high-throughput-sequencing

nim wrapper for htslib for parsing genomics data files

Python library to access Gene Expression Omnibus Database (GEO)

VarSim: A high-fidelity simulation validation framework for high-throughput genome sequencing with cancer applications

Sequence alignment tools

Find and visualize rearrangements in DNA sequences

Validation and manipulation of FASTQ files, scRNA-seq barcode pre-processing and UMI quantification.

use the noise

command-line querying+conversion of bigwigs and a nim wrapper for dpryan's libbigwig

A toolset for handling sequencing data with unique molecular identifiers (UMIs)

mSWEEP High-resolution sweep metagenomics using fast probabilistic inference

vSNP -- validate SNPs

uORF-Tools are a workflow and a collection of tools for the analysis of 'Upstream Open Reading Frames' (short uORFs)

Processing, quality control and analysis of GAM datsets

basepair bio: a single binary with many useful genomics subtools.

Sargasso disambiguates mixed-species high-throughput sequencing data.

mGEMS Genomic epidemiology with mixed samples

Bayesian modelling approach for detecting RNA flexibility changes in high-throughput structure probing data under different conditions, based on an extension of the BUM-HMM method.

Resolution-independent normalization of Hi-C data

HTSinfer infers metadata from High Throughput Sequencing (HTS) data

nim-lang wrapper for https://github.com/38/d4-format

Comparison of gene usage in immune repertoires under different biological conditions

Jupyter server for Duke Biostatistics and Bioinformatics high-throughput sequencing and analysis workshop summer 2017

Barcode Generator

This package creates segmentation of the genome into regions of biological significance from high-throughput sequencing data.

Custom plugins for the MultiQC tool.

A series of scripts used for transferring and validating files with gluster, and for submitting condor jobs

This package identifies differential expression in high-throughput 'count' data, such as that derived from next-generation sequencing machines, calculating estimated posterior likelihoods of differential expression (or more complex hypotheses) via empirical Bayesian methods.

Distributed iterative finite element analysis with high throughput computing