expansions of short tandem repeats

fastqtl

Fork of FastQTL for SVs

forest-confidence-interval

Confidence intervals for scikit-learn forest algorithms

gatk-sv-single-sample

WDLs for the Single Sample GATK-SV pipeline

giab_data_indexes

This repository contains data indexes from NIST's Genome in a Bottle project.

gnomad-sv-pipeline

Code and custom scripts relevant to gnomAD-SV (Collins*, Brand*, et al., 2019)

gnomad_qc

gtexv6prarevariation

Repository to reproduce analyses from the GTEx V6P Rare Variation Manuscript

hail

Scalable genomic data analysis.

hera

hic_data

A (continuously updated) collection of references to Hi-C data. Predominantly human/mouse Hi-C data, with replicates.

hubpredictor

HubPredictor is the R function to run Bayesian Additive Regression Trees (BART) model for predicting chromatin interaction hubs using histone marks information.

microbiomeanalystr

A companion R package for the MicrobiomeAnalyst web server

mopline

Detection and genotyping of structural variants

prenatalsvdiscoveryproject

pydeepsea

DeepSEA implements in PyTorch

qiita

Qiita - A multi-omics databasing effort

samplot

Plot structural variant signals from many BAMs and CRAMs

slivar

genetic variant expressions, annotation, and filtering for great good.