Aksh77

dndscv

dN/dS methods to quantify selection in cancer and somatic evolution

gReLU

gReLU is a python library to train, interpret, and apply deep learning models to DNA sequences.

CHM13

The complete sequence of a human genome

baskerville

Machine learning methods for DNA sequence analysis.

borzoi

RNA-seq prediction with deep convolutional neural networks.

atacseq

ATAC-seq peak-calling and QC analysis pipeline

ProteinGym

Official repository for the ProteinGym benchmarks

BMMB554

Introduction to data driven life sciences

conda

A system-level, binary package and environment manager running on all major operating systems and platforms.

matplotlib-venn

Area-weighted venn-diagrams for Python/matplotlib

AMBER

Automated Modelling for Biological Evidence-based Research

RepeatMasker

RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.

gggenomes

A grammar of graphics for comparative genomics

bwa

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

manta

Structural variant and indel caller for mapped sequencing data

deepTools

Tools to process and analyze deep sequencing data.

jbrowse

JBrowse 1, a full-featured genome browser built with JavaScript and HTML5. For JBrowse 2, see https://github.com/GMOD/jbrowse-components.

igv-notebook

Module for embedding igv.js in an IPython notebook

fastp

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

CNVpytor

a python extension of CNVnator -- a tool for CNV analysis from depth-of-coverage by mapped reads

bedtools2

bedtools - the swiss army knife for genome arithmetic

igv.js

Embeddable genomic visualization component based on the Integrative Genomics Viewer

nfs-ganesha-server-and-external-provisioner

NFS Ganesha Server and Volume Provisioner.

elasticsearch-dsl-py

High level Python client for Elasticsearch

project-based-learning

Curated list of project-based tutorials

cbioportal

cBioPortal for Cancer Genomics

Scribblr

biovalidator

JSON validator derived from AJV supporting ontology and taxonomy validation.

OpenPBTA-analysis

The analysis repository for the Open Pediatric Brain Tumor Atlas Project

Deep-Learning-for-Computational-Phenotyping

computational phenotyping using deep learning model on EHR data