genomics-data

Development repository for the Bioconductor package 'mixOmics '

Highly performant data storage in C++ for importing, querying and transforming variant data with C/C++/Java/Spark bindings. Used in gatk4.

Ontology for consent codes and data use requirements

Pandas ExtensionDtypes for dealing with genomics data

Sentieon DNAseq

🧬 gnomAD Python API is used to obtain data from gnomAD (genome aggregation database).

Sentieon DNAscope + Machine Learning Model

Datastores for reads, not your papa's FASTQ files.

🧮 🔢 Generate multi-sample k-mer count matrix from WGS

Experimental R bindings to the native GenomicsDB library

FauxFlow - Analyze Single Cell Genomics Data in a Flow Cytometry Paradigm

Genomic Data Commons API wrapper

This repo contains pipeline implemented using the nextflow workflow management system for the analysis of genomics data

R script employed in the manuscript 'Genomic signatures of clonality in the deep water kelp Laminaria rodriguezii' to compute the distribution of FIS across loci into discrete classes

Using Convolutional Neural Networks to model an association between a genomic sequence and the number of sequenced reads that align to it

R AnnotationDB resources like org.db, tx.db for various fungal species

An Acute Myeloid Leukemia diagnostics project based on the research outlined in Scalable Prediction of Acute Myeloid Leukemia Using High-Dimensional Machine Learning and Blood Transcriptomics by Stefanie WarnatHerresthal, Konstantinos Perrakis, Bernd Taschler, Torsten Haferlach, Sach Mukherjee & Joachim L. Schultze.

Genomic linked data converter. Interchange GFF, GVF, VCF files via JSON.

Code and data related to analysis of genomics data

In this project, we address three potential challenges for secure sharing and count query execution on the genomic data: data privacy, query privacy, and output privacy.

Covers the following bash commands cat, chmod, cd, cp, curl, head, history, ls, less, man, mkdir, mv, nano, pwd, rm, tail, wc, wget

Implementation of https://www.biorxiv.org/content/10.1101/2021.04.29.442004v1

List of online databases and resources for Mycobacterium Tuberculosis

Python code for the processing of the input data for SDA tensor and matrix decomposition and the resulting output data.

Level 4 Data Management for Genomics Data

Jupyter notebook generator to download and execute the processing files for GGR related datasets

Miscellaneous R script to wrangle data and generate visualizations

Manifestation of the Lottery Ticket Phenomena in supervised, reinforcement and unsupervised learning.

A bash script for downloading sequence datasets from PlasmoDb, a Plasmodium informatics resourse

Here, I stored various scripts relevant to the study of sapovirus evolution. The scripts are relevant to (1) the mining of inter-genotype evolution, (2) within and between-host sapovirus genome evolutionary analyses, (3) sapovirus genetic divergence and diversity.