ngs-analysis

Publication quality NGS track plotting

SalmonTE is an ultra-Fast and Scalable Quantification Pipeline of Transpose Element (TE) Abundances

WisecondorX — An evolved WISECONDOR

A comprehensive R package to construct interactive and reproducible biological data analysis applications based on the R platform

Metagenomic pipeline and other general scripts used in the lab.

is an open-source LIMS (laboratory Information Management System) for Next Generation Sequencing sample management, statistics and reports, and bioinformatics analysis service management.

PlasmidID is a mapping-based, assembly-assisted plasmid identification tool that analyzes and gives graphic solution for plasmid identification.

Toolbox for generic NGS analyses - A framework to quickly build pipelines and to perform large-scale NGS analysis

A set of CWL tools and workflows used by NCBI Computational Biology Branch for NGS data analysis

R package: Simulate Expression data from igraph network using mvtnorm (CRAN; JOSS)

Project Manager for NGS data analysis

Utilities for analyzing next generation sequencing data.

Ultrafast sequence typing and gene detection from NGS raw reads

A toolkit for NGS analysis with Python

HemTools: a collection of NGS pipelines and bioinformatic analyses

Using combined evidence from replicates to evaluate ChIP-seq peaks

Bayesian Markov Model motif discovery tool version 2 - An expectation maximization algorithm for the de novo discovery of enriched motifs as modelled by higher-order Markov models.

生物信息学项目实践仓库🏆🥇

Computational Suite for Bioinformaticians and Biologists (CSBB) is a RShiny application developed with an intention to empower researchers from wet and dry lab to perform downstream Bioinformatics analysis

RNA-seq pipeline for raw sequence alignment and transcript/gene quantification.

Ensemble Learning for Harmonization and Annotation of Single Cells (ELeFHAnt) provides an easy to use R package for users to annotate clusters of single cells, harmonize labels across single cell datasets to generate a unified atlas and infer relationship among celltypes between two datasets. It provides users with a flexibility of choosing a machine learning based classifiers or let ELeFHAnt automatically use the power of robust classifiers like randomForest and SVM (Support Vector Machines) to make predictions. It has three functions 1) CelltypeAnnotation 2) LabelHarmonization 3) DeduceRelationship.

Tools for analyzing NGS sequence data and aligned protein sequences

In this training course you will find theory and practice material for introducing yourself to wgs analysis for bacterial, including outbreak investigation.

The ChIP-Seq peak calling algorithm using convolution neural networks

A python package storing different tools for different NGS operations

Multple methods for BSA Pipeline

Workshop • Intro to Bioinformatics using NGS data • 5 days

deepEA: a containerized web server for interactive analysis of epitranscriptome sequencing data

Algorithm to implement Fraction and Allelic Copy number Estimate from Tumor/normal Sequencing. Package created to test FACETS with both matched and unmatched normal.